Starting phenix.real_space_refine on Wed Mar 4 21:18:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6xqb_22288/03_2026/6xqb_22288.cif Found real_map, /net/cci-nas-00/data/ceres_data/6xqb_22288/03_2026/6xqb_22288.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6xqb_22288/03_2026/6xqb_22288.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6xqb_22288/03_2026/6xqb_22288.map" model { file = "/net/cci-nas-00/data/ceres_data/6xqb_22288/03_2026/6xqb_22288.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6xqb_22288/03_2026/6xqb_22288.cif" } resolution = 3.4 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= 0.002 sd= 0.038 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: 8 Type Number sf(0) Gaussians Zn 2 6.06 5 P 15 5.49 5 Mg 1 5.21 5 S 61 5.16 5 C 5262 2.51 5 N 1392 2.21 5 O 1603 1.98 5 H 7987 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16323 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 12682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 801, 12682 Classifications: {'peptide': 801} Link IDs: {'PTRANS': 25, 'TRANS': 775} Chain breaks: 5 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1713 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 993 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "D" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 444 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 229 Classifications: {'RNA': 7} Modifications used: {'3*END': 1, 'rna3p_pur': 4, 'rna3p_pyr': 3} Link IDs: {'rna3p': 6} Chain: "F" Number of atoms: 259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 259 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 4} Link IDs: {'rna3p': 7} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3213 SG CYS A 301 37.207 66.986 36.975 1.00131.34 S ATOM 3290 SG CYS A 306 37.350 65.836 33.243 1.00128.23 S ATOM 3355 SG CYS A 310 40.424 66.248 34.854 1.00134.44 S ATOM 6095 SG CYS A 487 19.687 63.110 45.316 1.00126.47 S ATOM 8612 SG CYS A 645 17.972 62.844 42.341 1.00141.82 S ATOM 8622 SG CYS A 646 22.155 64.389 43.308 1.00142.48 S Time building chain proxies: 2.97, per 1000 atoms: 0.18 Number of scatterers: 16323 At special positions: 0 Unit cell: (84.55, 97.01, 108.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 2 29.99 S 61 16.00 P 15 15.00 Mg 1 11.99 O 1603 8.00 N 1392 7.00 C 5262 6.00 H 7987 1.00 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=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 414.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 642 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " Number of angles added : 3 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1934 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 8 sheets defined 53.2% alpha, 11.5% beta 7 base pairs and 10 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 139 through 149 removed outlier: 3.684A pdb=" N LYS A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N TYR A 149 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 159 Processing helix chain 'A' and resid 170 through 177 removed outlier: 3.520A pdb=" N VAL A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 198 removed outlier: 3.867A pdb=" N ALA A 185 " --> pdb=" O ARG A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 242 Processing helix chain 'A' and resid 243 through 246 removed outlier: 4.018A pdb=" N THR A 246 " --> pdb=" O PRO A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 246' Processing helix chain 'A' and resid 249 through 260 removed outlier: 4.264A pdb=" N ALA A 253 " --> pdb=" O ALA A 250 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU A 254 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N VAL A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASP A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A 260 " --> pdb=" O VAL A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 287 Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 303 through 315 removed outlier: 3.614A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 319 removed outlier: 3.585A pdb=" N THR A 319 " --> pdb=" O LEU A 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 316 through 319' Processing helix chain 'A' and resid 367 through 376 removed outlier: 4.455A pdb=" N ALA A 376 " --> pdb=" O LEU A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 383 removed outlier: 4.222A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 425 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 455 through 459 Processing helix chain 'A' and resid 465 through 480 removed outlier: 5.132A pdb=" N LYS