Starting phenix.real_space_refine on Wed Mar 4 03:23:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7doi_30794/03_2026/7doi_30794.cif Found real_map, /net/cci-nas-00/data/ceres_data/7doi_30794/03_2026/7doi_30794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7doi_30794/03_2026/7doi_30794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7doi_30794/03_2026/7doi_30794.map" model { file = "/net/cci-nas-00/data/ceres_data/7doi_30794/03_2026/7doi_30794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7doi_30794/03_2026/7doi_30794.cif" } resolution = 2.6 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= 0.007 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 32 5.49 5 Mg 4 5.21 5 S 70 5.16 5 C 6337 2.51 5 N 1691 2.21 5 O 1992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 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: 10128 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 7305 Classifications: {'peptide': 906} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 875} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 875 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 526 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 68} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 256 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 5} Link IDs: {'rna3p': 11} Chain: "T" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 310 Classifications: {'RNA': 15} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 10} Link IDs: {'rna3p': 14} Chain: "G" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 808 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain breaks: 1 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: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 24 Unusual residues: {' MG': 4, ' ZN': 2, 'POP': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "P" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HCU': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2430 SG CYS A 301 51.638 67.160 47.100 1.00 31.29 S ATOM 2471 SG CYS A 306 51.444 66.425 43.040 1.00 28.10 S ATOM 2503 SG CYS A 310 54.950 66.284 45.465 1.00 24.11 S ATOM 3911 SG CYS A 487 33.332 61.554 55.485 1.00 32.99 S ATOM 5164 SG CYS A 645 32.357 61.308 51.380 1.00 39.17 S ATOM 5170 SG CYS A 646 35.439 63.877 53.211 1.00 37.97 S Time building chain proxies: 2.16, per 1000 atoms: 0.21 Number of scatterers: 10128 At special positions: 0 Unit cell: (112.245, 94.072, 131.487, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 70 16.00 P 32 15.00 Mg 4 11.99 O 1992 8.00 N 1691 7.00 C 6337 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 509.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 295 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 310 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 306 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 301 " pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 487 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 646 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 645 " Number of angles added : 3 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2294 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 11 sheets defined 47.1% alpha, 19.2% beta 10 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 4 through 13 removed outlier: 3.503A pdb=" N GLY A 13 " --> pdb=" O ASN A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 16 No H-bonds generated for 'chain 'A' and resid 14 through 16' Processing helix chain 'A' and resid 77 through 91 removed outlier: 3.644A pdb=" N LEU A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.650A pdb=" N LEU A 127 " --> pdb=" O THR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 149 Processing helix chain 'A' and resid 153 through 159 removed outlier: 3.898A pdb=" N PHE A 157 " --> pdb=" O ASP A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 177 Processing helix chain 'A' and resid 178 through 199 Processing helix chain 'A' and resid 234 through 248 Proline residue: A 243 - end of helix removed outlier: 4.177A pdb=" N THR A 246 " --> pdb=" O MET A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 5.835A pdb=" N VAL A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ASP A 258 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR A 259 " --> pdb=" O HIS A 256 " (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 318 removed outlier: 3.713A pdb=" N PHE A 313 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 Processing helix chain 'A' and resid 377 through 385 removed outlier: 4.540A pdb=" N HIS A 381 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 426 Processing helix chain 'A' and resid 447 through 454 Processing helix chain 'A' and resid 455 through 458 removed outlier: 3.562A pdb=" N TYR A 458 " --> pdb=" O TYR A 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 455 through 458' Processing helix chain 'A' and resid 465 through 480 removed outlier: 3.957A pdb=" N TYR A 479 " --> pdb=" O VAL A 475 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE A 480 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 509 removed outlier: 3.689A pdb=" N LYS A 508 " --> pdb=" O PRO A 505 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP A 509 " --> pdb=" O PHE A 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 505 through 509' Processing helix chain 'A' and resid 511 through 519 removed outlier: 3.851A pdb=" N TYR A 515 " --> pdb=" O LYS A 511 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 531 Processing helix chain 'A' and resid 561 through 581 removed outlier: 6.099A pdb=" N LYS A 574 " --> pdb=" O GLN A 570 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N LEU A 575 " --> pdb=" O PHE