Starting phenix.real_space_refine on Mon Jul 28 14:59:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7doi_30794/07_2025/7doi_30794.cif Found real_map, /net/cci-nas-00/data/ceres_data/7doi_30794/07_2025/7doi_30794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7doi_30794/07_2025/7doi_30794.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7doi_30794/07_2025/7doi_30794.map" model { file = "/net/cci-nas-00/data/ceres_data/7doi_30794/07_2025/7doi_30794.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7doi_30794/07_2025/7doi_30794.cif" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10128 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 7305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 7305 Classifications: {'peptide': 906} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 875} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 875 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 108} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 526 Classifications: {'peptide': 69} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 68} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 256 Classifications: {'RNA': 12} Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 5} Link IDs: {'rna3p': 11} Chain: "T" Number of atoms: 310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 310 Classifications: {'RNA': 15} Modifications used: {'rna3p_pur': 5, 'rna3p_pyr': 10} Link IDs: {'rna3p': 14} Chain: "G" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 808 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 24 Unusual residues: {' MG': 4, ' ZN': 2, 'POP': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "P" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'HCU': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2430 SG CYS A 301 51.638 67.160 47.100 1.00 31.29 S ATOM 2471 SG CYS A 306 51.444 66.425 43.040 1.00 28.10 S ATOM 2503 SG CYS A 310 54.950 66.284 45.465 1.00 24.11 S ATOM 3911 SG CYS A 487 33.332 61.554 55.485 1.00 32.99 S ATOM 5164 SG CYS A 645 32.357 61.308 51.380 1.00 39.17 S ATOM 5170 SG CYS A 646 35.439 63.877 53.211 1.00 37.97 S Time building chain proxies: 6.55, per 1000 atoms: 0.65 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: 2.65 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 3.69 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: 4.20 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2404 1.33 - 1.45: 2329 1.45 - 1.57: 5500 1.57 - 1.69: 57 1.69 - 1.81: 105 Bond restraints: 10395 Sorted by residual: bond pdb=" O3 HCU P1201 " pdb=" P1 HCU P1201 " ideal model delta sigma weight residual 1.668 1.429 0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C9 HCU P1201 " pdb=" O3 HCU P1201 " ideal model delta sigma weight residual 1.417 1.222 0.195 2.00e-02 2.50e+03 9.52e+01 bond pdb=" O4 HCU P1201 " pdb=" P1 HCU P1201 " ideal model delta sigma weight residual 1.519 1.337 0.182 2.00e-02 2.50e+03 8.25e+01 bond pdb=" C SER A 15 " pdb=" N ALA A 16 " ideal model delta sigma weight residual 1.331 1.218 0.114 1.36e-02 5.41e+03 6.99e+01 bond pdb=" C7 HCU P1201 " pdb=" C8 HCU P1201 " ideal model delta sigma weight residual 1.535 1.375 0.160 2.00e-02 2.50e+03 6.39e+01 ... (remaining 10390 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.96: 14130 3.96 - 7.91: 91 7.91 - 11.87: 13 11.87 - 15.82: 1 15.82 - 19.78: 5 Bond angle restraints: 14240 Sorted by residual: angle pdb=" O2' U T 10 " pdb=" C2' U T 10 " pdb=" C1' U T 10 " ideal model delta sigma weight residual 108.40 88.67 19.73 1.50e+00 4.44e-01 1.73e+02 angle pdb=" C4' U P 20 " pdb=" C3' U P 20 " pdb=" O3' U P 20 " ideal model delta sigma weight residual 113.00 123.85 -10.85 1.50e+00 4.44e-01 5.23e+01 angle pdb=" O3' U P 20 " pdb=" C3' U P 20 " pdb=" C2' U P 20 " ideal model delta sigma weight residual 113.70 103.30 10.40 1.50e+00 4.44e-01 4.80e+01 angle pdb=" C3' U T 10 " pdb=" C2' U T 10 " pdb=" O2' U T 10 " ideal model delta sigma weight residual 110.70 120.83 -10.13 1.50e+00 4.44e-01 4.56e+01 angle pdb=" C7 HCU P1201 " pdb=" C8 HCU P1201 " pdb=" C9 HCU P1201 " ideal model delta sigma weight residual 112.97 132.75 -19.78 3.00e+00 1.11e-01 4.35e+01 ... (remaining 14235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5581 17.95 - 35.89: 495 35.89 - 53.84: 88 53.84 - 71.79: 33 71.79 - 89.73: 6 Dihedral angle restraints: 6203 sinusoidal: 2658 harmonic: 3545 Sorted by residual: dihedral pdb=" O4' U T 10 " pdb=" C2' U T 10 " pdb=" C1' U T 10 " pdb=" C3' U T 10 " ideal model delta sinusoidal sigma weight residual 25.00 -13.69 38.69 1 8.00e+00 1.56e-02 3.29e+01 dihedral pdb=" CA ASP G 163 " pdb=" C ASP G 163 " pdb=" N SER G 164 " pdb=" CA SER G 164 " ideal model delta harmonic sigma weight residual 180.00 152.07 27.93 