A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.812A pdb=" N VAL A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 508 Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.726A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 532 removed outlier: 3.532A pdb=" N LYS A 532 " --> pdb=" O PHE A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 573 removed outlier: 3.682A pdb=" N THR A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR A 567 " --> pdb=" O CYS A 563 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN A 573 " --> pdb=" O ARG A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 581 removed outlier: 3.912A pdb=" N ALA A 581 " --> pdb=" O LYS A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 607 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 627 through 638 removed outlier: 3.739A pdb=" N ARG A 631 " --> pdb=" O PRO A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 662 Processing helix chain 'A' and resid 686 through 710 removed outlier: 3.893A pdb=" N SER A 709 " --> pdb=" O ASN A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 732 Processing helix chain 'A' and resid 738 through 752 removed outlier: 4.021A pdb=" N VAL A 742 " --> pdb=" O ASP A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 774 Processing helix chain 'A' and resid 778 through 789 removed outlier: 4.050A pdb=" N PHE A 782 " --> pdb=" O SER A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 843 removed outlier: 3.905A pdb=" N ILE A 837 " --> pdb=" O ASP A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 865 removed outlier: 3.834A pdb=" N ASP A 865 " --> pdb=" O SER A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 872 Processing helix chain 'A' and resid 874 through 895 removed outlier: 3.505A pdb=" N ALA A 878 " --> pdb=" O ASN A 874 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU A 894 " --> pdb=" O LYS A 890 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 915 removed outlier: 3.703A pdb=" N SER A 913 " --> pdb=" O ASN A 909 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG A 914 " --> pdb=" O ASP A 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 95 through 98 Processing helix chain 'B' and resid 101 through 108 removed outlier: 3.533A pdb=" N ASN B 105 " --> pdb=" O ASP B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 114 removed outlier: 4.530A pdb=" N GLY B 113 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N CYS B 114 " --> pdb=" O ARG B 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 110 through 114' Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 135 through 142 removed outlier: 3.559A pdb=" N ASN B 140 " --> pdb=" O ASN B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.751A pdb=" N ASN B 179 " --> pdb=" O ASN B 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 20 removed outlier: 3.548A pdb=" N LEU C 20 " --> pdb=" O VAL C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 40 Processing helix chain 'C' and resid 44 through 62 removed outlier: 3.634A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 99 removed outlier: 3.515A pdb=" N THR D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP D 99 " --> pdb=" O LEU D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 112 removed outlier: 3.610A pdb=" N ASP D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA3, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.416A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.416A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL B 115 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 389 through 390 removed outlier: 6.826A pdb=" N LEU A 389 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 397 through 400 removed outlier: 7.200A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AA8, first strand: chain 'A' and resid 816 through 822 369 hydrogen bonds defined for protein. 1011 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 7 basepair parallelities 10 stacking parallelities Total time for adding SS restraints: 3.80 Time building geometry restraints manager: 1.