Starting phenix.real_space_refine on Fri Sep 11 16:55:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7doi_30794/09_2026/7doi_30794.cif Found real_map, /net/cci-nas-00/data/ceres_data/7doi_30794/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7doi_30794/09_2026/7doi_30794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7doi_30794/09_2026/7doi_30794.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7doi_30794/09_2026/7doi_30794.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7doi_30794/09_2026/7doi_30794.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7doi_30794/09_2026/7doi_30794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7doi_30794/09_2026/7doi_30794.map" } 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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: {'RNAv2': 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: 2.40, per 1000 atoms: 0.24 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: 0.98 Conformation dependent library (CDL) restraints added in 371.4 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: 1.24 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: 2.47 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 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: 14111 3.96 - 7.91: 112 7.91 - 11.87: 13 11.87 - 15.82: 1 15.82 - 19.78: 3 Bond angle restraints: 14240 Sorted by residual: 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 angle pdb=" O2' U T 10 " pdb=" C2' U T 10 " pdb=" C1' U T 10 " ideal model delta sigma weight residual 108.20 88.67 19.53 3.00e+00 1.11e-01 4.24e+01 angle pdb=" C LYS G 139 " pdb=" N ASN G 140 " pdb=" CA ASN G 140 " ideal model delta sigma weight residual 121.14 111.07 10.07 1.75e+00 3.27e-01 3.31e+01 angle pdb=" O VAL G 131 " pdb=" C VAL G 131 " pdb=" N ILE G 132 " ideal model delta sigma weight residual 122.97 130.47 -7.50 1.32e+00 5.74e-01 3.23e+01 angle pdb=" CA LYS G 139 " pdb=" C LYS G 139 " pdb=" N ASN G 140 " ideal model delta sigma weight residual 118.14 111.04 7.10 1.31e+00 5.83e-01 2.93e+01 ... (remaining 14235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.07: 5829 25.07 - 50.14: 260 50.14 - 75.22: 30 75.22 - 100.29: 2 100.29 - 125.36: 2 Dihedral angle restraints: 6123 sinusoidal: 2578 harmonic: 3545 Sorted by residual: 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 36.34 1.47 34.88 1 3.10e+00 1.04e-01 1.79e+02 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 25.59 -13.69 39.29 3 3.80e+00 6.93e-02 1.08e+02 dihedral pdb=" O5' U T 10 " pdb=" C5' U T 10 " pdb=" C4' U T 10 " pdb=" C3' U T 10 " ideal model delta sinusoidal sigma weight residual -60.00 -1.75 -58.25 3 6.40e+00 2.44e-02 5.20e+01 ... (remaining 6120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.286: 1627 0.286 - 0.573: 2 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 -2.50 -2.20 -0.30 2.00e-01 2.50e+01 2.30e+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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.920 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 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= 1.310 Angle : 1.080 19.776 14243 Z= 0.634 Chirality : 0.078 1.432 1630 Planarity : 0.006 0.066 1714 Dihedral : 14.050 125.358 3829 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/Z covalent geometry : bond 0.00892 / 0.49 (10395) covalent geometry : angle 1.07299 / 0.63 (14240) hydrogen bonds : bond 0.19326 / 13.10 ( 459) hydrogen bonds : angle 6.75122 / 4.70 ( 1367) metal coordination : bond 0.15895 / 10.91 ( 7) metal coordination : angle 8.45212 / 5.56 ( 3) Misc. bond : bond 0.70975 / 35.69 ( 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 : 0.284 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: 0.5879 time to fit residues: 93.5131 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 : 0.392 ------------------------------------------------------------------------------- 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: 0.6980 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3690 r_free = 0.3690 target = 