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" C4' U T 10 " pdb=" C3' U T 10 " pdb=" C2' U T 10 " pdb=" C1' U T 10 " ideal model delta sinusoidal sigma weight residual 36.00 1.47 34.53 1 8.00e+00 1.56e-02 2.64e+01 ... (remaining 6200 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.286: 1628 0.286 - 0.573: 1 0.573 - 0.859: 0 0.859 - 1.146: 0 1.146 - 1.432: 1 Chirality restraints: 1630 Sorted by residual: chirality pdb=" C8 HCU P1201 " pdb=" C10 HCU P1201 " pdb=" C7 HCU P1201 " pdb=" C9 HCU P1201 " both_signs ideal model delta sigma weight residual False -2.60 -1.17 -1.43 2.00e-01 2.50e+01 5.13e+01 chirality pdb=" CA TRP A 916 " pdb=" N TRP A 916 " pdb=" C TRP A 916 " pdb=" CB TRP A 916 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" C3' U T 10 " pdb=" C4' U T 10 " pdb=" O3' U T 10 " pdb=" C2' U T 10 " both_signs ideal model delta sigma weight residual False -2.48 -2.20 -0.28 2.00e-01 2.50e+01 1.99e+00 ... (remaining 1627 not shown) Planarity restraints: 1714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U T 10 " -0.054 2.00e-02 2.50e+03 2.90e-02 1.89e+01 pdb=" N1 U T 10 " 0.063 2.00e-02 2.50e+03 pdb=" C2 U T 10 " 0.001 2.00e-02 2.50e+03 pdb=" O2 U T 10 " 0.001 2.00e-02 2.50e+03 pdb=" N3 U T 10 " 0.007 2.00e-02 2.50e+03 pdb=" C4 U T 10 " -0.000 2.00e-02 2.50e+03 pdb=" O4 U T 10 " -0.023 2.00e-02 2.50e+03 pdb=" C5 U T 10 " -0.003 2.00e-02 2.50e+03 pdb=" C6 U T 10 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS G 139 " 0.013 2.00e-02 2.50e+03 2.70e-02 7.30e+00 pdb=" C LYS G 139 " -0.047 2.00e-02 2.50e+03 pdb=" O LYS G 139 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN G 140 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP G 182 " -0.044 5.00e-02 4.00e+02 6.62e-02 7.00e+00 pdb=" N PRO G 183 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO G 183 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 183 " -0.037 5.00e-02 4.00e+02 ... (remaining 1711 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.60: 86 2.60 - 3.17: 7903 3.17 - 3.75: 16222 3.75 - 4.32: 23573 4.32 - 4.90: 37481 Nonbonded interactions: 85265 Sorted by model distance: nonbonded pdb=" OD2 ASP A 218 " pdb="MG MG A1006 " model vdw 2.021 2.170 nonbonded pdb="MG MG A1006 " pdb=" O4 POP A1008 " model vdw 2.073 2.170 nonbonded pdb=" OD1 ASN A 209 " pdb="MG MG A1007 " model vdw 2.120 2.170 nonbonded pdb=" N3 U T 10 " pdb=" O1 HCU P1201 " model vdw 2.153 3.120 nonbonded pdb=" OG SER A 501 " pdb=" OP1 C T 9 " model vdw 2.198 3.040 ... (remaining 85260 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'B' and (resid 84 through 95 or (resid 96 and (name N or name CA or name \ C or name O or name CB )) or resid 97 through 110 or (resid 111 and (name N or n \ ame CA or name C or name O or name CB )) or resid 112 through 179 or resid 182 t \ hrough 191)) selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 32.000 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 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:13.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.891 10405 Z= 1.313 Angle : 1.072 19.776 14243 Z= 0.663 Chirality : 0.073 1.432 1630 Planarity : 0.006 0.066 1714 Dihedral : 14.384 89.733 3909 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 5.88 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.019 0.003 TRP A 916 HIS 0.015 0.002 HIS A 613 PHE 0.031 0.003 PHE A 741 TYR 0.024 0.003 TYR A 788 ARG 0.020 0.001 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.19326 ( 459) hydrogen bonds : angle 6.75122 ( 1367) metal coordination : bond 0.15895 ( 7) metal coordination : angle 8.45212 ( 3) covalent geometry : bond 0.00900 (10395) covalent geometry : angle 1.06464 (14240) Misc. bond : bond 0.70975 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2362 Ramachandran restraints generated. 1181 Oldfield, 0 Emsley, 1181 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 147 time to evaluate : 1.009 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: 1.2514 time to fit residues: 199.4440 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 : 1.008 ------------------------------------------------------------------------------- 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 100 optimal weight: 0.4980 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 93 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 9 ASN A 113 HIS A 158 ASN A 224 GLN A 357 GLN A 362 HIS A 381 HIS A 408 GLN A 468 GLN A 492 GLN A 568 ASN A 691 ASN A 705 ASN A 773 GLN B 109 ASN B 157 GLN B 179 ASN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN G 105 ASN G 108 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.132534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.098994 restraints weight = 12718.088| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.87 r_work: 0.3132 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10405 Z= 0.117 Angle : 0.520 7.815 14243 Z= 0.278 Chirality : 0.040 0.188 1630 Planarity : 0.005 0.086 1714 Dihedral : 10.539 73.296 1715 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.71 % Allowed : 8.94 % Favored : 89.