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 7963 1.03 - 1.22: 42 1.22 - 1.42: 3706 1.42 - 1.62: 4725 1.62 - 1.82: 93 Bond restraints: 16529 Sorted by residual: bond pdb=" C GLY A 203 " pdb=" N VAL A 204 " ideal model delta sigma weight residual 1.332 1.273 0.059 1.73e-02 3.34e+03 1.16e+01 bond pdb=" CB VAL A 473 " pdb=" CG2 VAL A 473 " ideal model delta sigma weight residual 1.521 1.411 0.110 3.30e-02 9.18e+02 1.10e+01 bond pdb=" C GLN A 573 " pdb=" N LYS A 574 " ideal model delta sigma weight residual 1.332 1.290 0.043 1.40e-02 5.10e+03 9.28e+00 bond pdb=" CA ILE B 120 " pdb=" C ILE B 120 " ideal model delta sigma weight residual 1.524 1.494 0.030 1.05e-02 9.07e+03 8.26e+00 bond pdb=" CB VAL A 637 " pdb=" CG2 VAL A 637 " ideal model delta sigma weight residual 1.521 1.430 0.091 3.30e-02 9.18e+02 7.65e+00 ... (remaining 16524 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.39: 29219 3.39 - 6.78: 489 6.78 - 10.16: 13 10.16 - 13.55: 6 13.55 - 16.94: 2 Bond angle restraints: 29729 Sorted by residual: angle pdb=" N GLY A 503 " pdb=" CA GLY A 503 " pdb=" C GLY A 503 " ideal model delta sigma weight residual 111.85 117.17 -5.32 1.06e+00 8.90e-01 2.51e+01 angle pdb=" CA LEU A 241 " pdb=" CB LEU A 241 " pdb=" CG LEU A 241 " ideal model delta sigma weight residual 116.30 133.24 -16.94 3.50e+00 8.16e-02 2.34e+01 angle pdb=" CA LEU A 247 " pdb=" CB LEU A 247 " pdb=" CG LEU A 247 " ideal model delta sigma weight residual 116.30 131.87 -15.57 3.50e+00 8.16e-02 1.98e+01 angle pdb=" CA PRO A 830 " pdb=" C PRO A 830 " pdb=" N TYR A 831 " ideal model delta sigma weight residual 114.65 120.20 -5.55 1.27e+00 6.20e-01 1.91e+01 angle pdb=" N PHE A 321 " pdb=" CA PHE A 321 " pdb=" C PHE A 321 " ideal model delta sigma weight residual 110.36 104.55 5.81 1.34e+00 5.57e-01 1.88e+01 ... (remaining 29724 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.42: 6972 17.42 - 34.83: 634 34.83 - 52.25: 177 52.25 - 69.67: 81 69.67 - 87.08: 16 Dihedral angle restraints: 7880 sinusoidal: 4275 harmonic: 3605 Sorted by residual: dihedral pdb=" CA ASP A 465 " pdb=" C ASP A 465 " pdb=" N ILE A 466 " pdb=" CA ILE A 466 " ideal model delta harmonic sigma weight residual -180.00 -136.97 -43.03 0 5.00e+00 4.00e-02 7.41e+01 dihedral pdb=" CA VAL A 234 " pdb=" C VAL A 234 " pdb=" N ASP A 235 " pdb=" CA ASP A 235 " ideal model delta harmonic sigma weight residual -180.00 -139.49 -40.51 0 5.00e+00 4.00e-02 6.56e+01 dihedral pdb=" CA LEU B 180 " pdb=" C LEU B 180 " pdb=" N ALA B 181 " pdb=" CA ALA B 181 " ideal model delta harmonic sigma weight residual 180.00 141.10 38.90 0 5.00e+00 4.00e-02 6.05e+01 ... (remaining 7877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1052 0.076 - 0.152: 253 0.152 - 0.229: 27 0.229 - 0.305: 2 0.305 - 0.381: 1 Chirality restraints: 1335 Sorted by residual: chirality pdb=" CB VAL A 473 " pdb=" CA VAL A 473 " pdb=" CG1 VAL A 473 " pdb=" CG2 VAL A 473 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CA PRO A 296 " pdb=" N PRO A 296 " pdb=" C PRO A 296 " pdb=" CB PRO A 296 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CB VAL A 763 " pdb=" CA VAL A 763 " pdb=" CG1 VAL A 763 " pdb=" CG2 VAL A 763 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 1332 not shown) Planarity restraints: 2410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 166 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.19e+00 pdb=" C VAL A 166 " 0.052 2.00e-02 2.50e+03 pdb=" O VAL A 166 " -0.020 2.00e-02 2.50e+03 pdb=" N GLU A 167 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 134 " 0.015 2.00e-02 2.50e+03 3.02e-02 9.11e+00 pdb=" C ASP B 134 " -0.052 2.00e-02 2.50e+03 pdb=" O ASP B 134 " 0.020 2.00e-02 2.50e+03 pdb=" N TYR B 135 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 238 " -0.015 2.00e-02 2.50e+03 2.92e-02 8.51e+00 pdb=" C TYR A 238 " 0.050 2.00e-02 2.50e+03 pdb=" O TYR A 238 " -0.019 2.00e-02 2.50e+03 pdb=" N SER A 239 " -0.017 2.00e-02 2.50e+03 ... (remaining 2407 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 1295 2.19 - 2.79: 34516 2.79 - 3.39: 46566 3.39 - 4.00: 59821 4.00 - 4.60: 90605 Nonbonded interactions: 232803 Sorted by model distance: nonbonded pdb="HE21 GLN A 210 " pdb=" O GLY A 214 " model vdw 1.583 2.450 nonbonded pdb=" OD1 ASP A 194 " pdb=" HH TYR A 289 " model vdw 1.601 2.450 nonbonded pdb=" O ASP A 454 " pdb=" H ARG A 457 " model vdw 1.648 2.450 nonbonded pdb=" O VAL A 234 " pdb=" H TYR A 237 " model vdw 1.650 2.450 nonbonded pdb=" O PHE A 480 " pdb=" HZ1 LYS A 641 " model vdw 1.655 2.450 ... (remaining 232798 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 'E' and resid 3 through 8) selection = (chain 'F' and resid 3 through 8) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 0.130 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.580 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5560 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 : 0.014 0.690 8549 Z= 0.588 Angle : 1.334 32.088 11664 Z= 0.717 Chirality : 0.064 0.381 1335 Planarity : 0.008 0.059 1427 Dihedral : 13.837 78.509 3174 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.15 % Favored : 84.85 % Rotamer: Outliers : 0.23 % Allowed : 3.97 % Favored : 95.