0.131594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.098017 restraints weight = 12711.161| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.86 r_work: 0.3117 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10405 Z= 0.131 Angle : 0.561 7.589 14243 Z= 0.290 Chirality : 0.044 0.232 1630 Planarity : 0.004 0.058 1714 Dihedral : 8.729 90.507 1635 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.09 % Allowed : 8.66 % Favored : 89.25 % 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: -1.03 (0.23), residues: 1181 helix: -0.50 (0.21), residues: 530 sheet: -0.50 (0.40), residues: 155 loop : -0.76 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 553 TYR 0.019 0.001 TYR A 921 PHE 0.018 0.001 PHE A 652 TRP 0.026 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (10395) covalent geometry : angle 0.56075 / 0.29 (14240) hydrogen bonds : bond 0.04914 / 3.29 ( 459) hydrogen bonds : angle 4.46123 / 3.10 ( 1367) metal coordination : bond 0.00965 / 0.51 ( 7) metal coordination : angle 2.02464 / 1.33 ( 3) Misc. bond : bond 0.00187 / 0.09 ( 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: 22 poor density : 124 time to evaluate : 0.364 Fit side-chains REVERT: A 92 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7452 (p0) REVERT: A 360 ASN cc_start: 0.7114 (p0) cc_final: 0.6558 (p0) REVERT: A 370 GLU cc_start: 0.7699 (pt0) cc_final: 0.7025 (pm20) REVERT: A 714 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8369 (mmmm) REVERT: A 798 LYS cc_start: 0.8248 (mmtp) cc_final: 0.7797 (mmtt) REVERT: A 846 ASP cc_start: 0.7887 (t0) cc_final: 0.7586 (t0) REVERT: A 893 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.6863 (p0) REVERT: A 916 TRP cc_start: 0.7399 (OUTLIER) cc_final: 0.6502 (p90) REVERT: B 94 MET cc_start: 0.7434 (mtm) cc_final: 0.7231 (mtp) REVERT: B 155 GLU cc_start: 0.8324 (pt0) cc_final: 0.7945 (pt0) REVERT: B 164 SER cc_start: 0.8762 (m) cc_final: 0.8310 (p) REVERT: B 165 LYS cc_start: 0.8581 (mptt) cc_final: 0.8305 (mmtm) REVERT: B 179 ASN cc_start: 0.8543 (m-40) cc_final: 0.8058 (t0) REVERT: G 174 MET cc_start: 0.5084 (OUTLIER) cc_final: 0.4827 (pmm) outliers start: 22 outliers final: 5 residues processed: 128 average time/residue: 0.5944 time to fit residues: 81.8061 Evaluate side-chains 121 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 111 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 92 ASP 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 46 THR Chi-restraints excluded: chain G residue 174 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 91 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 99 optimal weight: 0.0050 chunk 38 optimal weight: 0.7980 chunk 83 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 22 optimal weight: 10.0000 chunk 63 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 overall best weight: 1.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3684 r_free = 0.3684 target = 0.131062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.097260 restraints weight = 12923.971| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.89 r_work: 0.3102 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10405 Z= 0.146 Angle : 0.540 6.854 14243 Z= 0.277 Chirality : 0.044 0.218 1630 Planarity : 0.004 0.113 1714 Dihedral : 8.019 81.080 1635 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.66 % Allowed : 10.09 % Favored : 87.25 % 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 (0.23), residues: 1181 helix: 0.11 (0.22), residues: 536 sheet: -0.23 (0.41), residues: 153 loop : -0.58 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 553 TYR 0.017 0.002 TYR A 788 PHE 0.018 0.002 PHE A 741 TRP 0.025 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (10395) covalent geometry : angle 0.53924 / 0.28 (14240) hydrogen bonds : bond 0.04464 / 2.99 ( 459) hydrogen bonds : angle 4.19473 / 2.91 ( 1367) metal coordination : bond 0.00430 / 0.23 ( 7) metal coordination : angle 1.82740 / 1.21 ( 3) Misc. bond : bond 0.00202 / 0.10 ( 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: 28 poor density : 123 time