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.22), residues: 1181 helix: -0.44 (0.22), residues: 521 sheet: -0.43 (0.41), residues: 153 loop : -0.76 (0.25), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.016 0.001 PHE A 652 TYR 0.017 0.001 TYR A 921 ARG 0.003 0.000 ARG A 513 Details of bonding type rmsd hydrogen bonds : bond 0.04866 ( 459) hydrogen bonds : angle 4.44270 ( 1367) metal coordination : bond 0.01465 ( 7) metal coordination : angle 2.10210 ( 3) covalent geometry : bond 0.00239 (10395) covalent geometry : angle 0.51907 (14240) Misc. bond : bond 0.00150 ( 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 143 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 1.077 Fit side-chains REVERT: A 92 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7454 (p0) REVERT: A 360 ASN cc_start: 0.7088 (p0) cc_final: 0.6561 (p0) REVERT: A 370 GLU cc_start: 0.7702 (pt0) cc_final: 0.7025 (pm20) REVERT: A 644 THR cc_start: 0.8935 (p) cc_final: 0.8590 (m) REVERT: A 714 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8363 (mmmm) REVERT: A 798 LYS cc_start: 0.8239 (mmtp) cc_final: 0.7782 (mmtt) REVERT: A 846 ASP cc_start: 0.7870 (t0) cc_final: 0.7586 (t0) REVERT: A 893 ASP cc_start: 0.7384 (OUTLIER) cc_final: 0.6838 (p0) REVERT: A 916 TRP cc_start: 0.7370 (OUTLIER) cc_final: 0.6466 (p90) REVERT: B 155 GLU cc_start: 0.8393 (pt0) cc_final: 0.7974 (pt0) REVERT: B 164 SER cc_start: 0.8755 (m) cc_final: 0.8277 (p) REVERT: B 165 LYS cc_start: 0.8585 (mptt) cc_final: 0.8306 (mmtm) REVERT: B 171 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: B 179 ASN cc_start: 0.8524 (m-40) cc_final: 0.8043 (t0) REVERT: C 62 MET cc_start: 0.7929 (ptp) cc_final: 0.7616 (ptp) REVERT: G 103 LEU cc_start: 0.8263 (mt) cc_final: 0.8043 (mt) REVERT: G 174 MET cc_start: 0.5086 (OUTLIER) cc_final: 0.4829 (pmm) outliers start: 18 outliers final: 4 residues processed: 129 average time/residue: 1.2583 time to fit residues: 174.8060 Evaluate side-chains 122 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 171 GLU 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 4 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 58 optimal weight: 0.0670 chunk 33 optimal weight: 0.0040 chunk 35 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 0.1980 chunk 54 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 overall best weight: 1.4534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.131850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.098010 restraints weight = 12891.499| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 1.89 r_work: 0.3114 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10405 Z= 0.128 Angle : 0.494 6.468 14243 Z= 0.264 Chirality : 0.041 0.200 1630 Planarity : 0.004 0.041 1714 Dihedral : 10.272 73.425 1715 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.28 % Allowed : 9.80 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.23), residues: 1181 helix: 0.19 (0.22), residues: 534 sheet: -0.15 (0.42), residues: 143 loop : -0.53 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.017 0.001 PHE A 741 TYR 0.018 0.001 TYR A 788 ARG 0.009 0.000 ARG A 553 Details of bonding type rmsd hydrogen bonds : bond 0.04281 ( 459) hydrogen bonds : angle 4.14023 ( 1367) metal coordination : bond 0.00514 ( 7) metal coordination : angle 1.85884 ( 3) covalent geometry : bond 0.00281 (10395) covalent geometry : angle 0.49346 (14240) Misc. bond : bond 0.00104 ( 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 144 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 1.087 Fit side-chains REVERT: A 291 ASP cc_start: 0.8260 (m-30) cc_final: 0.7955 (m-30) REVERT: A 360 ASN cc_start: 0.7102 (p0) cc_final: 0.6537 (p0) REVERT: A 370 GLU cc_start: 0.7797 (pt0) cc_final: 0.7448 (pm20) REVERT: A 404 ASN cc_start: 0.8481 (m-40) cc_final: 0.8101 (m-40) REVERT: A 644 THR cc_start: 0.8974 (OUTLIER) cc_final: 0.8646 (m) REVERT: A 666 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8720 (mtt) REVERT: A 714 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8372 (mmmm) REVERT: A 798 LYS cc_start: 0.8251 (mmtp) cc_final: 0.7795 (mmtt) REVERT: A 846 ASP cc_start: 0.7907 (t0) cc_final: 0.7608 (t0) REVERT: A 889 ARG cc_start: 0.7699 (tpt-90) cc_final: 0.7338 (tmt90) REVERT: A 893 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.6856 (p0) REVERT: A 916 TRP cc_start: 0.7394 (OUTLIER) cc_final: 0.6526 (p90) REVERT: B 155 GLU