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.72 % 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: -5.15 (0.20), residues: 990 helix: -3.28 (0.17), residues: 427 sheet: -2.91 (0.47), residues: 86 loop : -3.65 (0.24), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.003 ARG A 132 TYR 0.031 0.005 TYR A 788 PHE 0.044 0.005 PHE A 326 TRP 0.023 0.004 TRP A 290 HIS 0.022 0.005 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.01185 ( 8542) covalent geometry : angle 1.27679 (11661) hydrogen bonds : bond 0.15727 ( 380) hydrogen bonds : angle 7.65771 ( 1051) metal coordination : bond 0.27511 ( 7) metal coordination : angle 24.15317 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 170 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 515 TYR cc_start: 0.6852 (m-80) cc_final: 0.6213 (m-10) REVERT: A 859 PHE cc_start: 0.7511 (t80) cc_final: 0.6713 (t80) REVERT: A 884 TYR cc_start: 0.8757 (m-10) cc_final: 0.8551 (m-10) REVERT: A 885 LEU cc_start: 0.8528 (mt) cc_final: 0.8304 (tp) REVERT: B 104 ASN cc_start: 0.6760 (t160) cc_final: 0.6324 (m110) REVERT: C 47 GLU cc_start: 0.8062 (mp0) cc_final: 0.7726 (mp0) REVERT: D 87 MET cc_start: 0.6526 (ttm) cc_final: 0.5334 (mmp) outliers start: 2 outliers final: 1 residues processed: 171 average time/residue: 0.1913 time to fit residues: 45.0085 Evaluate side-chains 133 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 132 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 463 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 ASN A 414 ASN A 491 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 611 ASN A 705 ASN B 104 ASN B 118 ASN C 31 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.154110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.138545 restraints weight = 101141.648| |-----------------------------------------------------------------------------| r_work (start): 0.4501 rms_B_bonded: 5.80 r_work (final): 0.4501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5588 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8549 Z= 0.147 Angle : 0.695 8.900 11664 Z= 0.367 Chirality : 0.040 0.141 1335 Planarity : 0.005 0.053 1427 Dihedral : 13.043 73.943 1340 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 1.36 % Allowed : 8.85 % Favored : 89.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -3.78 (0.23), residues: 990 helix: -2.13 (0.21), residues: 443 sheet: -2.40 (0.53), residues: 80 loop : -2.88 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 457 TYR 0.015 0.002 TYR A 719 PHE 0.019 0.001 PHE A 471 TRP 0.010 0.001 TRP A 598 HIS 0.009 0.002 HIS A 572 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8542) covalent geometry : angle 0.68958 (11661) hydrogen bonds : bond 0.04784 ( 380) hydrogen bonds : angle 5.73718 ( 1051) metal coordination : bond 0.01386 ( 7) metal coordination : angle 5.59018 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.7497 (m-30) cc_final: 0.7000 (p0) REVERT: A 479 TYR cc_start: 0.7387 (OUTLIER) cc_final: 0.6609 (t80) REVERT: A 519 MET cc_start: 0.2165 (mtp) cc_final: 0.1842 (mtp) REVERT: A 859 PHE cc_start: 0.7595 (t80) cc_final: 0.6739 (t80) REVERT: A 884 TYR cc_start: 0.8665 (m-10) cc_final: 0.8308 (m-10) REVERT: A 885 LEU cc_start: 0.8493 (mt) cc_final: 0.8019 (tt) REVERT: A 886 GLN cc_start: 0.9162 (mm110) cc_final: 0.8462 (mm-40) REVERT: A 888 ILE cc_start: 0.7529 (mt) cc_final: 0.7282 (mt) REVERT: B 104 ASN cc_start: 0.7092 (t0) cc_final: 0.6560 (m110) REVERT: D 87 MET cc_start: 0.6839 (ttm) cc_final: 0.5623 (mmt) outliers start: 12 outliers final: 10 residues processed: 157 average time/residue: 0.1688 time to fit residues: 37.3890 Evaluate side-chains 148 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 137 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain C residue 21 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 87 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 25 optimal weight: 0.0270 chunk 23 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 overall best weight: 2.