A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 627 through 639 Processing helix chain 'A' and resid 640 through 642 No H-bonds generated for 'chain 'A' and resid 640 through 642' Processing helix chain 'A' and resid 647 through 663 removed outlier: 3.508A pdb=" N LEU A 663 " --> pdb=" O CYS A 659 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 709 Processing helix chain 'A' and resid 711 through 715 removed outlier: 3.673A pdb=" N ILE A 715 " --> pdb=" O GLY A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 733 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 768 through 773 Processing helix chain 'A' and resid 778 through 789 Processing helix chain 'A' and resid 833 through 842 Processing helix chain 'A' and resid 854 through 867 Processing helix chain 'A' and resid 868 through 872 removed outlier: 3.589A pdb=" N LYS A 871 " --> pdb=" O PRO A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 874 through 893 removed outlier: 4.353A pdb=" N PHE A 881 " --> pdb=" O TYR A 877 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS A 882 " --> pdb=" O ALA A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 918 through 923 removed outlier: 3.546A pdb=" N GLU A 922 " --> pdb=" O PRO A 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 97 removed outlier: 4.191A pdb=" N LEU B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 108 removed outlier: 3.529A pdb=" N ILE B 106 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 134 through 142 Processing helix chain 'B' and resid 176 through 180 removed outlier: 3.590A pdb=" N LEU B 180 " --> pdb=" O SER B 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 20 removed outlier: 3.723A pdb=" N VAL C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 24 Processing helix chain 'C' and resid 25 through 40 removed outlier: 3.509A pdb=" N GLN C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 60 removed outlier: 3.529A pdb=" N ALA C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS C 51 " --> pdb=" O GLU C 47 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 85 through 96 removed outlier: 3.663A pdb=" N PHE G 92 " --> pdb=" O GLN G 88 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET G 94 " --> pdb=" O MET G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 112 Processing helix chain 'G' and resid 135 through 140 removed outlier: 3.787A pdb=" N ASN G 140 " --> pdb=" O ASN G 136 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 21 removed outlier: 5.460A pdb=" N SER A 68 " --> pdb=" O GLU A 58 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N TYR A 69 " --> pdb=" O ARG A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 31 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 224 removed outlier: 7.108A pdb=" N VAL A 233 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N GLY A 203 " --> pdb=" O VAL A 233 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.684A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N SER A 363 " --> pdb=" O LYS A 332 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N PHE A 334 " --> pdb=" O SER A 363 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 355 removed outlier: 6.684A pdb=" N LEU A 329 " --> pdb=" O THR A 344 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TYR A 346 " --> pdb=" O GLY A 327 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLY A 327 " --> pdb=" O TYR A 346 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.600A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 559 removed outlier: 6.600A pdb=" N THR A 540 " --> pdb=" O MET A 668 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 399 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N VAL A 675 " --> pdb=" O SER A 397 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N SER A 397 " --> pdb=" O VAL A 675 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N VAL A 398 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N LEU A 388 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 185 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL B 159 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR B 187 " --> pdb=" O GLN B 157 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL B 159 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA9, first strand: chain 'A' and resid 753 through 758 Processing sheet with id=AB1, first strand: chain 'A' and resid 815 through 822 removed outlier: 3.565A pdb=" N ASP A 825 " --> pdb=" O GLN A 822 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 127 through 132 removed outlier: 6.476A pdb=" N LEU G 189 " --> pdb=" O ILE G 156 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ILE G 156 " --> pdb=" O LEU G 189 " (cutoff:3.500A) 470 hydrogen bonds defined for protein. 1323 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2404 1.33 - 1.45: 2329 1.45 - 1.57: 5500 1.57 - 1.69: 57 1.69 - 1.81: 105 Bond restraints: 10395 Sorted by residual: bond pdb=" O3 HCU P1201 " pdb=" P1 HCU P1201 " ideal model delta sigma weight residual 1.668 1.429 0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C9 HCU P1201 " pdb=" O3 HCU P1201 " ideal model delta sigma weight residual 1.417 1.222 0.195 2.00e-02 2.50e+03 9.52e+01 bond pdb=" O4 HCU P1201 " pdb=" P1 HCU P1201 " ideal model delta sigma weight residual 1.519 1.337 0.182 2.00e-02 2.50e+03 8.25e+01 bond pdb=" C SER A 15 " pdb=" N ALA A 16 " ideal model delta sigma weight residual 1.331 1.218 0.114 1.36e-02 5.41e+03 6.99e+01 bond pdb=" C7 HCU P1201 " pdb=" C8 HCU P1201 " ideal model delta sigma weight residual 1.535 1.375 0.160 2.00e-02 2.50e+03 6.39e+01 ... (remaining 10390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.96: 14130 3.96 - 7.91: 91 7.91 - 