to evaluate : 0.453 Fit side-chains REVERT: A 291 ASP cc_start: 0.8254 (m-30) cc_final: 0.7940 (m-30) REVERT: A 360 ASN cc_start: 0.7142 (p0) cc_final: 0.6557 (p0) REVERT: A 370 GLU cc_start: 0.7837 (pt0) cc_final: 0.7512 (pm20) REVERT: A 404 ASN cc_start: 0.8500 (m-40) cc_final: 0.8118 (m-40) REVERT: A 644 THR cc_start: 0.8985 (OUTLIER) cc_final: 0.8654 (m) REVERT: A 666 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8724 (mtt) REVERT: A 714 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8369 (mmmm) REVERT: A 798 LYS cc_start: 0.8279 (mmtp) cc_final: 0.7810 (mmtt) REVERT: A 846 ASP cc_start: 0.7966 (t0) cc_final: 0.7656 (t0) REVERT: A 889 ARG cc_start: 0.7671 (tpt-90) cc_final: 0.7312 (tmt90) REVERT: A 893 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.6842 (p0) REVERT: A 916 TRP cc_start: 0.7519 (OUTLIER) cc_final: 0.6624 (p90) REVERT: B 94 MET cc_start: 0.7412 (mtm) cc_final: 0.7120 (mtm) REVERT: B 109 ASN cc_start: 0.7965 (m-40) cc_final: 0.7758 (m-40) REVERT: B 155 GLU cc_start: 0.8375 (pt0) cc_final: 0.8024 (pt0) REVERT: B 164 SER cc_start: 0.8820 (m) cc_final: 0.8382 (p) REVERT: B 165 LYS cc_start: 0.8536 (mptt) cc_final: 0.8259 (mmtm) REVERT: B 179 ASN cc_start: 0.8620 (m-40) cc_final: 0.8051 (t0) outliers start: 28 outliers final: 13 residues processed: 131 average time/residue: 0.5537 time to fit residues: 78.2654 Evaluate side-chains 136 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 92 optimal weight: 20.0000 chunk 36 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 6 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 40 optimal weight: 7.9990 chunk 88 optimal weight: 0.1980 chunk 109 optimal weight: 0.9980 chunk 112 optimal weight: 0.3980 chunk 68 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3728 r_free = 0.3728 target = 0.134480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.100950 restraints weight = 12970.471| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 1.90 r_work: 0.3161 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10405 Z= 0.093 Angle : 0.479 7.290 14243 Z= 0.244 Chirality : 0.042 0.191 1630 Planarity : 0.004 0.077 1714 Dihedral : 7.576 67.192 1635 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.90 % Allowed : 11.99 % Favored : 86.11 % 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: 0.12 (0.24), residues: 1181 helix: 0.62 (0.23), residues: 524 sheet: -0.05 (0.42), residues: 143 loop : -0.31 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 553 TYR 0.013 0.001 TYR A 788 PHE 0.015 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/Z covalent geometry : bond 0.00193 / 0.09 (10395) covalent geometry : angle 0.47904 / 0.24 (14240) hydrogen bonds : bond 0.03410 / 2.25 ( 459) hydrogen bonds : angle 3.92192 / 2.71 ( 1367) metal coordination : bond 0.00197 / 0.09 ( 7) metal coordination : angle 1.35701 / 0.86 ( 3) Misc. bond : bond 0.00093 / 0.05 ( 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 145 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7826 (mt0) cc_final: 0.7589 (mt0) REVERT: A 291 ASP cc_start: 0.8285 (m-30) cc_final: 0.7999 (m-30) REVERT: A 360 ASN cc_start: 0.7136 (p0) cc_final: 0.6760 (p0) REVERT: A 370 GLU cc_start: 0.7765 (pt0) cc_final: 0.7446 (pm20) REVERT: A 404 ASN cc_start: 0.8527 (m-40) cc_final: 0.8156 (m-40) REVERT: A 519 MET cc_start: 0.8295 (mtm) cc_final: 0.8083 (ttm) REVERT: A 629 MET cc_start: 0.9336 (mmp) cc_final: 0.9055 (mmm) REVERT: A 644 THR cc_start: 0.8946 (p) cc_final: 0.8667 (m) REVERT: A 714 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8357 (mmmm) REVERT: A 798 LYS cc_start: 0.8259 (mmtp) cc_final: 0.7846 (mmmt) REVERT: A 846 ASP cc_start: 0.8004 (t0) cc_final: 0.7703 (t0) REVERT: A 889 ARG cc_start: 0.7725 (tpt-90) cc_final: 0.7418 (tmt90) REVERT: A 893 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.6872 (p0) REVERT: A 916 TRP cc_start: 0.7433 (OUTLIER) cc_final: 0.6538 (p90) REVERT: B 94 MET cc_start: 0.7438 (mtm) cc_final: 0.7113 (mtm) REVERT: B 155 GLU cc_start: 0.8349 (pt0) cc_final: 0.8011 (pt0) REVERT: B 164 