Starting phenix.real_space_refine on Fri Mar 6 06:19:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vya_32198/03_2026/7vya_32198.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vya_32198/03_2026/7vya_32198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vya_32198/03_2026/7vya_32198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vya_32198/03_2026/7vya_32198.map" model { file = "/net/cci-nas-00/data/ceres_data/7vya_32198/03_2026/7vya_32198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vya_32198/03_2026/7vya_32198.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 28 7.16 5 Zn 1 6.06 5 P 11 5.49 5 Mg 1 5.21 5 S 188 5.16 5 C 17737 2.51 5 N 4885 2.21 5 O 5180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28031 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3318 Classifications: {'peptide': 431} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 409} Chain: "B" Number of atoms: 1412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1412 Classifications: {'peptide': 176} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 165} Chain: "C" Number of atoms: 1248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1248 Classifications: {'peptide': 156} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 145} Chain: "E" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 971 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "F" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 691 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "G" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 910 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 910 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 103} Chain: "I" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 780 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 11, 'TRANS': 85} Chain breaks: 1 Chain: "J" Number of atoms: 2359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2359 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 16, 'TRANS': 280} Chain breaks: 3 Chain: "K" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 355 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "L" Number of atoms: 1016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1016 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain: "M" Number of atoms: 5296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 690, 5296 Classifications: {'peptide': 690} Link IDs: {'PTRANS': 32, 'TRANS': 657} Chain: "N" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1204 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 11, 'TRANS': 132} Chain: "O" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1671 Classifications: {'peptide': 217} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Chain: "P" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1738 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 15, 'TRANS': 192} Chain: "Q" Number of atoms: 3044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3044 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 20, 'TRANS': 358} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'2MR:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 741 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "W" Number of atoms: 218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 218 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 23} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 83 Unusual residues: {'FMN': 1, 'NAI': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'PEE': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'8Q1': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 21 Unusual residues: {' MG': 1, 'FES': 1, 'SF4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'CDL': 1, 'PLX': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 49 Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2706 SG CYS A 382 48.135 48.231 104.012 1.00 12.56 S ATOM 3048 SG CYS A 425 47.684 44.741 109.630 1.00 17.81 S ATOM 2726 SG CYS A 385 44.694 44.054 104.264 1.00 15.03 S ATOM 2687 SG CYS A 379 43.290 49.265 108.324 1.00 16.08 S ATOM 3949 SG CYS B 113 36.031 65.527 70.194 1.00 28.65 S ATOM 3968 SG CYS B 116 40.983 62.336 73.518 1.00 28.65 S ATOM 3991 SG CYS B 119 41.999 65.050 68.063 1.00 28.65 S ATOM 4320 SG CYS B 162 38.734 59.572 69.013 1.00 28.65 S ATOM 4018 SG CYS B 123 48.013 67.124 62.940 1.00 28.65 S ATOM 4244 SG CYS B 152 45.437 65.605 57.208 1.00 28.65 S ATOM 4291 SG CYS B 158 43.527 62.202 62.185 1.00 28.65 S ATOM 4270 SG CYS B 155 49.463 61.689 60.200 1.00 28.65 S ATOM 5712 SG CYS C 166 51.494 64.825 52.598 1.00 28.65 S ATOM 4984 SG CYS C 72 52.083 66.338 46.238 1.00 11.08 S ATOM 4978 SG CYS C 71 55.883 63.591 48.118 1.00 11.39 S ATOM 5482 SG CYS C 136 54.475 69.342 50.815 1.00 20.64 S ATOM 14538 SG CYS M 131 41.257 62.515 85.622 1.00 22.94 S ATOM 14517 SG CYS M 128 44.137 57.602 82.293 1.00 28.65 S ATOM 14578 SG CYS M 137 46.954 60.853 87.303 1.00 15.42 S ATOM 14910 SG CYS M 179 46.350 61.045 98.459 1.00 28.65 S ATOM 15264 SG CYS M 226 43.154 63.984 94.451 1.00 19.45 S ATOM 14934 SG CYS M 182 41.404 64.206 100.637 1.00 28.65 S ATOM 14887 SG CYS M 176 40.274 58.774 97.266 1.00 20.94 S ATOM 14135 SG CYS M 78 57.481 54.944 101.112 1.00 17.45 S ATOM 14236 SG CYS M 92 56.120 57.041 103.627 1.00 12.00 S ATOM 14024 SG CYS M 64 51.680 57.676 101.842 1.00 28.65 S ATOM 14110 SG CYS M 75 52.145 55.742 98.654 1.00 16.94 S ATOM 21073 SG CYS O 135 31.016 32.726 113.102 1.00 47.88 S ATOM 21107 SG CYS O 140 30.663 29.379 114.101 1.00 50.11 S ATOM 21387 SG CYS O 176 35.692 33.871 115.533 1.00 48.14 S ATOM 21410 SG CYS O 180 35.480 30.182 115.933 1.00 57.41 S ATOM 27168 SG CYS T 86 27.929 52.911 78.535 1.00 15.04 S ATOM 27346 SG CYS T 111 29.451 56.281 79.491 1.00 16.86 S Time building chain proxies: 5.35, per 1000 atoms: 0.19 Number of scatterers: 28031 At special positions: 0 Unit cell: (122.459, 137.498, 158.982, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 28 26.01 S 188 16.00 P 11 15.00 Mg 1 11.99 O 5180 8.00 N 4885 7.00 C 17737 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS F 24 " - pdb=" SG