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 136 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4740 r_free = 0.4740 target = 0.150976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.135187 restraints weight = 102201.017| |-----------------------------------------------------------------------------| r_work (start): 0.4457 rms_B_bonded: 5.83 r_work (final): 0.4457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5753 moved from start: 0.3260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8549 Z= 0.177 Angle : 0.676 7.624 11664 Z= 0.362 Chirality : 0.040 0.140 1335 Planarity : 0.005 0.051 1427 Dihedral : 12.697 73.741 1340 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Rotamer: Outliers : 1.70 % Allowed : 10.90 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -3.23 (0.24), residues: 990 helix: -1.55 (0.22), residues: 446 sheet: -2.43 (0.51), residues: 80 loop : -2.67 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 624 TYR 0.017 0.002 TYR A 521 PHE 0.019 0.002 PHE A 753 TRP 0.010 0.002 TRP A 598 HIS 0.007 0.002 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 8542) covalent geometry : angle 0.67250 (11661) hydrogen bonds : bond 0.04678 ( 380) hydrogen bonds : angle 5.44249 ( 1051) metal coordination : bond 0.01545 ( 7) metal coordination : angle 4.44240 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.7600 (m-30) cc_final: 0.7048 (p0) REVERT: A 479 TYR cc_start: 0.7396 (OUTLIER) cc_final: 0.6654 (t80) REVERT: A 525 ASP cc_start: 0.8306 (t0) cc_final: 0.8104 (p0) REVERT: A 885 LEU cc_start: 0.8562 (mt) cc_final: 0.8157 (tt) REVERT: A 886 GLN cc_start: 0.9229 (mm110) cc_final: 0.8542 (mm-40) REVERT: A 887 TYR cc_start: 0.8551 (t80) cc_final: 0.7937 (t80) REVERT: B 90 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7312 (tmm) REVERT: B 104 ASN cc_start: 0.7085 (t0) cc_final: 0.6494 (m110) REVERT: D 87 MET cc_start: 0.6920 (ttm) cc_final: 0.5654 (mmt) outliers start: 15 outliers final: 11 residues processed: 154 average time/residue: 0.1908 time to fit residues: 40.8029 Evaluate side-chains 147 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 134 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain B residue 90 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 31 optimal weight: 9.9990 chunk 34 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 18 optimal weight: 0.0470 chunk 5 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 overall best weight: 1.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4753 r_free = 0.4753 target = 0.152121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.136424 restraints weight = 101384.559| |-----------------------------------------------------------------------------| r_work (start): 0.4475 rms_B_bonded: 5.80 r_work (final): 0.4475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5715 moved from start: 0.3848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8549 Z= 0.136 Angle : 0.596 6.746 11664 Z= 0.318 Chirality : 0.038 0.130 1335 Planarity : 0.004 0.048 1427 Dihedral : 12.381 73.649 1340 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 2.50 % Allowed : 10.33 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.69 (0.25), residues: 990 helix: -0.95 (0.23), residues: 439 sheet: -2.38 (0.49), residues: 91 loop : -2.48 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 624 TYR 0.013 0.001 TYR A 515 PHE 0.023 0.002 PHE A 782 TRP 0.014 0.002 TRP A 617 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 8542) covalent geometry : angle 0.59417 (11661) hydrogen bonds : bond 0.03974 ( 380) hydrogen bonds : angle 4.98908 ( 1051) metal coordination : bond 0.00693 ( 7) metal coordination : angle 3.21278 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 140 ASP cc_start: 0.7783 (m-30) cc_final: 0.7180 (p0) REVERT: A 163 TYR cc_start: 0.8599 (p90) cc_final: 0.7721 (p90) REVERT: A 479 TYR cc_start: 0.7266 (OUTLIER) cc_final: 0.6670 (t80) REVERT: A 588 VAL cc_start: 0.8103 (OUTLIER) cc_final: 0.7890 (m) REVERT: A 859 PHE cc_start: 0.7743 (t80) cc_final: 0.6841 (t80) REVERT: A 884 TYR cc_start: 0.8727 (m-10) cc_final: 0.8420 (m-10) REVERT: A 885 LEU cc_start: 0.8578 (mt) cc_final: 0.8322 (tt) REVERT: A 888 ILE cc_start: 0.7698 (mt) cc_final: 0.7398 (mt) REVERT: B 104 ASN cc_start: 0.7039 (t0) cc_final: 0.6464 (m110) REVERT: D 87 MET cc_start: 0.6822 (ttm) cc_final: 0.5486 (mmt) outliers start: 22 outliers final: 14 residues processed: 145 average time/residue: 0.1803 time to fit residues: 36.6322 Evaluate side-chains 145 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 129 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain D residue 90 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 57 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 21 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 695 ASN A 773 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4692 r_free = 0.4692 target = 0.147800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.131813 restraints weight = 