SER cc_start: 0.8766 (m) cc_final: 0.8299 (p) REVERT: B 165 LYS cc_start: 0.8560 (mptt) cc_final: 0.8260 (mmtm) REVERT: B 171 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7584 (mp0) REVERT: B 174 MET cc_start: 0.7639 (tpt) cc_final: 0.7380 (tpt) REVERT: B 179 ASN cc_start: 0.8655 (m-40) cc_final: 0.8092 (t0) REVERT: G 85 SER cc_start: 0.8241 (p) cc_final: 0.7997 (t) outliers start: 20 outliers final: 8 residues processed: 131 average time/residue: 0.5740 time to fit residues: 81.2092 Evaluate side-chains 131 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 119 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain G residue 182 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 105 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.130949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.096951 restraints weight = 12912.491| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.88 r_work: 0.3099 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1852 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= 0.166 Angle : 0.539 6.572 14243 Z= 0.277 Chirality : 0.045 0.202 1630 Planarity : 0.005 0.125 1714 Dihedral : 7.622 71.477 1635 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.76 % Allowed : 12.46 % Favored : 84.78 % 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: 0.15 (0.24), residues: 1181 helix: 0.63 (0.23), residues: 527 sheet: -0.02 (0.41), residues: 143 loop : -0.30 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 553 TYR 0.018 0.002 TYR A 788 PHE 0.021 0.002 PHE A 859 TRP 0.023 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (10395) covalent geometry : angle 0.53838 / 0.28 (14240) hydrogen bonds : bond 0.04355 / 2.93 ( 459) hydrogen bonds : angle 4.03557 / 2.79 ( 1367) metal coordination : bond 0.00435 / 0.23 ( 7) metal coordination : angle 1.57965 / 1.05 ( 3) Misc. bond : bond 0.00220 / 0.10 ( 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 152 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 291 ASP cc_start: 0.8317 (m-30) cc_final: 0.8037 (m-30) REVERT: A 360 ASN cc_start: 0.7105 (p0) cc_final: 0.6777 (p0) REVERT: A 370 GLU cc_start: 0.7676 (pt0) cc_final: 0.7443 (pm20) REVERT: A 404 ASN cc_start: 0.8487 (m-40) cc_final: 0.8167 (m-40) REVERT: A 519 MET cc_start: 0.8390 (OUTLIER) cc_final: 0.8054 (ttm) REVERT: A 522 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7758 (mp0) REVERT: A 644 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8725 (m) REVERT: A 714 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8409 (mmmm) REVERT: A 798 LYS cc_start: 0.8307 (mmtp) cc_final: 0.7877 (mmmt) REVERT: A 846 ASP cc_start: 0.8117 (t0) cc_final: 0.7846 (t0) REVERT: A 889 ARG cc_start: 0.7755 (tpt-90) cc_final: 0.7448 (tmt90) REVERT: A 893 ASP cc_start: 0.7472 (OUTLIER) cc_final: 0.6978 (p0) REVERT: A 916 TRP cc_start: 0.7504 (OUTLIER) cc_final: 0.6550 (p90) REVERT: B 94 MET cc_start: 0.7488 (mtm) cc_final: 0.7250 (mtm) REVERT: B 155 GLU cc_start: 0.8390 (pt0) cc_final: 0.8066 (pt0) REVERT: B 165 LYS cc_start: 0.8544 (mptt) cc_final: 0.8286 (mmtm) REVERT: B 168 GLN cc_start: 0.8345 (mm-40) cc_final: 0.7922 (mm-40) REVERT: B 179 ASN cc_start: 0.8689 (m-40) cc_final: 0.8046 (t0) outliers start: 29 outliers final: 15 residues processed: 133 average time/residue: 0.5612 time to fit residues: 80.6887 Evaluate side-chains 142 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 568 ASN Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 644 THR 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: 0.9980 chunk 113 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 86 optimal weight: 0.2980 chunk 63 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 105 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.131240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.097382 restraints weight = 12880.512| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.88 r_work: 0.3106 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10405 Z= 0.146 Angle : 0.524 6.546 14243 Z= 0.269 Chirality : 0.044 0.200 1630 Planarity : 0.004 0.109 1714 Dihedral : 7.577 71.170 1635 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.66 % Allowed : 13.32 % Favored : 84.02 % 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: 0.20 (0.24), residues: 1181 helix: 0.68 (0.23), residues: 527 sheet: 0.00 (0.41), residues: 143 loop : -0.28 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 18 TYR 0.015 0.002 TYR A 788 PHE 0.022 0.002 PHE A 859 TRP 0.023 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (10395) covalent geometry : angle 0.52357 / 0.27 (14240) hydrogen bonds : bond 0.04107 / 2.75 ( 459) hydrogen bonds : angle 3.99780 / 2.76 ( 1367) metal coordination : bond 0.00421 / 0.22 ( 7) metal coordination : angle 2.04907 / 1.36 ( 3) Misc. bond : bond 0.00227 / 0.11 ( 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 154 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 291 ASP cc_start: 0.8358 (m-30) cc_final: 0.8077 (m-30) REVERT: A 360 ASN cc_start: 0.7174 (p0) cc_final: 0.6889 (p0) REVERT: A 370 GLU cc_start: 0.7750 (pt0) cc_final: 0.7424 (pm20) REVERT: A 404 ASN cc_start: 0.8456 (m-40) cc_final: 0.8180 (m-40) REVERT: A 519 MET cc_start: 0.8378 (OUTLIER) cc_final: 0.8125 (ttm) REVERT: A 522 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: A 644 THR cc_start: 0.8981 (OUTLIER) cc_final: 0.8672 (m) REVERT: A 714 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8400 (mmmm) REVERT: A 798 LYS cc_start: 0.8323 (mmtp) cc_final: 0.7884 (mmmt) REVERT: A 846 ASP cc_start: 0.8143 (t0) cc_final: 0.7850 (t0) REVERT: A 889 ARG cc_start: 0.7785 (tpt-90) cc_final: 0.7445 (tmt90) REVERT: A 893 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.6924 (p0) REVERT: A 916 TRP cc_start: 0.7538 (OUTLIER) cc_final: 0.6536 (p90) REVERT: B 94 MET cc_start: 0.7419 (mtm) cc_final: 0.7122 (mtm) REVERT: B 155 GLU cc_start: 0.8400 (pt0) cc_final: 0.8079 (pt0) REVERT: B 164 SER cc_start: 0.8809 (m) cc_final: 0.8417 (p) REVERT: B 165 LYS cc_start: 0.8544 (mptt) cc_final: 0.8289 (mmtm) REVERT: B 168 GLN cc_start: 0.8335 (mm-40) cc_final: 0.7930 (mm-40) REVERT: B 174 MET cc_start: 0.7674 (tpt) cc_final: 0.7404 (tpt) REVERT: B 179 ASN cc_start: 0.8709 (m-40) cc_final: 0.8056 (t0) outliers start: 28 outliers final: 17 residues processed: 136 average time/residue: 0.5866 time to fit residues: 86.1212 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 : 0.352 ------------------------------------------------------------------------------- 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 235 ASP 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 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 174 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: 3.9990 chunk 6 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 52 optimal weight: 0.3980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3693 r_free = 0.3693 target = 0.132222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.098304 restraints weight = 12864.617| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.88 r_work: 0.3118 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10405 Z= 0.124 Angle : 0.506 6.998 14243 Z= 0.258 Chirality : 0.043 0.190 1630 Planarity : 0.004 0.084 1714 Dihedral : 7.461 67.649 1635 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.76 % Allowed : 14.08 % Favored : 83.16 % 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: 0.28 (0.24), residues: 1181 helix: 0.77 (0.23), residues: 527 sheet: 0.04 (0.41), residues: 143 loop : -0.25 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 467 TYR 0.014 0.001 TYR A 788 PHE 0.022 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/Z covalent geometry : bond 0.00278 / 0.12 (10395) covalent geometry : angle 0.50524 / 0.26 (14240) hydrogen bonds : bond 0.03878 / 2.60 ( 459) hydrogen bonds : angle 3.94333 / 2.72 ( 1367) metal coordination : bond 0.00316 / 0.16 ( 7) metal coordination : angle 1.34198 / 0.89 ( 3) Misc. bond : bond 0.00187 / 0.09 ( 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 153 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 