CYS F 58 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 92 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 64 " pdb=" FES O 301 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 135 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb=" SF4 A 501 " pdb="FE2 SF4 A 501 " - pdb=" SG CYS A 425 " pdb="FE3 SF4 A 501 " - pdb=" SG CYS A 385 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " pdb="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb=" SF4 B 301 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 116 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 113 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 119 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 162 " pdb=" SF4 B 302 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb=" SF4 C 301 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 71 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 166 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 72 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 136 " pdb="FE3 SF4 C 301 " - pdb=" NE2 HIS Q 223 " pdb=" SF4 M 801 " pdb="FE3 SF4 M 801 " - pdb=" NE2 HIS M 124 " pdb="FE4 SF4 M 801 " - pdb=" SG CYS M 137 " pdb="FE1 SF4 M 801 " - pdb=" SG CYS M 131 " pdb="FE2 SF4 M 801 " - pdb=" SG CYS M 128 " pdb=" SF4 M 802 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " pdb="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 86 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 111 " pdb="ZN ZN T 201 " - pdb=" NE2 HIS T 95 " 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6472 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 31 sheets defined 45.2% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 removed outlier: 3.671A pdb=" N ARG A 40 " --> pdb=" O ASP A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 64 through 72 removed outlier: 3.885A pdb=" N GLY A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 83 removed outlier: 3.513A pdb=" N ILE A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 102 Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 134 through 150 removed outlier: 4.129A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 179 Processing helix chain 'A' and resid 204 through 207 Processing helix chain 'A' and resid 208 through 217 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 245 through 258 Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 258 through 265 removed outlier: 3.834A pdb=" N PHE A 262 " --> pdb=" O GLY A 258 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N PHE A 265 " --> pdb=" O TRP A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 329 through 333 Processing helix chain 'A' and resid 338 through 345 Processing helix chain 'A' and resid 362 through 378 Processing helix chain 'A' and resid 382 through 402 removed outlier: 3.567A pdb=" N LYS A 401 " --> pdb=" O ALA A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 420 removed outlier: 3.853A pdb=" N ILE A 409 " --> pdb=" O ARG A 405 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ASP A 410 " --> pdb=" O PRO A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 458 Proline residue: A 434 - end of helix Proline residue: A 444 - end of helix Processing helix chain 'B' and resid 49 through 63 Processing helix chain 'B' and resid 63 through 78 removed outlier: 3.571A pdb=" N PHE B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 123 Processing helix chain 'B' and resid 156 through 162 Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 186 through 209 removed outlier: 5.921A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'C' and resid 42 through 61 removed outlier: 3.547A pdb=" N SER C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 80 removed outlier: 3.897A pdb=" N GLU C 75 " --> pdb=" O CYS C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 113 through 123 Processing helix chain 'C' and resid 134 through 140 Processing helix chain 'C' and resid 141 through 144 Processing helix chain 'C' and resid 152 through 156 Processing helix chain 'C' and resid 169 through 187 Processing helix chain 'C' and resid 188 through 196 removed outlier: 3.853A pdb=" N ILE C 192 " --> pdb=" O LYS C 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 50 removed outlier: 3.726A pdb=" N ALA E 28 " --> pdb=" O ASP E 24 " (cutoff:3.500A) Proline residue: E 44 - end of helix Processing helix chain 'E' and resid 55 through 70 removed outlier: 4.113A pdb=" N ASN E 70 " --> pdb=" O MET E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 95 Processing helix chain 'E' and resid 99 through 105 Processing helix chain 'E' and resid 106 through 108 No H-bonds generated for 'chain 'E' and resid 106 through 108' Processing helix chain 'E' and resid 117 through 125 Processing helix chain 'F' and resid 27 through 29 No H-bonds generated for 'chain 'F' and resid 27 through 29' Processing helix chain 'F' and resid 30 through 48 removed outlier: 3.529A pdb=" N ILE F 37 " --> pdb=" O VAL F 33 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL F 42 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLU F 43 " --> pdb=" O LYS F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 97 Processing helix chain 'G' and resid 75 through 89 Processing helix chain 'G' and resid 111 through 127 Processing helix chain 'G' and resid 131 through 136 Processing helix chain 'G' and resid 140 through 153 Processing helix chain 'H' and resid 19 through 36 removed outlier: 3.951A pdb=" N ARG H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 62 Processing helix chain 'H' and resid 64 through 73 Processing helix chain 'H' and resid 76 through 98 Processing helix chain 'I' and resid 5 through 17 Processing helix chain 'I' and resid 53 through 57 Processing helix chain 'I' and resid 59 through 63 Processing helix chain 'J' and resid 37 through 41 Processing helix chain 'J' and resid 63 through 75 removed outlier: 3.509A pdb=" N ARG J 67 " --> pdb=" O GLY J 63 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 92 removed outlier: 3.870A pdb=" N THR J 91 " --> pdb=" O GLU