cc_start: 0.8382 (pt0) cc_final: 0.7974 (pt0) REVERT: B 164 SER cc_start: 0.8805 (m) cc_final: 0.8334 (p) REVERT: B 165 LYS cc_start: 0.8533 (mptt) cc_final: 0.8243 (mmtm) REVERT: B 171 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7773 (mp0) REVERT: B 179 ASN cc_start: 0.8607 (m-40) cc_final: 0.8040 (t0) REVERT: C 62 MET cc_start: 0.7808 (ptp) cc_final: 0.7519 (ptp) outliers start: 24 outliers final: 11 residues processed: 128 average time/residue: 1.2423 time to fit residues: 171.5353 Evaluate side-chains 130 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 1.083 ------------------------------------------------------------------------------- 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 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 19 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 31 optimal weight: 0.0020 chunk 65 optimal weight: 0.9980 chunk 84 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 overall best weight: 2.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 416 ASN A 642 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.129653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.095784 restraints weight = 12840.826| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.87 r_work: 0.3081 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10405 Z= 0.197 Angle : 0.539 8.245 14243 Z= 0.288 Chirality : 0.044 0.205 1630 Planarity : 0.004 0.058 1714 Dihedral : 10.334 73.690 1715 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.76 % Allowed : 11.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.24), residues: 1181 helix: 0.30 (0.23), residues: 535 sheet: -0.27 (0.39), residues: 165 loop : -0.44 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 916 HIS 0.006 0.001 HIS A 613 PHE 0.022 0.002 PHE A 741 TYR 0.019 0.002 TYR A 606 ARG 0.005 0.000 ARG A 553 Details of bonding type rmsd hydrogen bonds : bond 0.04800 ( 459) hydrogen bonds : angle 4.21205 ( 1367) metal coordination : bond 0.00502 ( 7) metal coordination : angle 1.79624 ( 3) covalent geometry : bond 0.00453 (10395) covalent geometry : angle 0.53818 (14240) Misc. bond : bond 0.00111 ( 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 150 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 1.014 Fit side-chains REVERT: A 291 ASP cc_start: 0.8290 (m-30) cc_final: 0.8005 (m-30) REVERT: A 334 PHE cc_start: 0.8088 (m-80) cc_final: 0.7881 (m-80) REVERT: A 360 ASN cc_start: 0.7185 (p0) cc_final: 0.6854 (p0) REVERT: A 370 GLU cc_start: 0.7697 (pt0) cc_final: 0.7153 (pt0) REVERT: A 404 ASN cc_start: 0.8480 (m-40) cc_final: 0.8101 (m-40) REVERT: A 519 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.8102 (ttm) REVERT: A 644 THR cc_start: 0.9005 (OUTLIER) cc_final: 0.8678 (m) REVERT: A 666 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8752 (mtt) REVERT: A 714 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8378 (mmmm) REVERT: A 798 LYS cc_start: 0.8306 (mmtp) cc_final: 0.7872 (mmtt) REVERT: A 846 ASP cc_start: 0.8082 (t0) cc_final: 0.7789 (t0) REVERT: A 889 ARG cc_start: 0.7687 (tpt-90) cc_final: 0.7335 (tmt90) REVERT: A 893 ASP cc_start: 0.7477 (OUTLIER) cc_final: 0.6879 (p0) REVERT: A 916 TRP cc_start: 0.7578 (OUTLIER) cc_final: 0.6581 (p90) REVERT: B 155 GLU cc_start: 0.8407 (pt0) cc_final: 0.8060 (pt0) REVERT: B 165 LYS cc_start: 0.8517 (mptt) cc_final: 0.8213 (mmtm) REVERT: B 179 ASN cc_start: 0.8701 (m-40) cc_final: 0.8050 (t0) outliers start: 29 outliers final: 14 residues processed: 130 average time/residue: 1.1427 time to fit residues: 160.8916 Evaluate side-chains 141 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 1.163 ------------------------------------------------------------------------------- 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 519 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 818 MET 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 26 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 57 optimal weight: 0.8980 chunk 25 optimal weight: 0.0670 chunk 112 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 734 ASN B 109 ASN C 31 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN G 105 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.131748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.098017 restraints weight = 12698.370| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.87 r_work: 0.3119 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10405 Z= 0.120 Angle : 0.478 6.517 14243 Z= 0.256 Chirality : 0.041 0.199 1630 Planarity : 0.003 0.037 1714 Dihedral : 9.991 73.455 1715 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.47 % Allowed : 11.99 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.24), residues: 1181 helix: 0.57 (0.23), residues: 527 