101725.524| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 5.76 r_work (final): 0.4400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5892 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8549 Z= 0.209 Angle : 0.681 8.372 11664 Z= 0.367 Chirality : 0.041 0.137 1335 Planarity : 0.005 0.049 1427 Dihedral : 12.448 73.659 1340 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer: Outliers : 2.27 % Allowed : 11.92 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.83 (0.25), residues: 990 helix: -0.97 (0.23), residues: 433 sheet: -2.41 (0.49), residues: 90 loop : -2.66 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 624 TYR 0.016 0.002 TYR A 238 PHE 0.028 0.002 PHE A 753 TRP 0.013 0.002 TRP A 617 HIS 0.009 0.002 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 8542) covalent geometry : angle 0.67841 (11661) hydrogen bonds : bond 0.04610 ( 380) hydrogen bonds : angle 5.38464 ( 1051) metal coordination : bond 0.01553 ( 7) metal coordination : angle 4.02203 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 859 PHE cc_start: 0.7809 (t80) cc_final: 0.6790 (t80) REVERT: A 884 TYR cc_start: 0.8849 (m-10) cc_final: 0.8507 (m-10) REVERT: A 885 LEU cc_start: 0.8638 (mt) cc_final: 0.8231 (tt) REVERT: A 886 GLN cc_start: 0.9296 (mm110) cc_final: 0.8629 (mm-40) REVERT: A 888 ILE cc_start: 0.7726 (mt) cc_final: 0.7339 (mt) REVERT: B 104 ASN cc_start: 0.6853 (t0) cc_final: 0.6189 (m110) REVERT: D 87 MET cc_start: 0.6946 (ttm) cc_final: 0.5547 (mmt) outliers start: 20 outliers final: 18 residues processed: 147 average time/residue: 0.1656 time to fit residues: 35.1206 Evaluate side-chains 146 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 479 TYR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 92 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 78 optimal weight: 10.0000 chunk 70 optimal weight: 8.9990 chunk 25 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.148452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.132592 restraints weight = 101485.851| |-----------------------------------------------------------------------------| r_work (start): 0.4412 rms_B_bonded: 5.71 r_work (final): 0.4412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5867 moved from start: 0.4692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8549 Z= 0.168 Angle : 0.631 8.121 11664 Z= 0.336 Chirality : 0.039 0.129 1335 Planarity : 0.004 0.048 1427 Dihedral : 12.295 73.639 1340 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 2.27 % Allowed : 13.39 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.66 (0.25), residues: 990 helix: -0.79 (0.24), residues: 438 sheet: -2.46 (0.48), residues: 96 loop : -2.60 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 624 TYR 0.014 0.002 TYR A 238 PHE 0.020 0.002 PHE A 753 TRP 0.011 0.002 TRP A 598 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00355 ( 8542) covalent geometry : angle 0.62835 (11661) hydrogen bonds : bond 0.04218 ( 380) hydrogen bonds : angle 5.15838 ( 1051) metal coordination : bond 0.01165 ( 7) metal coordination : angle 3.60650 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 GLU cc_start: 0.8229 (mp0) cc_final: 0.7821 (mm-30) REVERT: A 859 PHE cc_start: 0.7835 (t80) cc_final: 0.6893 (t80) REVERT: A 884 TYR cc_start: 0.8764 (m-10) cc_final: 0.8428 (m-10) REVERT: A 885 LEU cc_start: 0.8644 (mt) cc_final: 0.8241 (tt) REVERT: A 886 GLN cc_start: 0.9304 (mm110) cc_final: 0.8636 (mm-40) REVERT: A 888 ILE cc_start: 0.7721 (mt) cc_final: 0.7364 (mt) REVERT: B 104 ASN cc_start: 0.6660 (t0) cc_final: 0.5978 (m110) REVERT: D 87 MET cc_start: 0.6891 (ttm) cc_final: 0.5460 (mmt) outliers start: 20 outliers final: 18 residues processed: 146 average time/residue: 0.1701 time to fit residues: 35.8416 Evaluate side-chains 147 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 92 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 74 optimal weight: 7.9990 chunk 85 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.150266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.134962 restraints weight = 100787.442| |-----------------------------------------------------------------------------| r_work (start): 0.4452 rms_B_bonded: 5.68 r_work (final): 0.4452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5796 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8549 Z= 0.125 Angle : 0.591 7.801 11664 Z= 0.309 Chirality : 0.038 0.126 1335 Planarity : 0.004 0.042 1427 Dihedral : 12.068 73.522 1340 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.19 % Favored : 90.81 % Rotamer: Outliers : 2.16 % Allowed : 13.85 