J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 98 Proline residue: J 96 - end of helix No H-bonds generated for 'chain 'J' and resid 93 through 98' Processing helix chain 'J' and resid 112 through 120 removed outlier: 4.079A pdb=" N ILE J 116 " --> pdb=" O ASP J 112 " (cutoff:3.500A) Processing helix chain 'J' and resid 140 through 146 Processing helix chain 'J' and resid 146 through 160 Processing helix chain 'J' and resid 178 through 195 Processing helix chain 'J' and resid 213 through 219 Processing helix chain 'J' and resid 242 through 255 Processing helix chain 'J' and resid 273 through 284 Processing helix chain 'J' and resid 316 through 323 removed outlier: 3.518A pdb=" N GLU J 320 " --> pdb=" O ARG J 316 " (cutoff:3.500A) Processing helix chain 'J' and resid 334 through 339 Processing helix chain 'J' and resid 344 through 354 removed outlier: 3.976A pdb=" N LYS J 348 " --> pdb=" O PRO J 344 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N ILE J 350 " --> pdb=" O GLU J 346 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLU J 351 " --> pdb=" O LEU J 347 " (cutoff:3.500A) Processing helix chain 'K' and resid 75 through 81 removed outlier: 4.254A pdb=" N HIS K 78 " --> pdb=" O ASN K 75 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N GLU K 80 " --> pdb=" O GLN K 77 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR K 81 " --> pdb=" O HIS K 78 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 94 Processing helix chain 'K' and resid 95 through 97 No H-bonds generated for 'chain 'K' and resid 95 through 97' Processing helix chain 'L' and resid 61 through 66 removed outlier: 4.248A pdb=" N GLY L 66 " --> pdb=" O THR L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 72 Processing helix chain 'L' and resid 119 through 124 removed outlier: 3.928A pdb=" N SER L 122 " --> pdb=" O ASP L 119 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ASN L 123 " --> pdb=" O PRO L 120 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU L 124 " --> pdb=" O LEU L 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 119 through 124' Processing helix chain 'L' and resid 130 through 141 Processing helix chain 'L' and resid 160 through 165 removed outlier: 3.646A pdb=" N SER L 165 " --> pdb=" O ALA L 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 57 Processing helix chain 'M' and resid 106 through 123 removed outlier: 4.472A pdb=" N ASN M 123 " --> pdb=" O PHE M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 137 through 147 Processing helix chain 'M' and resid 173 through 176 Processing helix chain 'M' and resid 180 through 189 Processing helix chain 'M' and resid 200 through 204 Processing helix chain 'M' and resid 220 through 226 removed outlier: 3.952A pdb=" N ASP M 224 " --> pdb=" O GLY M 220 " (cutoff:3.500A) Processing helix chain 'M' and resid 287 through 293 Processing helix chain 'M' and resid 294 through 299 Processing helix chain 'M' and resid 318 through 333 removed outlier: 3.654A pdb=" N MET M 329 " --> pdb=" O ARG M 325 " (cutoff:3.500A) Processing helix chain 'M' and resid 334 through 336 No H-bonds generated for 'chain 'M' and resid 334 through 336' Processing helix chain 'M' and resid 347 through 360 Processing helix chain 'M' and resid 381 through 386 removed outlier: 3.932A pdb=" N LEU M 386 " --> pdb=" O SER M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 389 through 394 removed outlier: 3.527A pdb=" N GLY M 393 " --> pdb=" O THR M 389 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL M 394 " --> pdb=" O THR M 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 389 through 394' Processing helix chain 'M' and resid 395 through 397 No H-bonds generated for 'chain 'M' and resid 395 through 397' Processing helix chain 'M' and resid 406 through 411 Processing helix chain 'M' and resid 411 through 426 removed outlier: 3.585A pdb=" N ASP M 426 " --> pdb=" O TRP M 422 " (cutoff:3.500A) Processing helix chain 'M' and resid 449 through 458 removed outlier: 4.093A pdb=" N GLN M 453 " --> pdb=" O PRO M 449 " (cutoff:3.500A) Processing helix chain 'M' and resid 460 through 468 removed outlier: 4.198A pdb=" N GLN M 464 " --> pdb=" O HIS M 460 " (cutoff:3.500A) Processing helix chain 'M' and resid 479 through 482 Processing helix chain 'M' and resid 485 through 505 Processing helix chain 'M' and resid 521 through 528 Processing helix chain 'M' and resid 534 through 540 Processing helix chain 'M' and resid 618 through 630 Processing helix chain 'M' and resid 638 through 650 Processing helix chain 'M' and resid 651 through 654 removed outlier: 3.661A pdb=" N VAL M 654 " --> pdb=" O PRO M 651 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 651 through 654' Processing helix chain 'M' and resid 664 through 673 removed outlier: 3.629A pdb=" N LYS M 673 " --> pdb=" O ASN M 669 " (cutoff:3.500A) Processing helix chain 'M' and resid 690 through 694 Processing helix chain 'M' and resid 698 through 703 Processing helix chain 'M' and resid 704 through 716 Processing helix chain 'N' and resid 3 through 16 Processing helix chain 'N' and resid 19 through 31 Processing helix chain 'N' and resid 78 through 82 removed outlier: 3.851A pdb=" N VAL N 82 " --> pdb=" O GLY N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 91 Processing helix chain 'O' and resid 56 through 70 removed outlier: 3.888A pdb=" N TYR O 70 " --> pdb=" O ILE O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 77 removed outlier: 3.722A pdb=" N ALA O 77 " --> pdb=" O HIS O 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 74 through 77' Processing helix chain 'O' and resid 78 through 91 Processing helix chain 'O' and resid 94 through 106 Processing helix chain 'O' and resid 108 through 119 removed outlier: 3.662A pdb=" N VAL O 112 " --> pdb=" O PRO O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 143 removed outlier: 3.816A pdb=" N ARG O 143 " --> pdb=" O PRO O 139 " (cutoff:3.500A) Processing helix chain 'O' and resid 145 through 157 removed outlier: 3.518A pdb=" N LEU O 149 " --> pdb=" O SER O 145 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 183 