sheet: -0.06 (0.42), residues: 143 loop : -0.32 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.017 0.001 PHE A 859 TYR 0.015 0.001 TYR A 788 ARG 0.004 0.000 ARG A 553 Details of bonding type rmsd hydrogen bonds : bond 0.03954 ( 459) hydrogen bonds : angle 4.03486 ( 1367) metal coordination : bond 0.00272 ( 7) metal coordination : angle 1.54878 ( 3) covalent geometry : bond 0.00263 (10395) covalent geometry : angle 0.47702 (14240) Misc. bond : bond 0.00159 ( 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 151 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 1.147 Fit side-chains revert: symmetry clash REVERT: A 291 ASP cc_start: 0.8310 (m-30) cc_final: 0.8046 (m-30) REVERT: A 360 ASN cc_start: 0.7132 (p0) cc_final: 0.6807 (p0) REVERT: A 370 GLU cc_start: 0.7753 (pt0) cc_final: 0.7429 (pm20) REVERT: A 404 ASN cc_start: 0.8533 (m-40) cc_final: 0.8159 (m-40) REVERT: A 522 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: A 644 THR cc_start: 0.8967 (p) cc_final: 0.8665 (m) REVERT: A 666 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8686 (mtt) REVERT: A 714 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8395 (mmmm) REVERT: A 798 LYS cc_start: 0.8318 (mmtp) cc_final: 0.7890 (mmtt) REVERT: A 846 ASP cc_start: 0.8121 (t0) cc_final: 0.7821 (t0) REVERT: A 889 ARG cc_start: 0.7757 (tpt-90) cc_final: 0.7435 (tmt90) REVERT: A 893 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.6899 (p0) REVERT: A 916 TRP cc_start: 0.7473 (OUTLIER) cc_final: 0.6490 (p90) REVERT: B 155 GLU cc_start: 0.8391 (pt0) cc_final: 0.8042 (pt0) REVERT: B 164 SER cc_start: 0.8811 (m) cc_final: 0.8407 (p) REVERT: B 165 LYS cc_start: 0.8544 (mptt) cc_final: 0.8277 (mmtm) REVERT: B 174 MET cc_start: 0.7829 (tpt) cc_final: 0.7565 (tpt) REVERT: B 179 ASN cc_start: 0.8705 (m-40) cc_final: 0.8047 (t0) outliers start: 26 outliers final: 15 residues processed: 133 average time/residue: 1.1667 time to fit residues: 169.1427 Evaluate side-chains 143 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 522 GLU Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 847 ILE Chi-restraints excluded: chain A residue 893 ASP Chi-restraints excluded: chain A residue 916 TRP Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain C residue 15 SER Chi-restraints excluded: chain C residue 46 THR Chi-restraints excluded: chain G residue 87 MET Chi-restraints excluded: chain G residue 174 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 45 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 734 ASN B 109 ASN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.131532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.097437 restraints weight = 12696.171| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 1.88 r_work: 0.3105 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10405 Z= 0.142 Angle : 0.488 5.799 14243 Z= 0.262 Chirality : 0.042 0.201 1630 Planarity : 0.003 0.037 1714 Dihedral : 9.927 73.438 1715 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.76 % Allowed : 12.37 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.24), residues: 1181 helix: 0.64 (0.23), residues: 527 sheet: -0.05 (0.42), residues: 143 loop : -0.29 (0.27), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 916 HIS 0.006 0.001 HIS C 36 PHE 0.021 0.002 PHE A 859 TYR 0.015 0.002 TYR A 788 ARG 0.006 0.000 ARG A 553 Details of bonding type rmsd hydrogen bonds : bond 0.04180 ( 459) hydrogen bonds : angle 4.03932 ( 1367) metal coordination : bond 0.00351 ( 7) metal coordination : angle 1.60604 ( 3) covalent geometry : bond 0.00322 (10395) covalent geometry : angle 0.48715 (14240) Misc. bond : bond 0.00103 ( 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 157 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 1.126 Fit side-chains revert: symmetry clash REVERT: A 291 ASP cc_start: 0.8351 (m-30) cc_final: 0.8082 (m-30) REVERT: A 360 ASN cc_start: 0.7138 (p0) cc_final: 0.6827 (p0) REVERT: A 370 GLU cc_start: 0.7795 (pt0) cc_final: 0.7445 (pm20) REVERT: A 404 ASN cc_start: 0.8486 (m-40) cc_final: 0.8197 (m-40) REVERT: A 522 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7687 (mp0) REVERT: A 644 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8727 (m) REVERT: A 666 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8728 (mtt) REVERT: A 714 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8387 (mmmm) REVERT: A 798 LYS cc_start: 0.8291 (mmtp) cc_final: 0.7860 (mmmt) REVERT: A 846 ASP cc_start: 0.8140 (t0) cc_final: 0.7821 (t0) REVERT: A 889 ARG cc_start: 0.7782 (tpt-90) cc_final: 0.7442 (tmt90) REVERT: A 893 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.6927 (p0) REVERT: A 916 TRP cc_start: 0.7548 (OUTLIER) cc_final: 0.6536 (p90) REVERT: B 155 GLU cc_start: 