160 LYS cc_start: 0.6928 (mmmt) cc_final: 0.6610 (mmmt) REVERT: A 291 ASP cc_start: 0.8337 (m-30) cc_final: 0.8071 (m-30) REVERT: A 360 ASN cc_start: 0.7202 (p0) cc_final: 0.6890 (p0) REVERT: A 370 GLU cc_start: 0.7724 (pt0) cc_final: 0.7435 (pm20) REVERT: A 404 ASN cc_start: 0.8402 (m-40) cc_final: 0.8087 (m-40) REVERT: A 519 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8082 (ttm) REVERT: A 522 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7695 (mp0) REVERT: A 629 MET cc_start: 0.9362 (mmp) cc_final: 0.9013 (mmm) REVERT: A 644 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8650 (m) REVERT: A 666 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8647 (mtt) REVERT: A 714 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8402 (mmmm) REVERT: A 798 LYS cc_start: 0.8318 (mmtp) cc_final: 0.7899 (mmmt) REVERT: A 846 ASP cc_start: 0.7998 (t0) cc_final: 0.7709 (t0) REVERT: A 889 ARG cc_start: 0.7763 (tpt-90) cc_final: 0.7420 (tmt90) REVERT: A 893 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.6949 (p0) REVERT: A 916 TRP cc_start: 0.7507 (OUTLIER) cc_final: 0.6535 (p90) REVERT: B 94 MET cc_start: 0.7348 (mtm) cc_final: 0.7048 (mtm) REVERT: B 155 GLU cc_start: 0.8379 (pt0) cc_final: 0.8063 (pt0) REVERT: B 164 SER cc_start: 0.8793 (m) cc_final: 0.8407 (p) REVERT: B 165 LYS cc_start: 0.8545 (mptt) cc_final: 0.8285 (mmtm) REVERT: B 168 GLN cc_start: 0.8338 (mm-40) cc_final: 0.7930 (mm-40) outliers start: 29 outliers final: 17 residues processed: 137 average time/residue: 0.5430 time to fit residues: 80.4658 Evaluate side-chains 145 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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 235 ASP 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 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 174 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: 5.9990 chunk 106 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 1 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 362 HIS A 734 ASN B 158 GLN C 36 HIS C 37 ASN 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 = 0.3659 r_free = 0.3659 target = 0.129534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.095535 restraints weight = 12843.173| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 1.86 r_work: 0.3078 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10405 Z= 0.209 Angle : 0.578 9.588 14243 Z= 0.296 Chirality : 0.046 0.205 1630 Planarity : 0.004 0.084 1714 Dihedral : 7.697 76.779 1635 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.57 % Allowed : 14.27 % Favored : 83.16 % 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: 0.62 (0.23), residues: 529 sheet: -0.18 (0.39), residues: 161 loop : -0.30 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 553 TYR 0.021 0.002 TYR A 606 PHE 0.023 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/Z covalent geometry : bond 0.00487 / 0.21 (10395) covalent geometry : angle 0.57739 / 0.30 (14240) hydrogen bonds : bond 0.04747 / 3.20 ( 459) hydrogen bonds : angle 4.13449 / 2.86 ( 1367) metal coordination : bond 0.00516 / 0.28 ( 7) metal coordination : angle 1.76282 / 1.15 ( 3) Misc. bond : bond 0.00233 / 0.11 ( 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 150 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 161 ASP cc_start: 0.7932 (m-30) cc_final: 0.7697 (m-30) REVERT: A 291 ASP cc_start: 0.8377 (m-30) cc_final: 0.8116 (m-30) REVERT: A 370 GLU cc_start: 0.7650 (pt0) cc_final: 0.7310 (pm20) REVERT: A 404 ASN cc_start: 0.8348 (m-40) cc_final: 0.8134 (m-40) REVERT: A 519 MET cc_start: 0.8361 (OUTLIER) cc_final: 0.8050 (ttm) REVERT: A 522 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: A 566 MET cc_start: 0.8565 (ttm) cc_final: 0.8323 (ttm) REVERT: A 644 THR cc_start: 0.8987 (OUTLIER) cc_final: 0.8639 (m) REVERT: A 666 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8697 (mtt) REVERT: A 714 LYS cc_start: 0.8732 (mppt) cc_final: 0.8411 (mmmm) REVERT: A 798 LYS cc_start: 0.8345 (mmtp) cc_final: 0.7897 (mmmt) REVERT: A 846 ASP cc_start: 0.8150 (t0) cc_final: 0.7867 (t0) REVERT: A 893 ASP cc_start: 0.7409 (OUTLIER) cc_final: 0.6855 (p0) REVERT: A 916 TRP cc_start: 0.7601 (OUTLIER) cc_final: 0.6660 (p90) REVERT: B 155 GLU cc_start: 0.8425 (pt0) cc_final: 0.8104 (pt0) REVERT: B 165 LYS cc_start: 0.8505 (mptt) cc_final: 0.8269 (mmtm) REVERT: B 168 GLN cc_start: 0.8304 (mm-40) cc_final: 0.7927 (mm-40) outliers start: 27 outliers final: 17 residues processed: 135 average time/residue: 0.5401 time to fit residues: 78.8005 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 : 0.304 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 82 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 94 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 362 HIS 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 = 0.3682 r_free = 0.3682 target = 0.131225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.097354 restraints weight = 12886.538| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.87 r_work: 0.3106 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2977 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10405 Z= 0.139 Angle : 0.532 9.026 14243 Z= 0.271 Chirality : 0.044 0.205 1630 Planarity : 0.004 0.064 1714 Dihedral : 7.565 72.984 1635 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.57 % Allowed : 14.84 % Favored : 82.59 % 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: 0.21 (0.24), residues: 1181 helix: 0.72 (0.23), residues: 527 sheet: -0.03 (0.40), residues: 153 loop : -0.29 (0.28), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 553 TYR 0.015 0.001 TYR A 788 PHE 0.027 0.001 PHE A 859 TRP 0.022 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (10395) covalent geometry : angle 0.53180 / 0.27 (14240) hydrogen bonds : bond 0.04048 / 2.71 ( 459) hydrogen bonds : angle 4.01499 / 2.78 ( 1367) metal coordination : bond 0.00336 / 0.18 ( 7) metal coordination : angle 1.49184 / 0.99 ( 3) Misc. bond : bond 0.00183 / 0.09 ( 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 152 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 125 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 LYS cc_start: 0.6940 (mmmt) cc_final: 0.6648 (mmmt) REVERT: A 291 ASP cc_start: 0.8359 (m-30) cc_final: 0.8102 (m-30) REVERT: A 370 GLU cc_start: 0.7732 (pt0) cc_final: 0.7417 (pm20) REVERT: A 404 ASN cc_start: 0.8410 (m-40) cc_final: 0.8102 (m-40) REVERT: A 519 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.8098 (ttm) REVERT: A 522 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: A 644 THR cc_start: 0.8971 (OUTLIER) cc_final: 0.8640 (m) REVERT: A 714 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8403 (mmmm) REVERT: A 798 LYS cc_start: 0.8337 (mmtp) cc_final: 0.7895 (mmmt) REVERT: A 846 ASP cc_start: 0.8100 (t0) cc_final: 0.7795 (t0) REVERT: A 893 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7010 (p0) REVERT: A 916 TRP cc_start: 0.7491 (OUTLIER) cc_final: 0.6546 (p90) REVERT: B 155 GLU cc_start: 0.8412 (pt0) cc_final: 0.8095 (pt0) REVERT: B 164 SER cc_start: 0.8805 (m) cc_final: 0.8436 (p) REVERT: B 165 LYS cc_start: 0.8510 (mptt) cc_final: 0.8269 (mmtm) REVERT: B 168 GLN cc_start: 0.8308 (mm-40) cc_final: 0.7924 (mm-40) REVERT: B 179 ASN cc_start: 0.8500 (m-40) cc_final: 0.7933 (t0) outliers start: 27 outliers final: 18 residues processed: 135 average time/residue: 0.5665 time to fit residues: 82.5327 Evaluate side-chains 147 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 605 VAL Chi-restraints excluded: chain A residue 644 THR 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 79 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 362 HIS A 496 ASN 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 = 0.3703 r_free = 0.3703 target = 0.132655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.098729 restraints weight = 12625.050| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.87 r_work: 0.3126 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10405 Z= 0.124 Angle : 0.522 8.901 14243 Z= 0.265 Chirality : 0.043 0.205 1630 Planarity : 0.003 0.058 1714 Dihedral : 