Processing helix chain 'O' and resid 197 through 211 Processing helix chain 'P' and resid 51 through 69 removed outlier: 3.592A pdb=" N HIS P 55 " --> pdb=" O ASN P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 92 through 103 Processing helix chain 'P' and resid 162 through 175 removed outlier: 4.011A pdb=" N TYR P 166 " --> pdb=" O ALA P 162 " (cutoff:3.500A) Processing helix chain 'P' and resid 242 through 246 Processing helix chain 'Q' and resid 119 through 125 removed outlier: 3.688A pdb=" N GLU Q 125 " --> pdb=" O GLU Q 121 " (cutoff:3.500A) Processing helix chain 'Q' and resid 128 through 133 Processing helix chain 'Q' and resid 133 through 140 removed outlier: 4.117A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG Q 138 " --> pdb=" O PRO Q 134 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASP Q 140 " --> pdb=" O PHE Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 160 removed outlier: 3.718A pdb=" N ASN Q 147 " --> pdb=" O SER Q 143 " (cutoff:3.500A) Processing helix chain 'Q' and resid 164 through 195 Processing helix chain 'Q' and resid 197 through 219 removed outlier: 4.252A pdb=" N PHE Q 201 " --> pdb=" O MET Q 197 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLU Q 206 " --> pdb=" O TRP Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 239 through 249 Processing helix chain 'Q' and resid 250 through 263 removed outlier: 3.682A pdb=" N ARG Q 254 " --> pdb=" O ASN Q 250 " (cutoff:3.500A) Processing helix chain 'Q' and resid 265 through 273 Processing helix chain 'Q' and resid 279 through 286 Processing helix chain 'Q' and resid 290 through 295 Processing helix chain 'Q' and resid 301 through 306 Processing helix chain 'Q' and resid 325 through 350 Processing helix chain 'Q' and resid 367 through 374 Processing helix chain 'Q' and resid 374 through 387 Processing helix chain 'Q' and resid 426 through 439 removed outlier: 3.993A pdb=" N ALA Q 430 " --> pdb=" O ALA Q 426 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 443 through 455 removed outlier: 3.760A pdb=" N VAL Q 447 " --> pdb=" O MET Q 443 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL Q 448 " --> pdb=" O LEU Q 444 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA Q 449 " --> pdb=" O ALA Q 445 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP Q 455 " --> pdb=" O ILE Q 451 " (cutoff:3.500A) Processing helix chain 'Q' and resid 457 through 463 Processing helix chain 'T' and resid 49 through 56 removed outlier: 3.592A pdb=" N ARG T 52 " --> pdb=" O ASP T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 66 through 73 Processing helix chain 'T' and resid 90 through 94 Processing sheet with id=AA1, first strand: chain 'A' and resid 194 through 199 removed outlier: 6.425A pdb=" N LEU A 113 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N TYR A 157 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL A 115 " --> pdb=" O TYR A 157 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR A 241 " --> pdb=" O TYR A 112 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 267 removed outlier: 3.709A pdb=" N ARG A 267 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 286 through 291 Processing sheet with id=AA4, first strand: chain 'B' and resid 38 through 40 removed outlier: 6.134A pdb=" N LYS B 39 " --> pdb=" O ILE Q 320 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 101 through 103 Processing sheet with id=AA6, first strand: chain 'B' and resid 128 through 134 removed outlier: 6.531A pdb=" N THR B 129 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N TYR B 145 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLU B 131 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG B 141 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 64 through 68 removed outlier: 6.593A pdb=" N MET C 65 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ALA C 106 " --> pdb=" O MET C 65 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N PHE C 67 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL C 130 " --> pdb=" O ILE C 161 " (cutoff:3.500A) removed outlier: 8.164A pdb=" N VAL C 163 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N SER C 132 " --> pdb=" O VAL C 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 53 through 58 removed outlier: 3.616A pdb=" N GLU F 18 " --> pdb=" O ARG F 68 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 67 through 69 removed outlier: 6.584A pdb=" N PHE P 87 " --> pdb=" O GLN P 74 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N VAL P 76 " --> pdb=" O GLU P 85 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU P 85 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LEU P 84 " --> pdb=" O ARG P 140 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N TYR P 146 " --> pdb=" O ILE P 88 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU P 133 " --> pdb=" O LEU P 111 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU P 111 " --> pdb=" O LEU P 133 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 103 through 106 removed outlier: 6.662A pdb=" N VAL J 80 " --> pdb=" O ILE J 104 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N MET J 106 " --> pdb=" O VAL J 80 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N VAL J 82 " --> pdb=" O MET J 106 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA J 56 " --> pdb=" O ILE J 81 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL J 58 " --> pdb=" O PRO J 83 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL J 126 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ILE J 167 " --> pdb=" O VAL J 126 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ASN J 128 " --> pdb=" O ILE J 167 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS J 202 " --> pdb=" O PHE J 265 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 206 through 207 Processing sheet with id=AB3, first strand: chain 'J' and resid 236 through 237 Processing sheet with id=AB4, first strand: chain 'L' and resid 126 through 128 Processing sheet with id=AB5, first strand: chain 'L' and resid 106 through 108 Processing sheet with id=AB6, first