0.8414 (pt0) cc_final: 0.8086 (pt0) REVERT: B 164 SER cc_start: 0.8790 (m) cc_final: 0.8383 (p) REVERT: B 165 LYS cc_start: 0.8486 (mptt) cc_final: 0.8220 (mmtm) outliers start: 29 outliers final: 15 residues processed: 136 average time/residue: 1.2858 time to fit residues: 189.1142 Evaluate side-chains 147 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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 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 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 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 12 optimal weight: 0.9980 chunk 51 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 734 ASN B 109 ASN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.132030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.098118 restraints weight = 12999.979| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.90 r_work: 0.3119 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2008 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= 0.121 Angle : 0.481 10.179 14243 Z= 0.254 Chirality : 0.041 0.198 1630 Planarity : 0.003 0.038 1714 Dihedral : 9.820 73.430 1715 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.28 % Allowed : 13.51 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.24), residues: 1181 helix: 0.73 (0.23), residues: 527 sheet: -0.03 (0.41), residues: 139 loop : -0.23 (0.27), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 PHE 0.024 0.001 PHE A 859 TYR 0.014 0.001 TYR A 788 ARG 0.006 0.000 ARG A 553 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 459) hydrogen bonds : angle 3.96609 ( 1367) metal coordination : bond 0.00382 ( 7) metal coordination : angle 1.91943 ( 3) covalent geometry : bond 0.00272 (10395) covalent geometry : angle 0.48007 (14240) Misc. bond : bond 0.00087 ( 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 152 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 2.170 Fit side-chains revert: symmetry clash REVERT: A 160 LYS cc_start: 0.6987 (mmmt) cc_final: 0.6606 (tptt) REVERT: A 291 ASP cc_start: 0.8370 (m-30) cc_final: 0.8091 (m-30) REVERT: A 360 ASN cc_start: 0.7181 (p0) cc_final: 0.6897 (p0) REVERT: A 370 GLU cc_start: 0.7733 (pt0) cc_final: 0.7417 (pm20) REVERT: A 404 ASN cc_start: 0.8450 (m-40) cc_final: 0.8102 (m-40) REVERT: A 644 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8736 (m) REVERT: A 666 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8692 (mtt) REVERT: A 714 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8405 (mmmm) REVERT: A 798 LYS cc_start: 0.8301 (mmtp) cc_final: 0.7870 (mmmt) REVERT: A 846 ASP cc_start: 0.8087 (t0) cc_final: 0.7791 (t0) REVERT: A 889 ARG cc_start: 0.7785 (tpt-90) cc_final: 0.7444 (tmt90) REVERT: A 893 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.6939 (p0) REVERT: A 916 TRP cc_start: 0.7510 (OUTLIER) cc_final: 0.6500 (p90) REVERT: B 155 GLU cc_start: 0.8390 (pt0) cc_final: 0.8068 (pt0) REVERT: B 164 SER cc_start: 0.8812 (m) cc_final: 0.8417 (p) REVERT: B 165 LYS cc_start: 0.8527 (mptt) cc_final: 0.8257 (mmtm) outliers start: 24 outliers final: 16 residues processed: 135 average time/residue: 1.3428 time to fit residues: 195.8407 Evaluate side-chains 147 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 124 MET Chi-restraints excluded: chain A residue 335 VAL Chi-restraints excluded: chain A residue 519 MET Chi-restraints excluded: chain A residue 605 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 666 MET Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 818 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 75 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 chunk 55 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 29 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 chunk 65 optimal weight: 0.8980 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 734 ASN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.130100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.096021 restraints weight = 12987.899| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.89 r_work: 0.3088 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10405 Z= 0.184 Angle : 0.528 8.828 14243 Z= 0.281 Chirality : 0.043 0.206 1630 Planarity : 0.004 0.072 1714 Dihedral : 9.971 73.667 1715 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.76 % Allowed : 13.61 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.24), residues: 1181 helix: 0.65 (0.23), residues: 523 sheet: -0.11 (0.40), residues: 149 loop : -0.31 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 916 HIS 0.005 0.001 HIS C 36 PHE 0.023 0.002 PHE A 859 TYR 0.018 0.002 TYR A 606 ARG 0.003 0.000 ARG A 555 Details of bonding type rmsd hydrogen bonds : bond 0.04530 ( 459) hydrogen bonds : angle 4.10792 ( 1367) metal coordination : bond 0.00391 ( 7) metal coordination : angle 1.55397 ( 3) covalent geometry : bond 0.00424 (10395) covalent geometry : angle 0.52796 (14240) Misc. bond : bond 0.00126 ( 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 155 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: A 291 ASP cc_start: 0.8398 (m-30) cc_final: 0.8137 (m-30) REVERT: A 370 GLU cc_start: 0.7657 (pt0) cc_final: 0.7317 (pm20) REVERT: A 404 ASN cc_start: 0.8463 (m-40) cc_final: 0.8184 (m-40) REVERT: A 522 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: A 644 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8735 (m) REVERT: A 666 MET cc_start: 0.9093 (OUTLIER) cc_final: 0.8722 (mtt) REVERT: A 714 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8406 (mmmm) REVERT: A 798 LYS cc_start: 0.8342 (mmtp) cc_final: 0.7892 (mmmt) REVERT: A 846 ASP cc_start: 0.8114 (t0) cc_final: 0.7842 (t0) REVERT: A 893 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.6966 (p0) REVERT: A 916 TRP cc_start: 0.7599 (OUTLIER) cc_final: 0.6609 (p90) REVERT: B 155 GLU cc_start: 0.8406 (pt0) cc_final: 0.8081 (pt0) REVERT: B 164 SER cc_start: 0.8850 (m) cc_final: 0.8472 (p) REVERT: B 165 LYS cc_start: 0.8475 (mptt) cc_final: 0.8222 (mmtm) REVERT: B 168 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7964 (mm-40) outliers start: 29 outliers final: 17 residues processed: 137 average time/residue: 1.2368 time to fit residues: 182.7395 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 : 1.113 ------------------------------------------------------------------------------- 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 666 MET Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain A residue 818 MET 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 106 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 41 optimal weight: 1.9990 chunk 106 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 104 optimal weight: 0.0980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 362 HIS A 734 ASN B 109 ASN B 158 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.133952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.100145 restraints weight = 12758.401| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.88 r_work: 0.3148 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10405 Z= 0.095 Angle : 0.467 8.832 14243 Z= 0.246 Chirality : 0.040 0.205 1630 Planarity : 0.003 0.056 1714 Dihedral : 9.750 73.450 1715 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.90 % Allowed : 15.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.25), residues: 1181 helix: 0.82 (0.23), residues: 528 sheet: -0.00 (0.42), residues: 143 loop : -0.21 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 PHE 0.029 0.001 PHE A 859 TYR 0.012 0.001 TYR A 788 ARG 0.004 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.03507 ( 459) hydrogen bonds : angle 3.91440 ( 1367) metal coordination : bond 0.00215 ( 7) metal coordination : angle 1.24372 ( 3) covalent geometry : bond 0.00202 (10395) covalent geometry : angle 0.46669 (14240) Misc. bond : bond 0.00032 ( 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 147 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7923 (mt0) cc_final: 0.7610 (mt0) REVERT: A 291 ASP cc_start: 0.8337 (m-30) cc_final: 0.8080 (m-30) REVERT: A 370 GLU cc_start: 0.7739 (pt0) cc_final: 0.7392 (pm20) REVERT: A 522 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: A 629 MET cc_start: 0.9365 (mmp) cc_final: 0.8988 (mmm) REVERT: A 644 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8609 (m) REVERT: A 666 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8653 (mtt) REVERT: A 714 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8373 (mmmm) REVERT: A 798 LYS cc_start: 0.8265 (mmtp) cc_final: 0.7851 (mmmt) REVERT: A 846 ASP cc_start: 0.7991 (t0) cc_final: 0.7658 (t0) REVERT: A 893 ASP cc_start: 0.7440 (OUTLIER) cc_final: 0.6977 (p0) REVERT: A 916 TRP cc_start: 0.7453 (OUTLIER) cc_final: 0.6540 (p90) REVERT: B 155 GLU cc_start: 0.8370 (pt0) cc_final: 0.8047 (pt0) REVERT: B 164 SER cc_start: 0.8731 (m) cc_final: 0.8312 (p) REVERT: B 165 LYS cc_start: 0.8498 (mptt) cc_final: 0.8210 (mmtm) REVERT: B 168 GLN cc_start: 0.8238 (mm-40) cc_final: 0.7931 (mm-40) REVERT: B 179 ASN cc_start: 0.8470 (m-40) cc_final: 0.7889 (t0) outliers start: 20 outliers final: 12 residues processed: 134 average time/residue: 1.1867 time to fit residues: 172.1733 Evaluate side-chains 139 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 1.055 ------------------------------------------------------------------------------- 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 16 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 83 optimal weight: 8.9990 chunk 100 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 61 optimal weight: 0.2980 chunk 32 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 734 ASN A 882 HIS B 109 ASN B 158 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.134070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.100339 restraints weight = 12888.924| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.89 r_work: 0.3154 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 10405 Z= 0.098 Angle : 0.462 8.491 14243 Z= 0.244 Chirality : 0.040 0.198 1630 Planarity : 0.003 0.043 1714 Dihedral : 9.659 73.429 1715 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.09 % Allowed : 15.