11.87: 13 11.87 - 15.82: 1 15.82 - 19.78: 5 Bond angle restraints: 14240 Sorted by residual: angle pdb=" O2' U T 10 " pdb=" C2' U T 10 " pdb=" C1' U T 10 " ideal model delta sigma weight residual 108.40 88.67 19.73 1.50e+00 4.44e-01 1.73e+02 angle pdb=" C4' U P 20 " pdb=" C3' U P 20 " pdb=" O3' U P 20 " ideal model delta sigma weight residual 113.00 123.85 -10.85 1.50e+00 4.44e-01 5.23e+01 angle pdb=" O3' U P 20 " pdb=" C3' U P 20 " pdb=" C2' U P 20 " ideal model delta sigma weight residual 113.70 103.30 10.40 1.50e+00 4.44e-01 4.80e+01 angle pdb=" C3' U T 10 " pdb=" C2' U T 10 " pdb=" O2' U T 10 " ideal model delta sigma weight residual 110.70 120.83 -10.13 1.50e+00 4.44e-01 4.56e+01 angle pdb=" C7 HCU P1201 " pdb=" C8 HCU P1201 " pdb=" C9 HCU P1201 " ideal model delta sigma weight residual 112.97 132.75 -19.78 3.00e+00 1.11e-01 4.35e+01 ... (remaining 14235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5581 17.95 - 35.89: 495 35.89 - 53.84: 88 53.84 - 71.79: 33 71.79 - 89.73: 6 Dihedral angle restraints: 6203 sinusoidal: 2658 harmonic: 3545 Sorted by residual: dihedral pdb=" O4' U T 10 " pdb=" C2' U T 10 " pdb=" C1' U T 10 " pdb=" C3' U T 10 " ideal model delta sinusoidal sigma weight residual 25.00 -13.69 38.69 1 8.00e+00 1.56e-02 3.29e+01 dihedral pdb=" CA ASP G 163 " pdb=" C ASP G 163 " pdb=" N SER G 164 " pdb=" CA SER G 164 " ideal model delta harmonic sigma weight residual 180.00 152.07 27.93 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" C4' U T 10 " pdb=" C3' U T 10 " pdb=" C2' U T 10 " pdb=" C1' U T 10 " ideal model delta sinusoidal sigma weight residual 36.00 1.47 34.53 1 8.00e+00 1.56e-02 2.64e+01 ... (remaining 6200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.286: 1628 0.286 - 0.573: 1 0.573 - 0.859: 0 0.859 - 1.146: 0 1.146 - 1.432: 1 Chirality restraints: 1630 Sorted by residual: chirality pdb=" C8 HCU P1201 " pdb=" C10 HCU P1201 " pdb=" C7 HCU P1201 " pdb=" C9 HCU P1201 " both_signs ideal model delta sigma weight residual False -2.60 -1.17 -1.43 2.00e-01 2.50e+01 5.13e+01 chirality pdb=" CA TRP A 916 " pdb=" N TRP A 916 " pdb=" C TRP A 916 " pdb=" CB TRP A 916 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" C3' U T 10 " pdb=" C4' U T 10 " pdb=" O3' U T 10 " pdb=" C2' U T 10 " both_signs ideal model delta sigma weight residual False -2.48 -2.20 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 1627 not shown) Planarity restraints: 1714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U T 10 " -0.054 2.00e-02 2.50e+03 2.90e-02 1.89e+01 pdb=" N1 U T 10 " 0.063 2.00e-02 2.50e+03 pdb=" C2 U T 10 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U T 10 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U T 10 " 0.007 2.00e-02 2.50e+03 pdb=" C4 U T 10 " -0.000 2.00e-02 2.50e+03 pdb=" O4 U T 10 " -0.023 2.00e-02 2.50e+03 pdb=" C5 U T 10 " -0.003 2.00e-02 2.50e+03 pdb=" C6 U T 10 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 139 " 0.013 2.00e-02 2.50e+03 2.70e-02 7.30e+00 pdb=" C LYS G 139 " -0.047 2.00e-02 2.50e+03 pdb=" O LYS G 139 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN G 140 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP G 182 " -0.044 5.00e-02 4.00e+02 6.62e-02 7.00e+00 pdb=" N PRO G 183 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO G 183 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 183 " -0.037 5.00e-02 4.00e+02 ... (remaining 1711 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 86 2.60 - 3.17: 7903 3.17 - 3.75: 16222 3.75 - 4.32: 23573 4.32 - 4.90: 37481 Nonbonded interactions: 85265 Sorted by model distance: nonbonded pdb=" OD2 ASP A 218 " pdb="MG MG A1006 " model vdw 2.021 2.170 nonbonded pdb="MG MG A1006 " pdb=" O4 POP A1008 " model vdw 2.073 2.170 nonbonded pdb=" OD1 ASN A 209 " pdb="MG MG A1007 " model vdw 2.120 2.170 nonbonded pdb=" N3 U T 10 " pdb=" O1 HCU P1201 " model vdw 2.153 3.120 nonbonded pdb=" OG SER A 501 " pdb=" OP1 C T 9 " model vdw 2.198 3.040 ... (remaining 85260 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 'B' and (resid 84 through 95 or (resid 96 and (name N or name CA or name \ C or name O or name CB )) or resid 97 through 110 or (resid 111 and (name N or n \ ame CA or name C or name O or name CB )) or resid 112 through 179 or resid 182 t \ hrough 191)) selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.170 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:6.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 : 0.016 0.891 10405 Z= 1.313 Angle : 1.072 19.776 14243 Z= 0.663 Chirality : 0.073 1.432 1630 Planarity : 0.006 0.066 1714 Dihedral : 14.384 89.733 3909 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 0.29 % Allowed : 5.14 % Favored : 94.58 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 5.00 % 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: -2.36 (0.21), residues: 1181 helix: -1.84 (0.19), residues: 501 sheet: -0.86 (0.39), residues: 155 loop : -1.33 (0.23), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 889 TYR 0.024 0.003 TYR A 788 PHE 0.031 0.003 PHE A 741 TRP 0.019 0.003 TRP A 916 HIS 0.015 0.002 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00900 (10395) covalent geometry : angle 1.06464 (14240) hydrogen bonds : bond 0.19326 ( 459) hydrogen bonds : angle 6.75122 ( 1367) metal coordination : bond 0.15895 ( 7) metal coordination : angle 8.45212 ( 3) Misc. bond : bond 0.70975 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 147 time to evaluate : 0.369 Fit side-chains REVERT: A 9 ASN cc_start: 0.8044 (m-40) cc_final: 0.7840 (m110) REVERT: A 360 ASN cc_start: 0.6946 (p0) cc_final: 0.6564 (p0) REVERT: A 370 GLU cc_start: 0.7191 (pt0) cc_final: 0.6965 (pt0) REVERT: A 519 MET cc_start: 0.8630 (mtp) cc_final: 0.8239 (mtm) REVERT: A 798 LYS cc_start: 0.8194 (mmtp) cc_final: 0.7946 (mmtt) REVERT: A 916 TRP cc_start: 0.7084 (OUTLIER) cc_final: 0.6484 (p90) REVERT: B 155 GLU cc_start: 0.7823 (pt0) cc_final: 0.7443 (pt0) REVERT: B 164 SER cc_start: 0.8658 (m) cc_final: 0.8427 (p) REVERT: B 165 LYS cc_start: 0.8527 (mptt) cc_final: 0.8242 (mmtm) REVERT: B 179 ASN cc_start: 0.8381 (m110) cc_final: 0.8173 (t0) REVERT: G 103 LEU cc_start: 0.8592 (mt) cc_final: 0.8389 (mt) REVERT: G 104 ASN cc_start: 0.8556 (m-40) cc_final: 0.8275 (m-40) outliers start: 3 outliers final: 1 residues processed: 148 average time/residue: 0.6008 time to fit residues: 95.1232 Evaluate side-chains 123 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 121 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 916 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 9 ASN A 113 HIS A 158 ASN A 224 GLN A 357 GLN A 362 HIS A 381 HIS A 408 GLN A 468 GLN A 492 GLN A 568 ASN A 691 ASN A 705 ASN A 773 GLN B 109 ASN B 157 GLN B 179 ASN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN G 105 ASN G 108 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.131813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.098149 restraints weight = 12742.620| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.87 r_work: 0.3117 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10405 Z= 0.131 Angle : 0.526 7.254 14243 Z= 0.282 Chirality : 0.041 0.190 1630 Planarity : 0.004 0.059 1714 Dihedral : 10.539 73.190 1715 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 1.90 % Allowed : 9.13 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.23), residues: 1181 helix: -0.52 (0.21), residues: 536 sheet: -0.49 (0.40), residues: 155 loop : -0.78 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 553 TYR 0.019 0.001 TYR A 921 PHE 0.018 0.001 PHE A 652 TRP 0.025 0.002 TRP A 916 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00282 (10395) covalent geometry : angle 0.52502 (14240) hydrogen bonds : bond 0.04815 ( 459) hydrogen bonds : angle 4.41505 ( 1367) metal coordination : bond 0.00994 ( 7) metal coordination : angle 1.98671 ( 3) Misc. bond : bond 0.00095 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.393 Fit side-chains REVERT: A 92 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7455 (p0) REVERT: A 360 ASN cc_start: 0.7115 (p0) cc_final: 0.6562 (p0) REVERT: A 370 GLU cc_start: 0.7703 (pt0) cc_final: 0.7026 (pm20) REVERT: A 644 THR cc_start: 0.8921 (p) cc_final: 0.8567 (m) REVERT: A 714 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8373 (mmmm) REVERT: A 798 LYS cc_start: 0.8254 (mmtp) cc_final: 0.7804 (mmtt) REVERT: A 846 ASP cc_start: 0.7873 (t0) cc_final: 0.7584 (t0) REVERT: A 893 ASP cc_start: 0.7378 (OUTLIER) cc_final: 0.6817 (p0) REVERT: A 916 TRP cc_start: 0.7424 (OUTLIER) cc_final: 0.6518 (p90) REVERT: B 155 GLU cc_start: 0.8343 (pt0) cc_final: 0.7957 (pt0) REVERT: B 164 SER cc_start: 0.8777 (m) cc_final: 0.8323 (p) REVERT: B 165 LYS cc_start: 0.8561 (mptt) cc_final: 0.8299 (mmtm) REVERT: B 179 ASN cc_start: 0.8540 (m-40) cc_final: 0.8057 (t0) REVERT: C 62 MET cc_start: 0.7831 (ptp) cc_final: 0.7460 (ptp) outliers start: 20 outliers final: 6 residues processed: 130 average time/residue: 0.6125 time to fit residues: 85.4256 Evaluate side-chains 122 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 ASP Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 916 TRP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 46 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 91 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 99 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 89 optimal weight: 7.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 642 HIS A 822 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN G 108 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.130296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.096441 restraints weight = 12939.702| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.88 r_work: 0.3091 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10405 Z= 0.162 Angle : 0.525 6.222 14243 Z= 0.281 Chirality : 0.042 0.202 1630 Planarity : 0.004 0.040 1714 Dihedral : 10.380 73.397 1715 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.95 % Allowed : 10.37 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.24), residues: 1181 helix: 0.08 (0.22), residues: 535 sheet: -0.23 (0.41), residues: 153 loop : -0.54 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 553 TYR 0.019 0.002 TYR A 788 PHE 0.020 0.002 PHE A 741 TRP 0.025 0.002 TRP A 916 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00367 (10395) covalent geometry : angle 0.52441 (14240) hydrogen bonds : bond 0.04684 ( 459) hydrogen bonds : angle 4.23434 ( 1367) metal coordination : bond 0.00472 ( 7) metal coordination : angle 1.86388 ( 3) Misc. bond : bond 0.00091 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 120 time to evaluate : 0.375 Fit side-chains REVERT: A 291 ASP cc_start: 0.8287 (m-30) cc_final: 0.8006 (m-30) REVERT: A 360 ASN cc_start: 0.7132 (p0) cc_final: 0.6541 (p0) REVERT: A 370 GLU cc_start: 0.7864 (pt0) cc_final: 0.7518 (pm20) REVERT: A 404 ASN cc_start: 0.8488 (m-40) cc_final: 0.8106 (m-40) REVERT: A 644 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8648 (m) REVERT: A 666 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8748 (mtt) REVERT: A 714 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8379 (mmmm) REVERT: A 798 LYS cc_start: 0.8282 (mmtp) cc_final: 0.7810 (mmtt) REVERT: A 846 ASP cc_start: 0.7969 (t0) cc_final: 0.7665 (t0) REVERT: A 889 ARG cc_start: 0.7666 (tpt-90) cc_final: 0.7319 (tmt90) REVERT: A 893 ASP cc_start: 