strand: chain 'M' and resid 39 through 43 removed outlier: 9.225A pdb=" N ILE M 102 " --> pdb=" O GLU M 33 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N PHE M 35 " --> pdb=" O ILE M 102 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLU M 81 " --> pdb=" O LEU M 103 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 169 through 171 Processing sheet with id=AB8, first strand: chain 'M' and resid 196 through 198 Processing sheet with id=AB9, first strand: chain 'M' and resid 246 through 251 removed outlier: 7.904A pdb=" N ASN M 260 " --> pdb=" O PRO M 275 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL M 262 " --> pdb=" O ILE M 273 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ILE M 273 " --> pdb=" O VAL M 262 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER M 264 " --> pdb=" O MET M 271 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 314 through 316 removed outlier: 6.640A pdb=" N ILE M 566 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU M 584 " --> pdb=" O ILE M 566 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N TYR M 568 " --> pdb=" O LEU M 584 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N CYS M 367 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ALA M 340 " --> pdb=" O CYS M 367 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 443 through 446 removed outlier: 7.011A pdb=" N VAL M 429 " --> pdb=" O ASP M 443 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N LEU M 445 " --> pdb=" O VAL M 429 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LEU M 431 " --> pdb=" O LEU M 445 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE M 400 " --> pdb=" O ALA M 430 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N ILE M 432 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU M 402 " --> pdb=" O ILE M 432 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL M 474 " --> pdb=" O ASN M 514 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU M 516 " --> pdb=" O VAL M 474 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N LEU M 476 " --> pdb=" O LEU M 516 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'M' and resid 595 through 597 Processing sheet with id=AC4, first strand: chain 'N' and resid 37 through 41 removed outlier: 6.634A pdb=" N TYR N 48 " --> pdb=" O VAL N 39 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 169 through 174 removed outlier: 3.696A pdb=" N CYS O 135 " --> pdb=" O MET O 185 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N MET O 185 " --> pdb=" O CYS O 135 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N TYR O 192 " --> pdb=" O GLY O 217 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 153 through 154 removed outlier: 6.767A pdb=" N ILE P 153 " --> pdb=" O ALA P 179 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'P' and resid 208 through 213 Processing sheet with id=AC8, first strand: chain 'Q' and resid 80 through 84 removed outlier: 3.629A pdb=" N ARG Q 96 " --> pdb=" O HIS Q 112 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N SER Q 102 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N VAL Q 106 " --> pdb=" O SER Q 102 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Q' and resid 227 through 228 Processing sheet with id=AD1, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id=AD2, first strand: chain 'T' and resid 30 through 31 removed outlier: 4.188A pdb=" N ARG T 30 " --> pdb=" O VAL T 38 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'T' and resid 83 through 86 Processing sheet with id=AD4, first strand: chain 'T' and resid 109 through 110 1131 hydrogen bonds defined for protein. 3168 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.70 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.41: 11582 1.41 - 1.63: 16739 1.63 - 1.85: 274 1.85 - 2.07: 1 2.07 - 2.29: 80 Bond restraints: 28676 Sorted by residual: bond pdb=" C3D NAI A 503 " pdb=" C4D NAI A 503 " ideal model delta sigma weight residual 1.524 1.262 0.262 2.00e-02 2.50e+03 1.71e+02 bond pdb=" C1D NAI A 503 " pdb=" C2D NAI A 503 " ideal model delta sigma weight residual 1.528 1.287 0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" C1B NAI A 503 " pdb=" O4B NAI A 503 " ideal model delta sigma weight residual 1.397 1.630 -0.233 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C1B NAI A 503 " pdb=" C2B NAI A 503 " ideal model delta sigma weight residual 1.528 1.297 0.231 2.00e-02 2.50e+03 1.33e+02 bond pdb=" CB7 CDL N 202 " pdb=" OB8 CDL N 202 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.18e+02 ... (remaining 28671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 38483 3.29 - 6.57: 296 6.57 - 9.86: 45 9.86 - 13.14: 14 13.14 - 16.43: 7 Bond angle restraints: 38845 Sorted by residual: angle pdb=" N GLY A 120 " pdb=" CA GLY A 120 " pdb=" C GLY A 120 " ideal model delta sigma weight residual 112.73 122.45 -9.72 1.20e+00 6.94e-01 6.57e+01 angle pdb=" PA NDP J 401 " pdb=" O3 NDP J 401 " pdb=" PN NDP J 401 " ideal model delta sigma weight residual 107.74 123.06 -15.32 1.95e+00 2.62e-01 6.15e+01 angle pdb=" C ARG A 405 " pdb=" N PRO A 406 " pdb=" CA PRO A 406 " ideal model delta sigma weight residual 119.05 126.96 -7.91 1.11e+00 8.12e-01 5.07e+01 angle pdb=" C5B NDP J 401 " pdb=" O5B NDP J 401 " pdb=" PA NDP J 401 " ideal model delta sigma weight residual 103.84 117.15 -13.31 1.91e+00 2.73e-01 4.83e+01 angle pdb=" C TYR B 106 " pdb=" N PRO B 107 " pdb=" CA PRO B 107 " ideal model delta sigma weight residual 119.05 126.77 -7.72 1.11e+00 8.12e-01 4.83e+01 ... (remaining 38840 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.11: 16990 35.11 - 70.22: 383 70.22 - 105.33: 38 105.33 - 140.45: 4 140.45 - 175.56: 3 Dihedral angle restraints: 17418 sinusoidal: 7355 harmonic: 10063 Sorted by residual: dihedral pdb=" CB CYS F 24 " pdb=" SG CYS F 24 " pdb=" SG CYS F 58 " pdb=" CB CYS F 58 " ideal model delta sinusoidal sigma weight residual -86.00 -136.02 50.02 1 1.00e+01 1.00e-02 3.43e+01 dihedral pdb=" CA LEU I 106 " pdb=" C LEU I 106 " pdb=" N SER I 107 " pdb=" CA SER I 107 " ideal model delta harmonic sigma weight