7.390 68.390 1635 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.38 % Allowed : 14.84 % Favored : 82.78 % 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: 0.78 (0.23), residues: 527 sheet: 0.02 (0.42), residues: 139 loop : -0.22 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 553 TYR 0.014 0.001 TYR A 788 PHE 0.031 0.001 PHE A 859 TRP 0.021 0.001 TRP A 916 HIS 0.003 0.001 HIS A 613 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (10395) covalent geometry : angle 0.52188 / 0.27 (14240) hydrogen bonds : bond 0.03868 / 2.58 ( 459) hydrogen bonds : angle 3.95852 / 2.74 ( 1367) metal coordination : bond 0.00314 / 0.17 ( 7) metal coordination : angle 1.40662 / 0.94 ( 3) Misc. bond : bond 0.00145 / 0.07 ( 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 150 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 160 LYS cc_start: 0.6949 (mmmt) cc_final: 0.6621 (mmmt) REVERT: A 291 ASP cc_start: 0.8374 (m-30) cc_final: 0.8107 (m-30) REVERT: A 370 GLU cc_start: 0.7761 (pt0) cc_final: 0.7420 (pm20) REVERT: A 404 ASN cc_start: 0.8309 (m-40) cc_final: 0.8073 (m-40) REVERT: A 519 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8089 (ttm) REVERT: A 522 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: A 629 MET cc_start: 0.9320 (mmp) cc_final: 0.9009 (mmm) REVERT: A 644 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8600 (m) REVERT: A 714 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8396 (mmmm) REVERT: A 798 LYS cc_start: 0.8289 (mmtp) cc_final: 0.7855 (mmmt) REVERT: A 846 ASP cc_start: 0.8051 (t0) cc_final: 0.7731 (t0) REVERT: A 855 MET cc_start: 0.6214 (mmm) cc_final: 0.5655 (tpt) REVERT: A 893 ASP cc_start: 0.7477 (OUTLIER) cc_final: 0.7016 (p0) REVERT: A 916 TRP cc_start: 0.7489 (OUTLIER) cc_final: 0.6574 (p90) REVERT: B 155 GLU cc_start: 0.8399 (pt0) cc_final: 0.8077 (pt0) REVERT: B 164 SER cc_start: 0.8798 (m) cc_final: 0.8415 (p) REVERT: B 165 LYS cc_start: 0.8505 (mptt) cc_final: 0.8242 (mmtm) REVERT: B 168 GLN cc_start: 0.8296 (mm-40) cc_final: 0.7913 (mm-40) REVERT: B 179 ASN cc_start: 0.8507 (m-40) cc_final: 0.7917 (t0) outliers start: 25 outliers final: 18 residues processed: 133 average time/residue: 0.5722 time to fit residues: 82.2091 Evaluate side-chains 147 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 605 VAL Chi-restraints excluded: chain A residue 644 THR 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 50 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 21 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 67 optimal weight: 0.0980 chunk 28 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 114 optimal weight: 0.6980 chunk 53 optimal weight: 6.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 109 ASN 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 = 0.3723 r_free = 0.3723 target = 0.134186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.100408 restraints weight = 12830.046| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.89 r_work: 0.3157 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10405 Z= 0.097 Angle : 0.496 8.783 14243 Z= 0.250 Chirality : 0.042 0.207 1630 Planarity : 0.003 0.040 1714 Dihedral : 7.223 59.818 1635 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.09 % Allowed : 15.22 % Favored : 82.68 % 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: 0.41 (0.25), residues: 1181 helix: 0.89 (0.24), residues: 528 sheet: 0.09 (0.42), residues: 143 loop : -0.20 (0.27), residues: 510 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 0.030 0.001 PHE A 859 TRP 0.019 0.001 TRP A 916 HIS 0.004 0.001 HIS C 36 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (10395) covalent geometry : angle 0.49592 / 0.25 (14240) hydrogen bonds : bond 0.03399 / 2.25 ( 459) hydrogen bonds : angle 3.86578 / 2.67 ( 1367) metal coordination : bond 0.00206 / 0.10 ( 7) metal coordination : angle 1.26322 / 0.84 ( 3) Misc. bond : bond 0.00101 / 0.05 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3904.26 seconds wall clock time: 67 minutes 18.15 seconds (4038.15 seconds total)