0.7368 (OUTLIER) cc_final: 0.6791 (p0) REVERT: A 916 TRP cc_start: 0.7535 (OUTLIER) cc_final: 0.6597 (p90) REVERT: B 155 GLU cc_start: 0.8394 (pt0) cc_final: 0.8086 (pt0) REVERT: B 164 SER cc_start: 0.8811 (m) cc_final: 0.8342 (p) REVERT: B 165 LYS cc_start: 0.8524 (mptt) cc_final: 0.8253 (mmtm) REVERT: B 179 ASN cc_start: 0.8627 (m-40) cc_final: 0.8045 (t0) outliers start: 31 outliers final: 14 residues processed: 131 average time/residue: 0.5640 time to fit residues: 79.7274 Evaluate side-chains 135 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 916 TRP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 182 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 92 optimal weight: 6.9990 chunk 36 optimal weight: 0.0010 chunk 43 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 104 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 88 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 112 optimal weight: 0.2980 chunk 68 optimal weight: 3.9990 chunk 94 optimal weight: 0.7980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 734 ASN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN G 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.134081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.100509 restraints weight = 13003.646| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.90 r_work: 0.3154 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10405 Z= 0.091 Angle : 0.450 6.182 14243 Z= 0.240 Chirality : 0.039 0.163 1630 Planarity : 0.003 0.037 1714 Dihedral : 10.141 73.401 1715 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.00 % Allowed : 11.99 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.24), residues: 1181 helix: 0.57 (0.23), residues: 524 sheet: -0.03 (0.42), residues: 143 loop : -0.29 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 553 TYR 0.012 0.001 TYR A 788 PHE 0.024 0.001 PHE A 859 TRP 0.022 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00187 (10395) covalent geometry : angle 0.44913 (14240) hydrogen bonds : bond 0.03461 ( 459) hydrogen bonds : angle 3.95914 ( 1367) metal coordination : bond 0.00216 ( 7) metal coordination : angle 1.37921 ( 3) Misc. bond : bond 0.00052 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 291 ASP cc_start: 0.8295 (m-30) cc_final: 0.8020 (m-30) REVERT: A 360 ASN cc_start: 0.7125 (p0) cc_final: 0.6717 (p0) REVERT: A 370 GLU cc_start: 0.7753 (pt0) cc_final: 0.7423 (pm20) REVERT: A 404 ASN cc_start: 0.8491 (m-40) cc_final: 0.8130 (m-40) REVERT: A 519 MET cc_start: 0.8341 (mtm) cc_final: 0.8120 (ttm) REVERT: A 644 THR cc_start: 0.8962 (p) cc_final: 0.8683 (m) REVERT: A 714 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8362 (mmmm) REVERT: A 798 LYS cc_start: 0.8267 (mmtp) cc_final: 0.7850 (mmtt) REVERT: A 846 ASP cc_start: 0.8004 (t0) cc_final: 0.7704 (t0) REVERT: A 889 ARG cc_start: 0.7715 (tpt-90) cc_final: 0.7401 (tmt90) REVERT: A 893 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.6856 (p0) REVERT: A 916 TRP cc_start: 0.7422 (OUTLIER) cc_final: 0.6544 (p90) REVERT: B 155 GLU cc_start: 0.8349 (pt0) cc_final: 0.8005 (pt0) REVERT: B 164 SER cc_start: 0.8770 (m) cc_final: 0.8310 (p) REVERT: B 165 LYS cc_start: 0.8557 (mptt) cc_final: 0.8269 (mmtm) REVERT: B 171 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7565 (mp0) REVERT: B 179 ASN cc_start: 0.8619 (m-40) cc_final: 0.8060 (t0) outliers start: 21 outliers final: 7 residues processed: 133 average time/residue: 0.5563 time to fit residues: 79.7758 Evaluate side-chains 130 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 119 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 916 TRP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain G residue 87 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 71 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 chunk 33 optimal weight: 0.9990 chunk 94 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 734 ASN B 109 ASN C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.130448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.096558 restraints weight = 12896.589| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.87 r_work: 0.3093 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10405 Z= 0.176 Angle : 0.520 8.755 14243 Z= 0.277 Chirality : 0.043 0.201 1630 Planarity : 0.004 0.075 1714 Dihedral : 10.054 73.521 1715 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.57 % Allowed : 12.56 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.24), residues: 1181 helix: 0.59 (0.23), residues: 527 sheet: -0.03 (0.42), residues: 143 loop : -0.33 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 553 TYR 0.018 0.002 TYR A 788 PHE 0.025 0.002 PHE A 859 TRP 0.024 0.002 TRP A 916 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00406 (10395) covalent geometry : angle 0.51922 (14240) hydrogen bonds : bond 0.04410 ( 459) hydrogen bonds : angle 4.06820 ( 1367) metal coordination : bond 0.00445 ( 7) metal coordination : angle 1.56488 ( 3) Misc. bond : bond 0.00105 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.397 Fit side-chains revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7789 (OUTLIER) cc_final: 0.7589 (mpt-90) REVERT: A 291 ASP cc_start: 0.8357 (m-30) cc_final: 0.8075 (m-30) REVERT: A 360 ASN cc_start: 0.7181 (p0) cc_final: 0.6834 (p0) REVERT: A 370 GLU cc_start: 0.7692 (pt0) cc_final: 0.7359 (pm20) REVERT: A 404 ASN cc_start: 0.8580 (m-40) cc_final: 0.8214 (m-40) REVERT: A 519 MET cc_start: 0.8341 (OUTLIER) cc_final: 0.8033 (ttm) REVERT: A 522 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7743 (mp0) REVERT: A 644 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8663 (m) REVERT: A 666 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8713 (mtt) REVERT: A 714 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8407 (mmmm) REVERT: A 798 LYS cc_start: 0.8309 (mmtp) cc_final: 0.7875 (mmtt) REVERT: A 846 ASP cc_start: 0.8141 (t0) cc_final: 0.7849 (t0) REVERT: A 889 ARG cc_start: 0.7753 (tpt-90) cc_final: 0.7442 (tmt90) REVERT: A 893 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.6956 (p0) REVERT: A 916 TRP cc_start: 0.7503 (OUTLIER) cc_final: 0.6519 (p90) REVERT: B 155 GLU cc_start: 0.8403 (pt0) cc_final: 0.8077 (pt0) REVERT: B 165 LYS cc_start: 0.8535 (mptt) cc_final: 0.8275 (mmtm) REVERT: B 179 ASN cc_start: 0.8705 (m-40) cc_final: 0.8054 (t0) outliers start: 27 outliers final: 15 residues processed: 132 average time/residue: 0.5380 time to fit residues: 76.7719 Evaluate side-chains 145 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ARG Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 916 TRP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 182 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 82 optimal weight: 0.9990 chunk 113 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 9.9990 chunk 86 optimal weight: 0.2980 chunk 63 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 734 ASN B 109 ASN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN G 105 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.133570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.099830 restraints weight = 12969.863| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.90 r_work: 0.3145 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10405 Z= 0.099 Angle : 0.452 6.696 14243 Z= 0.241 Chirality : 0.040 0.193 1630 Planarity : 0.003 0.056 1714 Dihedral : 9.780 73.446 1715 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.19 % Allowed : 13.42 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.24), residues: 1181 helix: 0.76 (0.23), residues: 528 sheet: 0.03 (0.41), residues: 143 loop : -0.21 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 553 TYR 0.013 0.001 TYR A 788 PHE 0.019 0.001 PHE A 859 TRP 0.021 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00212 (10395) covalent geometry : angle 0.45177 (14240) hydrogen bonds : bond 0.03483 ( 459) hydrogen bonds : angle 3.88695 ( 1367) metal coordination : bond 0.00290 ( 7) metal coordination : angle 1.79694 ( 3) Misc. bond : bond 0.00110 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 291 ASP cc_start: 0.8374 (m-30) cc_final: 0.8104 (m-30) REVERT: A 360 ASN cc_start: 0.7148 (p0) cc_final: 0.6835 (p0) REVERT: A 370 GLU cc_start: 0.7752 (pt0) cc_final: 0.7413 (pm20) REVERT: A 404 ASN cc_start: 0.8446 (m-40) cc_final: 0.8100 (m-40) REVERT: A 519 MET cc_start: 0.8296 (OUTLIER) cc_final: 0.8072 (ttm) REVERT: A 644 THR cc_start: 0.8970 (p) cc_final: 0.8682 (m) REVERT: A 666 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8659 (mtt) REVERT: A 714 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8371 (mmmm) REVERT: A 798 LYS cc_start: 0.8256 (mmtp) cc_final: 0.7827 (mmmt) REVERT: A 846 ASP cc_start: 0.8039 (t0) cc_final: 0.7742 (t0) REVERT: A 889 ARG cc_start: 0.7779 (tpt-90) cc_final: 0.7458 (tmt90) REVERT: A 893 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.6927 (p0) REVERT: A 916 TRP cc_start: 0.7421 (OUTLIER) cc_final: 0.6495 (p90) REVERT: B 155 GLU cc_start: 0.8384 (pt0) cc_final: 0.8061 (pt0) REVERT: B 164 SER cc_start: 0.8815 (m) cc_final: 0.8418 (p) REVERT: B 165 LYS cc_start: 0.8558 (mptt) cc_final: 0.8256 (mmtm) REVERT: B 168 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7785 (mm-40) REVERT: B 171 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: B 174 MET cc_start: 0.7828 (tpt) cc_final: 0.7584 (tpt) REVERT: B 179 ASN cc_start: 0.8687 (m-40) cc_final: 0.8053 (t0) outliers start: 23 outliers final: 10 residues processed: 132 average time/residue: 0.5865 time to fit residues: 83.1903 Evaluate side-chains 139 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 916 TRP Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 182 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 78 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 49 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 734 ASN B 109 ASN C 36 HIS C 37 ASN G 105 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.129962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.095777 restraints weight = 12735.083| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.88 r_work: 0.3080 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10405 Z= 0.222 Angle : 0.549 6.673 14243 Z= 0.294 Chirality : 0.045 0.207 1630 Planarity : 0.004 0.074 1714 Dihedral : 10.016 73.710 1715 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.95 % Allowed : 13.32 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.24), residues: 1181 helix: 0.60 (0.23), residues: 525 sheet: -0.17 (0.39), residues: 165 loop : -0.29 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 467 TYR 0.021 0.002 TYR A 606 PHE 0.024 0.002 PHE A 741 TRP 0.025 0.002 TRP A 916 HIS 0.007 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00520 (10395) covalent geometry : angle 0.54874 (14240) hydrogen bonds : bond 0.04822 ( 459) hydrogen bonds : angle 4.14285 ( 1367) metal coordination : bond 0.00544 ( 7) metal coordination : angle 1.61583 ( 3) Misc. bond : bond 0.00137 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 291 ASP cc_start: 0.8406 (m-30) cc_final: 0.8140 (m-30) REVERT: A 360 ASN cc_start: 0.7146 (p0) cc_final: 0.6859 (p0) REVERT: A 370 GLU cc_start: 0.7709 (pt0) cc_final: 0.7128 (pt0) REVERT: A 404 ASN cc_start: 0.8495 (m-40) cc_final: 0.8228 (m-40) REVERT: A 519 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8060 (ttm) REVERT: A 522 