residual 180.00 154.75 25.25 0 5.00e+00 4.00e-02 2.55e+01 dihedral pdb=" CA SER O 224 " pdb=" C SER O 224 " pdb=" N CYS O 225 " pdb=" CA CYS O 225 " ideal model delta harmonic sigma weight residual 180.00 156.79 23.21 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 17415 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 3739 0.074 - 0.149: 444 0.149 - 0.223: 25 0.223 - 0.297: 7 0.297 - 0.372: 5 Chirality restraints: 4220 Sorted by residual: chirality pdb=" CA MET Q 222 " pdb=" N MET Q 222 " pdb=" C MET Q 222 " pdb=" CB MET Q 222 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.46e+00 chirality pdb=" CA ASN P 82 " pdb=" N ASN P 82 " pdb=" C ASN P 82 " pdb=" CB ASN P 82 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" C3D NDP J 401 " pdb=" C2D NDP J 401 " pdb=" C4D NDP J 401 " pdb=" O3D NDP J 401 " both_signs ideal model delta sigma weight residual False -2.71 -2.36 -0.35 2.00e-01 2.50e+01 3.10e+00 ... (remaining 4217 not shown) Planarity restraints: 4997 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2N NDP J 401 " -0.048 2.00e-02 2.50e+03 1.98e-01 4.91e+02 pdb=" C3N NDP J 401 " 0.387 2.00e-02 2.50e+03 pdb=" C4N NDP J 401 " -0.111 2.00e-02 2.50e+03 pdb=" C7N NDP J 401 " -0.169 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NDP J 401 " 0.115 2.00e-02 2.50e+03 2.05e-01 4.19e+02 pdb=" C2N NDP J 401 " 0.120 2.00e-02 2.50e+03 pdb=" C6N NDP J 401 " 0.120 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " -0.355 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C4N NDP J 401 " -0.095 2.00e-02 2.50e+03 1.41e-01 2.00e+02 pdb=" C5N NDP J 401 " 0.175 2.00e-02 2.50e+03 pdb=" C6N NDP J 401 " -0.176 2.00e-02 2.50e+03 pdb=" N1N NDP J 401 " 0.095 2.00e-02 2.50e+03 ... (remaining 4994 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1974 2.73 - 3.27: 27989 3.27 - 3.82: 46919 3.82 - 4.36: 60405 4.36 - 4.90: 101214 Nonbonded interactions: 238501 Sorted by model distance: nonbonded pdb=" O GLU B 111 " pdb=" NH1 ARG B 141 " model vdw 2.190 3.120 nonbonded pdb=" NE2 GLN Q 149 " pdb=" OD2 ASP Q 309 " model vdw 2.209 3.120 nonbonded pdb=" OG1 THR M 487 " pdb=" OE1 GLN M 677 " model vdw 2.211 3.040 nonbonded pdb=" OD1 ASP B 165 " pdb=" NH2 ARG Q 368 " model vdw 2.212 3.120 nonbonded pdb=" OE1 GLU B 110 " pdb=" O CYS T 114 " model vdw 2.214 3.040 ... (remaining 238496 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 29.630 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 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 : 0.011 0.924 28715 Z= 0.576 Angle : 0.968 47.469 38928 Z= 0.439 Chirality : 0.050 0.372 4220 Planarity : 0.007 0.205 4997 Dihedral : 15.289 175.557 10943 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.63 % Favored : 96.25 % Rotamer: Outliers : 0.23 % Allowed : 0.97 % Favored : 98.80 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.14), residues: 3439 helix: 0.68 (0.14), residues: 1320 sheet: 0.02 (0.26), residues: 390 loop : -0.49 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 109 TYR 0.041 0.002 TYR C 142 PHE 0.027 0.002 PHE Q 204 TRP 0.015 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00822 (28676) covalent geometry : angle 0.80899 (38845) SS BOND : bond 0.00499 ( 1) SS BOND : angle 2.03732 ( 2) hydrogen bonds : bond 0.15077 ( 1131) hydrogen bonds : angle 6.58161 ( 3168) metal coordination : bond 0.15496 ( 36) metal coordination : angle 11.68801 ( 81) Misc. bond : bond 0.51038 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 631 time to evaluate : 0.842 Fit side-chains revert: symmetry clash REVERT: A 29 LYS cc_start: 0.6940 (ttpt) cc_final: 0.6715 (ttpt) REVERT: A 134 ASP cc_start: 0.8248 (p0) cc_final: 0.7984 (p0) REVERT: A 405 ARG cc_start: 0.7284 (mtm110) cc_final: 0.7005 (mtp180) REVERT: A 450 MET cc_start: 0.8961 (mtt) cc_final: 0.8582 (mtt) REVERT: B 208 ASP cc_start: 0.8050 (t70) cc_final: 0.7642 (t0) REVERT: C 49 LYS cc_start: 0.8753 (mmtt) cc_final: 0.8440 (mmpt) REVERT: C 98 ARG cc_start: 0.6901 (ttp80) cc_final: 0.6686 (ttp-170) REVERT: C 126 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8230 (mt-10) REVERT: E 25 MET cc_start: 0.8345 (tpt) cc_final: 0.8039 (mmt) REVERT: E 30 ARG cc_start: 0.8193 (ttm110) cc_final: 0.7720 (mtm-85) REVERT: E 37 ARG cc_start: 0.7824 (ttm-80) cc_final: 0.7506 (mtt180) REVERT: F 35 ASP cc_start: 0.6797 (m-30) cc_final: 0.6584 (m-30) REVERT: G 114 ASP cc_start: 0.7515 (m-30) cc_final: 0.7176 (m-30) REVERT: I 62 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7969 (mt-10) REVERT: J 212 ARG cc_start: 0.7817 (mtt180) cc_final: 0.7528 (mtm-85) REVERT: L 105 GLU cc_start: 0.8643 (tt0) cc_final: 0.8415 (tt0) REVERT: M 144 MET cc_start: 0.8736 (mmm) cc_final: 0.8426 (mmm) REVERT: N 21 ARG cc_start: 0.7137 (mmt180) cc_final: 0.6456 (mpt90) REVERT: Q 261 MET cc_start: 0.8843 (mmm) cc_final: 0.8624 (mmt) REVERT: Q 282 ASP cc_start: 0.8412 (m-30) cc_final: 0.8122 (m-30) REVERT: T 119 ARG cc_start: 0.8167 (ttm-80) cc_final: 0.7939 (ttp-170) outliers start: 7 outliers final: 6 residues processed: 637 average time/residue: 0.8085 time to fit residues: 583.1096 Evaluate side-chains 441 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 435 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 83 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 133 HIS A 168 ASN A 244 ASN A 277 ASN F 62 GLN F 86 GLN F 93 ASN I 9 GLN I 21 GLN J 128 ASN J 166 HIS J 269 ASN J 278 GLN K 79 HIS K 110 HIS L 86 ASN M 74 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 336 ASN M 460 HIS M 499 ASN M 540 ASN ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 678 GLN N 31 ASN P 75 GLN P 77 GLN P 236 ASN Q 454 GLN W 24 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.112113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.089885 restraints weight = 37336.214| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 1.44 r_work: 0.2835 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.212 28715 Z= 0.167 Angle : 0.813 62.515 38928 Z= 0.310 Chirality : 0.045 0.190 4220 Planarity : 0.005 0.063 4997 Dihedral : 10.479 175.713 4097 