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.25 (0.26), residues: 990 helix: -0.41 (0.24), residues: 442 sheet: -2.36 (0.49), residues: 94 loop : -2.39 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 624 TYR 0.016 0.001 TYR A 515 PHE 0.016 0.001 PHE A 782 TRP 0.010 0.001 TRP A 617 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8542) covalent geometry : angle 0.58897 (11661) hydrogen bonds : bond 0.03742 ( 380) hydrogen bonds : angle 4.81120 ( 1051) metal coordination : bond 0.00865 ( 7) metal coordination : angle 3.08516 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 TYR cc_start: 0.8609 (p90) cc_final: 0.7804 (p90) REVERT: A 350 GLU cc_start: 0.8135 (mp0) cc_final: 0.7732 (mm-30) REVERT: B 104 ASN cc_start: 0.6713 (t0) cc_final: 0.6066 (m110) outliers start: 19 outliers final: 19 residues processed: 147 average time/residue: 0.1666 time to fit residues: 35.2387 Evaluate side-chains 151 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 745 PHE Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 92 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 54 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 81 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 12 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4674 r_free = 0.4674 target = 0.146510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.130579 restraints weight = 101442.913| |-----------------------------------------------------------------------------| r_work (start): 0.4365 rms_B_bonded: 5.67 r_work (final): 0.4365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8549 Z= 0.204 Angle : 0.674 8.250 11664 Z= 0.361 Chirality : 0.041 0.180 1335 Planarity : 0.005 0.045 1427 Dihedral : 12.148 73.440 1340 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 19.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.41 % Favored : 88.59 % Rotamer: Outliers : 3.06 % Allowed : 13.62 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.60 (0.25), residues: 990 helix: -0.64 (0.24), residues: 438 sheet: -2.47 (0.46), residues: 104 loop : -2.66 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 624 TYR 0.017 0.002 TYR A 238 PHE 0.023 0.002 PHE A 753 TRP 0.012 0.002 TRP A 216 HIS 0.009 0.002 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 8542) covalent geometry : angle 0.67165 (11661) hydrogen bonds : bond 0.04409 ( 380) hydrogen bonds : angle 5.23701 ( 1051) metal coordination : bond 0.01500 ( 7) metal coordination : angle 3.91359 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 GLU cc_start: 0.8248 (mp0) cc_final: 0.7860 (mm-30) REVERT: B 130 VAL cc_start: 0.0838 (OUTLIER) cc_final: 0.0576 (t) outliers start: 27 outliers final: 22 residues processed: 150 average time/residue: 0.1723 time to fit residues: 36.9097 Evaluate side-chains 151 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 463 MET Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 92 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 33 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.144851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.129248 restraints weight = 100764.081| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 5.60 r_work (final): 0.4338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5998 moved from start: 0.5952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8549 Z= 0.214 Angle : 0.694 7.814 11664 Z= 0.372 Chirality : 0.041 0.141 1335 Planarity : 0.005 0.052 1427 Dihedral : 12.152 73.362 1340 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 21.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.52 % Favored : 88.48 % Rotamer: Outliers : 2.84 % Allowed : 14.42 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.81 (0.25), residues: 990 helix: -0.86 (0.23), residues: 447 sheet: -2.47 (0.45), residues: 109 loop : -2.76 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 624 TYR 0.016 0.002 TYR A 674 PHE 0.025 0.002 PHE A 753 TRP 0.014 0.002 TRP A 216 HIS 0.009 0.002 HIS A 309 Details of bonding type rmsd covalent geometry : bond 0.00454 ( 8542) covalent geometry : angle 0.69032 (11661) hydrogen bonds : bond 0.04521 ( 380) hydrogen bonds : angle 5.36236 ( 1051) metal coordination : bond 0.01618 ( 7) metal coordination : angle 4.33052 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 PHE cc_start: 0.1885 (OUTLIER) cc_final: 0.1531 (t80) REVERT: A 350 GLU cc_start: 0.8295 (mp0) cc_final: 0.7897 (mm-30) REVERT: A 674 TYR cc_start: 0.7763 (m-80) cc_final: 0.7418 (m-80) outliers start: 25 outliers final: 22 residues processed: 147 average time/residue: 