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: A 644 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8738 (m) REVERT: A 666 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8744 (mtt) REVERT: A 714 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8399 (mmmm) REVERT: A 798 LYS cc_start: 0.8327 (mmtp) cc_final: 0.7854 (mmmt) REVERT: A 846 ASP cc_start: 0.8201 (t0) cc_final: 0.7910 (t0) REVERT: A 889 ARG cc_start: 0.7805 (tpt-90) cc_final: 0.7462 (tmt90) REVERT: A 893 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.6975 (p0) REVERT: A 916 TRP cc_start: 0.7604 (OUTLIER) cc_final: 0.6533 (p90) REVERT: B 155 GLU cc_start: 0.8433 (pt0) cc_final: 0.8100 (pt0) REVERT: B 165 LYS cc_start: 0.8426 (mptt) cc_final: 0.8216 (mmtm) REVERT: B 168 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7881 (mm-40) outliers start: 31 outliers final: 16 residues processed: 139 average time/residue: 0.5662 time to fit residues: 84.9730 Evaluate side-chains 148 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 568 ASN Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 916 TRP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 182 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 84 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 1 optimal weight: 0.0060 chunk 107 optimal weight: 10.0000 chunk 17 optimal weight: 0.5980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 734 ASN B 109 ASN G 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.133513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.099874 restraints weight = 12831.973| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.88 r_work: 0.3146 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10405 Z= 0.096 Angle : 0.466 11.275 14243 Z= 0.245 Chirality : 0.040 0.197 1630 Planarity : 0.003 0.052 1714 Dihedral : 9.743 73.444 1715 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.47 % Allowed : 13.99 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.25), residues: 1181 helix: 0.81 (0.23), residues: 527 sheet: 0.04 (0.42), residues: 143 loop : -0.22 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 553 TYR 0.012 0.001 TYR A 788 PHE 0.020 0.001 PHE A 859 TRP 0.020 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00205 (10395) covalent geometry : angle 0.46508 (14240) hydrogen bonds : bond 0.03491 ( 459) hydrogen bonds : angle 3.90919 ( 1367) metal coordination : bond 0.00300 ( 7) metal coordination : angle 1.66501 ( 3) Misc. bond : bond 0.00051 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 160 LYS cc_start: 0.6779 (mmmt) cc_final: 0.6490 (mmmt) REVERT: A 291 ASP cc_start: 0.8368 (m-30) cc_final: 0.8112 (m-30) REVERT: A 370 GLU cc_start: 0.7722 (pt0) cc_final: 0.7381 (pm20) REVERT: A 519 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.8089 (ttm) REVERT: A 522 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: A 644 THR cc_start: 0.8968 (p) cc_final: 0.8659 (m) REVERT: A 666 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8667 (mtt) REVERT: A 714 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8387 (mmmm) REVERT: A 798 LYS cc_start: 0.8300 (mmtp) cc_final: 0.7888 (mmmt) REVERT: A 846 ASP cc_start: 0.7940 (t0) cc_final: 0.7631 (t0) REVERT: A 889 ARG cc_start: 0.7764 (tpt-90) cc_final: 0.7407 (tmt90) REVERT: A 893 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.6958 (p0) REVERT: A 916 TRP cc_start: 0.7439 (OUTLIER) cc_final: 0.6478 (p90) REVERT: B 155 GLU cc_start: 0.8358 (pt0) cc_final: 0.8042 (pt0) REVERT: B 164 SER cc_start: 0.8818 (m) cc_final: 0.8430 (p) REVERT: B 165 LYS cc_start: 0.8546 (mptt) cc_final: 0.8258 (mmtm) REVERT: B 168 GLN cc_start: 0.8288 (mm-40) cc_final: 0.7939 (mm-40) REVERT: B 179 ASN cc_start: 0.8480 (m-40) cc_final: 0.7890 (t0) outliers start: 26 outliers final: 15 residues processed: 138 average time/residue: 0.5441 time to fit residues: 80.9446 Evaluate side-chains 144 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 859 PHE Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 916 TRP Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 174 MET Chi-restraints excluded: chain G residue 182 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 103 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 56 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 91 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 705 ASN A 734 ASN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN G 104 ASN G 105 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.129983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.095824 restraints weight = 12754.174| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.87 r_work: 0.3079 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10405 Z= 0.223 Angle : 0.563 9.708 14243 Z= 0.299 Chirality : 0.045 0.208 1630 Planarity : 0.004 0.071 1714 Dihedral : 10.008 73.647 1715 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.19 % Allowed : 14.84 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.24), residues: 1181 helix: 0.62 (0.23), residues: 525 sheet: -0.18 (0.39), residues: 165 loop : -0.32 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 553 TYR 0.023 0.002 TYR A 606 PHE 0.024 0.002 PHE A 741 TRP 0.024 0.002 TRP A 916 HIS 0.006 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00522 (10395) covalent geometry : angle 0.56256 (14240) hydrogen bonds : bond 0.04825 ( 459) hydrogen bonds : angle 4.15979 ( 1367) metal coordination : bond 0.00549 ( 7) metal coordination : angle 1.63894 ( 3) Misc. bond : bond 0.00170 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 291 ASP cc_start: 0.8419 (m-30) cc_final: 0.8160 (m-30) REVERT: A 370 GLU cc_start: 0.7709 (pt0) cc_final: 0.7175 (pt0) REVERT: A 519 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.8068 (ttm) REVERT: A 522 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7687 (mp0) REVERT: A 644 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8729 (m) REVERT: A 666 MET cc_start: 0.9123 (OUTLIER) cc_final: 0.8760 (mtt) REVERT: A 714 LYS cc_start: 0.8724 (OUTLIER) cc_final: 0.8405 (mmmm) REVERT: A 798 LYS cc_start: 0.8326 (mmtp) cc_final: 0.7854 (mmmt) REVERT: A 846 ASP cc_start: 0.8235 (t0) cc_final: 0.7901 (t0) REVERT: A 855 MET cc_start: 0.6475 (mmm) cc_final: 0.6205 (mmm) REVERT: A 893 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.6882 (p0) REVERT: A 916 TRP cc_start: 0.7621 (OUTLIER) cc_final: 0.6663 (p90) REVERT: B 155 GLU cc_start: 0.8433 (pt0) cc_final: 0.8100 (pt0) REVERT: B 165 LYS cc_start: 0.8408 (mptt) cc_final: 0.8165 (mmtm) REVERT: B 168 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7783 (mm-40) outliers start: 23 outliers final: 14 residues processed: 133 average time/residue: 0.5808 time to fit residues: 83.1065 Evaluate side-chains 145 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 859 PHE Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 916 TRP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 182 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 79 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 705 ASN A 734 ASN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN B 158 GLN G 104 ASN G 105 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.131034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.097227 restraints weight = 12769.164| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.87 r_work: 0.3106 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10405 Z= 0.145 Angle : 0.520 11.194 14243 Z= 0.274 Chirality : 0.042 0.199 1630 Planarity : 0.004 0.062 1714 Dihedral : 9.882 73.455 1715 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.09 % Allowed : 14.94 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.24), residues: 1181 helix: 0.71 (0.23), residues: 523 sheet: -0.06 (0.40), residues: 153 loop : -0.31 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 553 TYR 0.015 0.002 TYR A 788 PHE 0.022 0.001 PHE A 859 TRP 0.022 0.001 TRP A 916 HIS 0.004 0.001 HIS A 613 Details of bonding type rmsd covalent geometry : bond 0.00330 (10395) covalent geometry : angle 0.51961 (14240) hydrogen bonds : bond 0.04158 ( 459) hydrogen bonds : angle 4.05234 ( 1367) metal coordination : bond 0.00399 ( 7) metal coordination : angle 1.92848 ( 3) Misc. bond : bond 0.00111 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 LYS cc_start: 0.6996 (mmmt) cc_final: 0.6682 (tptt) REVERT: A 291 ASP cc_start: 0.8418 (m-30) cc_final: 0.8164 (m-30) REVERT: A 370 GLU cc_start: 0.7774 (pt0) cc_final: 0.7457 (pm20) REVERT: A 519 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.8094 (ttm) REVERT: A 522 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: A 644 THR cc_start: 0.9024 (OUTLIER) cc_final: 0.8671 (m) REVERT: A 666 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8714 (mtt) REVERT: A 714 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8405 (mmmm) REVERT: A 798 LYS cc_start: 0.8316 (mmtp) cc_final: 0.7879 (mmmt) REVERT: A 846 ASP cc_start: 0.8087 (t0) cc_final: 0.7785 (t0) REVERT: A 855 MET cc_start: 0.6377 (mmm) cc_final: 0.6137 (mmm) REVERT: A 893 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7028 (p0) REVERT: A 916 TRP cc_start: 0.7530 (OUTLIER) cc_final: 0.6573 (p90) REVERT: B 155 GLU cc_start: 0.8403 (pt0) cc_final: 0.8081 (pt0) REVERT: B 164 SER cc_start: 0.8809 (m) cc_final: 0.8423 (p) REVERT: B 165 LYS cc_start: 0.8520 (mptt) cc_final: 0.8255 (mmtm) REVERT: B 168 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7902 (mm-40) REVERT: B 179 ASN cc_start: 0.8493 (m-40) cc_final: 0.7914 (t0) outliers start: 22 outliers final: 13 residues processed: 133 average time/residue: 0.5679 time to fit residues: 81.3438 Evaluate side-chains 141 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 522 GLU Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 667 VAL Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 859 PHE Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 916 TRP Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 182 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 50 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 734 ASN ** A 790 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN G 104 ASN G 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.132672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.098887 restraints weight = 12852.232| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.89 r_work: 0.3131 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10405 Z= 0.115 Angle : 0.489 10.968 14243 Z= 0.257 Chirality : 0.041 0.205 1630 Planarity : 0.003 0.051 1714 Dihedral : 9.731 73.436 1715 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.90 % Allowed : 15.13 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.25), residues: 1181 helix: 0.79 (0.23), residues: 527 sheet: 0.03 (0.42), residues: 143 loop : -0.23 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 553 TYR 0.013 0.001 TYR A 788 PHE 0.022 0.001 PHE A 859 TRP 0.020 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd covalent geometry : bond 0.00257 (10395) covalent geometry : angle 0.48839 (14240) hydrogen bonds : bond 0.03712 ( 459) hydrogen bonds : angle 3.94992 ( 1367) metal coordination : bond 0.00195 ( 7) metal coordination : angle 1.15624 ( 3) Misc. bond : bond 0.00094 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3859.19 seconds wall clock time: 66 minutes 22.19 seconds (3982.19 seconds total)