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.25), residues: 1181 helix: 0.93 (0.24), residues: 527 sheet: 0.06 (0.42), residues: 143 loop : -0.18 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 PHE 0.028 0.001 PHE A 859 TYR 0.013 0.001 TYR A 788 ARG 0.004 0.000 ARG A 889 Details of bonding type rmsd hydrogen bonds : bond 0.03440 ( 459) hydrogen bonds : angle 3.84402 ( 1367) metal coordination : bond 0.00252 ( 7) metal coordination : angle 1.42359 ( 3) covalent geometry : bond 0.00213 (10395) covalent geometry : angle 0.46202 (14240) Misc. bond : bond 0.00091 ( 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 144 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 122 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 291 ASP cc_start: 0.8355 (m-30) cc_final: 0.8079 (m-30) REVERT: A 334 PHE cc_start: 0.7699 (m-80) cc_final: 0.7472 (m-80) REVERT: A 370 GLU cc_start: 0.7700 (pt0) cc_final: 0.7365 (pm20) REVERT: A 522 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: A 629 MET cc_start: 0.9381 (mmp) cc_final: 0.8999 (mmm) REVERT: A 644 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8675 (m) REVERT: A 714 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8378 (mmmm) REVERT: A 798 LYS cc_start: 0.8272 (mmtp) cc_final: 0.7834 (mmmt) REVERT: A 846 ASP cc_start: 0.7924 (t0) cc_final: 0.7604 (t0) REVERT: A 893 ASP cc_start: 0.7412 (OUTLIER) cc_final: 0.7007 (p0) REVERT: A 916 TRP cc_start: 0.7412 (OUTLIER) cc_final: 0.6559 (p90) REVERT: B 155 GLU cc_start: 0.8352 (pt0) cc_final: 0.8034 (pt0) REVERT: B 164 SER cc_start: 0.8817 (m) cc_final: 0.8405 (p) REVERT: B 165 LYS cc_start: 0.8559 (mptt) cc_final: 0.8287 (mmtm) REVERT: B 168 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7859 (mm-40) REVERT: B 171 GLU cc_start: 0.7848 (mp0) cc_final: 0.7640 (mp0) REVERT: B 179 ASN cc_start: 0.8466 (m-40) cc_final: 0.7889 (t0) outliers start: 22 outliers final: 11 residues processed: 132 average time/residue: 1.4359 time to fit residues: 205.9962 Evaluate side-chains 134 residues out of total 1058 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.173 ------------------------------------------------------------------------------- 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 335 VAL 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 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 182 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 119 random chunks: chunk 6 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 116 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 35 optimal weight: 0.0170 chunk 38 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 49 optimal weight: 7.9990 chunk 16 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.0822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 734 ASN B 158 GLN C 19 GLN ** C 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.133405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.099580 restraints weight = 12815.330| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.89 r_work: 0.3141 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10405 Z= 0.110 Angle : 0.485 10.092 14243 Z= 0.254 Chirality : 0.041 0.207 1630 Planarity : 0.003 0.051 1714 Dihedral : 9.651 73.436 1715 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.52 % Allowed : 15.60 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.25), residues: 1181 helix: 0.93 (0.23), residues: 528 sheet: 0.09 (0.42), residues: 143 loop : -0.19 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 916 HIS 0.005 0.001 HIS C 36 PHE 0.014 0.001 PHE A 741 TYR 0.014 0.001 TYR A 788 ARG 0.006 0.000 ARG A 553 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 459) hydrogen bonds : angle 3.87268 ( 1367) metal coordination : bond 0.00268 ( 7) metal coordination : angle 1.45945 ( 3) covalent geometry : bond 0.00245 (10395) covalent geometry : angle 0.48435 (14240) Misc. bond : bond 0.00101 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8616.54 seconds wall clock time: 153 minutes 26.68 seconds (9206.68 seconds total)