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.10 % Allowed : 10.69 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.14), residues: 3439 helix: 0.96 (0.14), residues: 1351 sheet: 0.22 (0.26), residues: 375 loop : -0.38 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 100 TYR 0.028 0.002 TYR P 64 PHE 0.021 0.002 PHE J 141 TRP 0.010 0.001 TRP M 319 HIS 0.011 0.001 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00389 (28676) covalent geometry : angle 0.58479 (38845) SS BOND : bond 0.00602 ( 1) SS BOND : angle 2.44103 ( 2) hydrogen bonds : bond 0.04720 ( 1131) hydrogen bonds : angle 5.18717 ( 3168) metal coordination : bond 0.03827 ( 36) metal coordination : angle 12.38680 ( 81) Misc. bond : bond 0.00952 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 469 time to evaluate : 1.074 Fit side-chains REVERT: A 134 ASP cc_start: 0.8637 (p0) cc_final: 0.8418 (p0) REVERT: A 340 ASP cc_start: 0.8080 (m-30) cc_final: 0.7830 (m-30) REVERT: A 405 ARG cc_start: 0.8016 (mtm110) cc_final: 0.7785 (mtp180) REVERT: A 450 MET cc_start: 0.9141 (mtt) cc_final: 0.8878 (mtt) REVERT: A 456 GLN cc_start: 0.7617 (mt0) cc_final: 0.7415 (mt0) REVERT: B 208 ASP cc_start: 0.8292 (t70) cc_final: 0.7785 (t0) REVERT: C 49 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8511 (mmtm) REVERT: C 126 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8703 (mt-10) REVERT: E 25 MET cc_start: 0.8615 (tpt) cc_final: 0.8407 (tpt) REVERT: E 52 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8640 (mt) REVERT: E 109 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8074 (mt-10) REVERT: F 91 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8445 (tt) REVERT: G 92 LYS cc_start: 0.7614 (mttp) cc_final: 0.7347 (mttp) REVERT: G 114 ASP cc_start: 0.7936 (m-30) cc_final: 0.7368 (m-30) REVERT: G 143 GLU cc_start: 0.6601 (pt0) cc_final: 0.6386 (pm20) REVERT: I 62 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8532 (mt-10) REVERT: J 212 ARG cc_start: 0.8233 (mtt180) cc_final: 0.7700 (mtm-85) REVERT: J 322 VAL cc_start: 0.8913 (p) cc_final: 0.8660 (m) REVERT: K 77 GLN cc_start: 0.8575 (mp10) cc_final: 0.8184 (mt0) REVERT: L 105 GLU cc_start: 0.9028 (tt0) cc_final: 0.8738 (tm-30) REVERT: M 44 GLU cc_start: 0.7774 (mp0) cc_final: 0.7493 (mp0) REVERT: M 97 MET cc_start: 0.8426 (mmm) cc_final: 0.8128 (mmm) REVERT: M 117 MET cc_start: 0.9313 (tpp) cc_final: 0.9097 (tpp) REVERT: M 144 MET cc_start: 0.9192 (mmm) cc_final: 0.8811 (mmm) REVERT: M 215 MET cc_start: 0.7723 (OUTLIER) cc_final: 0.6930 (mpt) REVERT: M 513 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8313 (mmm) REVERT: M 677 GLN cc_start: 0.7410 (tt0) cc_final: 0.7100 (tt0) REVERT: N 8 ARG cc_start: 0.6615 (mtm-85) cc_final: 0.6382 (mmt-90) REVERT: N 21 ARG cc_start: 0.7612 (mmt180) cc_final: 0.6296 (mpt90) REVERT: N 76 ASP cc_start: 0.8412 (m-30) cc_final: 0.8095 (m-30) REVERT: N 122 GLN cc_start: 0.8303 (mp10) cc_final: 0.7972 (mm-40) REVERT: O 106 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8381 (mp10) REVERT: P 83 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7970 (mt-10) REVERT: Q 81 THR cc_start: 0.8684 (m) cc_final: 0.8352 (t) REVERT: Q 84 PHE cc_start: 0.6617 (m-80) cc_final: 0.6238 (t80) REVERT: Q 282 ASP cc_start: 0.9099 (m-30) cc_final: 0.8746 (m-30) REVERT: Q 325 ASP cc_start: 0.9011 (p0) cc_final: 0.8786 (p0) REVERT: T 119 ARG cc_start: 0.8478 (ttm-80) cc_final: 0.8221 (ttm170) outliers start: 63 outliers final: 21 residues processed: 498 average time/residue: 0.7651 time to fit residues: 433.9068 Evaluate side-chains 452 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 424 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 99 GLN Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 554 CYS Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 203 GLU Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 282 optimal weight: 2.9990 chunk 143 optimal weight: 0.8980 chunk 334 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 239 optimal weight: 4.9990 chunk 254 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 333 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 295 optimal weight: 1.9990 chunk 327 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 GLN C 123 GLN F 93 ASN G 142 GLN H 50 GLN H 76 GLN I 9 GLN ** K 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN L 109 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 460 HIS ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 678 GLN ** N 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 31 ASN N 135 GLN Q 270 ASN T 63 ASN W 24 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.112112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.090196 restraints weight = 37446.360| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.37 r_work: 0.2831 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.209 28715 Z= 0.132 Angle : 0.735 58.236 38928 Z= 0.279 Chirality : 0.043 0.177 4220 Planarity : 0.005 0.057 4997 Dihedral : 9.922 174.815 4094 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.97 % Favored : 97.00 % Rotamer: Outliers : 2.14 % Allowed : 13.13 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.14), residues: 3439 helix: 1.18 (0.14), residues: 1347 sheet: 0.18 (0.26), residues: 385 loop : -0.33 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 538 TYR 0.020 0.001 TYR P 64 PHE 0.014 0.001 PHE Q 204 TRP 0.008 0.001 TRP M 422 HIS 0.009 0.001 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00300 (28676) covalent geometry : angle 0.52404 (38845) SS BOND : bond 0.00601 ( 1) SS BOND : angle 2.30468 ( 2) hydrogen bonds : bond 0.04210 ( 1131) hydrogen bonds : angle 4.94074 ( 3168) metal coordination : bond 0.03671 ( 36) metal coordination : angle 11.29867 ( 81) Misc. bond : bond 0.00375 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 449 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8110 (tp) REVERT: A 134 ASP cc_start: 0.8627 (p0) cc_final: 0.8389 (p0) REVERT: A 456 GLN cc_start: 0.7502 (mt0) cc_final: 0.7289 (mt0) REVERT: B 208 ASP cc_start: 0.8097 (t70) cc_final: 0.7583 (t0) REVERT: C 