0.1756 time to fit residues: 36.4519 Evaluate side-chains 148 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 344 THR Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 588 VAL Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 794 MET Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 92 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 51 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 chunk 76 optimal weight: 0.5980 chunk 65 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 85 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 67 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 ASN ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 118 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4690 r_free = 0.4690 target = 0.148755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.133434 restraints weight = 99503.685| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 5.62 r_work (final): 0.4400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5850 moved from start: 0.6130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8549 Z= 0.124 Angle : 0.608 7.391 11664 Z= 0.316 Chirality : 0.038 0.173 1335 Planarity : 0.004 0.044 1427 Dihedral : 11.900 73.296 1337 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.04 % Allowed : 15.32 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.24 (0.26), residues: 990 helix: -0.36 (0.24), residues: 449 sheet: -2.46 (0.44), residues: 113 loop : -2.43 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 624 TYR 0.013 0.001 TYR A 787 PHE 0.011 0.002 PHE A 321 TRP 0.009 0.001 TRP A 290 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 8542) covalent geometry : angle 0.60634 (11661) hydrogen bonds : bond 0.03782 ( 380) hydrogen bonds : angle 4.81841 ( 1051) metal coordination : bond 0.00660 ( 7) metal coordination : angle 3.21591 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1980 Ramachandran restraints generated. 990 Oldfield, 0 Emsley, 990 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 384 is missing expected H atoms. Skipping. Residue LYS 79 is missing expected H atoms. Skipping. Residue LYS 97 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 TYR cc_start: 0.8595 (p90) cc_final: 0.7920 (p90) REVERT: A 350 GLU cc_start: 0.8157 (mp0) cc_final: 0.7763 (mm-30) REVERT: A 756 MET cc_start: 0.5376 (tmm) cc_final: 0.4808 (tmm) REVERT: A 857 GLU cc_start: 0.8602 (tp30) cc_final: 0.8164 (tp30) REVERT: A 859 PHE cc_start: 0.7997 (t80) cc_final: 0.7145 (t80) outliers start: 18 outliers final: 17 residues processed: 146 average time/residue: 0.1635 time to fit residues: 33.9141 Evaluate side-chains 147 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 599 HIS Chi-restraints excluded: chain A residue 633 MET Chi-restraints excluded: chain A residue 648 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 696 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 737 VAL Chi-restraints excluded: chain A residue 742 VAL Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain B residue 143 ASP Chi-restraints excluded: chain B residue 146 THR Chi-restraints excluded: chain D residue 92 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 82 optimal weight: 0.0030 overall best weight: 1.9394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.147566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.132127 restraints weight = 101134.398| |-----------------------------------------------------------------------------| r_work (start): 0.4379 rms_B_bonded: 5.67 r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5898 moved from start: 0.6299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8549 Z= 0.140 Angle : 0.610 7.456 11664 Z= 0.319 Chirality : 0.038 0.134 1335 Planarity : 0.004 0.040 1427 Dihedral : 11.831 73.276 1337 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 1.93 % Allowed : 15.89 % Favored : 82.18 % 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: -2.20 (0.26), residues: 990 helix: -0.32 (0.24), residues: 450 sheet: -2.33 (0.48), residues: 103 loop : -2.45 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 624 TYR 0.014 0.001 TYR A 238 PHE 0.014 0.001 PHE A 753 TRP 0.010 0.002 TRP A 598 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8542) covalent geometry : angle 0.60797 (11661) hydrogen bonds : bond 0.03818 ( 380) hydrogen bonds : angle 4.85971 ( 1051) metal coordination : bond 0.01078 ( 7) metal coordination : angle 3.26902 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3056.11 seconds wall clock time: 52 minutes 47.01 seconds (3167.01 seconds total)