126 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8680 (mt-10) REVERT: E 25 MET cc_start: 0.8621 (tpt) cc_final: 0.8420 (tpt) REVERT: E 52 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8679 (mt) REVERT: E 66 MET cc_start: 0.9031 (mmp) cc_final: 0.8729 (mmp) REVERT: E 109 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: F 31 GLN cc_start: 0.8469 (tp40) cc_final: 0.7974 (tp40) REVERT: F 35 ASP cc_start: 0.8427 (m-30) cc_final: 0.7996 (m-30) REVERT: F 61 VAL cc_start: 0.7895 (t) cc_final: 0.7658 (p) REVERT: G 92 LYS cc_start: 0.7641 (mttp) cc_final: 0.7377 (mttp) REVERT: G 114 ASP cc_start: 0.8062 (m-30) cc_final: 0.7562 (m-30) REVERT: G 134 ASP cc_start: 0.8224 (p0) cc_final: 0.7982 (p0) REVERT: I 62 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8515 (mt-10) REVERT: I 70 MET cc_start: 0.8407 (tmt) cc_final: 0.8132 (tmt) REVERT: J 212 ARG cc_start: 0.8177 (mtt180) cc_final: 0.7674 (mtm-85) REVERT: J 322 VAL cc_start: 0.8947 (p) cc_final: 0.8668 (m) REVERT: L 105 GLU cc_start: 0.9001 (tt0) cc_final: 0.8721 (tm-30) REVERT: M 44 GLU cc_start: 0.7767 (mp0) cc_final: 0.7499 (mp0) REVERT: M 97 MET cc_start: 0.8489 (mmm) cc_final: 0.8203 (mmm) REVERT: M 144 MET cc_start: 0.9160 (mmm) cc_final: 0.8758 (mmm) REVERT: M 173 MET cc_start: 0.9223 (mmm) cc_final: 0.8974 (mmm) REVERT: M 215 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.6924 (mpt) REVERT: M 513 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8236 (mmm) REVERT: M 647 GLU cc_start: 0.8631 (tt0) cc_final: 0.8427 (tt0) REVERT: M 677 GLN cc_start: 0.7364 (tt0) cc_final: 0.7037 (tt0) REVERT: N 8 ARG cc_start: 0.6816 (mtm-85) cc_final: 0.6495 (mmt180) REVERT: N 21 ARG cc_start: 0.7626 (mmt180) cc_final: 0.6346 (mpt90) REVERT: N 76 ASP cc_start: 0.8390 (m-30) cc_final: 0.8058 (m-30) REVERT: N 122 GLN cc_start: 0.8291 (mp10) cc_final: 0.7950 (mm-40) REVERT: O 106 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8375 (mp10) REVERT: P 83 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8015 (mt-10) REVERT: Q 81 THR cc_start: 0.8664 (m) cc_final: 0.8305 (t) REVERT: Q 325 ASP cc_start: 0.9032 (p0) cc_final: 0.8811 (p0) REVERT: T 119 ARG cc_start: 0.8441 (ttm-80) cc_final: 0.8192 (ttm170) outliers start: 64 outliers final: 28 residues processed: 479 average time/residue: 0.8058 time to fit residues: 437.9662 Evaluate side-chains 456 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 421 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 111 GLU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain E residue 52 LEU Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 396 GLU Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 554 CYS Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 203 GLU Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 105 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 107 optimal weight: 0.8980 chunk 303 optimal weight: 3.9990 chunk 264 optimal weight: 0.9980 chunk 256 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 120 optimal weight: 0.0070 chunk 206 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 68 optimal weight: 0.5980 chunk 329 optimal weight: 0.0470 chunk 280 optimal weight: 2.9990 overall best weight: 0.4296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 GLN E 45 ASN F 93 ASN I 9 GLN ** K 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 460 HIS M 482 GLN ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 678 GLN ** N 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 135 GLN O 187 GLN P 77 GLN P 247 GLN Q 270 ASN W 24 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.114091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.092270 restraints weight = 37256.075| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.36 r_work: 0.2881 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.137 28715 Z= 0.102 Angle : 0.706 56.235 38928 Z= 0.263 Chirality : 0.042 0.174 4220 Planarity : 0.004 0.059 4997 Dihedral : 9.355 174.443 4092 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.17 % Favored : 96.80 % Rotamer: Outliers : 2.30 % Allowed : 13.96 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.14), residues: 3439 helix: 1.33 (0.14), residues: 1348 sheet: 0.15 (0.25), residues: 396 loop : -0.26 (0.15), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 89 TYR 0.016 0.001 TYR P 64 PHE 0.012 0.001 PHE Q 458 TRP 0.007 0.001 TRP N 61 HIS 0.008 0.001 HIS Q 223 Details of bonding type rmsd covalent geometry : bond 0.00222 (28676) covalent geometry : angle 0.49872 (38845) SS BOND : bond 0.00547 ( 1) SS BOND : angle 2.15302 ( 2) hydrogen bonds : bond 0.03579 ( 1131) hydrogen bonds : angle 4.75857 ( 3168) metal coordination : bond 0.02435 ( 36) metal coordination : angle 10.97493 ( 81) Misc. bond : bond 0.00138 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 451 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8099 (tp) REVERT: A 134 ASP cc_start: 0.8608 (p0) cc_final: 0.8322 (p0) REVERT: A 149 MET cc_start: 0.8977 (mtm) cc_final: 0.8722 (ptp) REVERT: A 340 ASP cc_start: 0.7947 (m-30) cc_final: 0.7731 (m-30) REVERT: A 456 GLN cc_start: 0.7572 (mt0) cc_final: 0.7355 (mt0) REVERT: B 208 ASP cc_start: 0.8063 (t70) cc_final: 0.7575 (t0) REVERT: C 47 VAL cc_start: 0.8695 (OUTLIER) cc_final: 0.8313 (p) REVERT: C 126 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8687 (mt-10) REVERT: C 195 ARG cc_start: 0.8467 (mtt-85) cc_final: 0.8150 (mtt90) REVERT: E 25 MET cc_start: 0.8588 (tpt) cc_final: 0.8151 (mmt) REVERT: F 91 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8633 (tt) REVERT: G 80 LYS cc_start: 0.7946 (tttt) cc_final: 0.7723 (ttpp) REVERT: G 92 LYS cc_start: 0.7558 (mttp) cc_final: 0.7285 (mttp) REVERT: G 114 ASP cc_start: 0.8056 (m-30) cc_final: 0.7629 (m-30) REVERT: I 62 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8490 (mt-10) REVERT: J 212 ARG cc_start: 0.8165 (mtt180) cc_final: 0.7667 (mtm-85) REVERT: J 322 VAL cc_start: 0.8952 (p) cc_final: 0.8665 (m) REVERT: L 105 GLU cc_start: 0.8992 (tt0) cc_final: 0.8738 (tm-30) REVERT: M 44 GLU cc_start: 0.7707 (mp0) cc_final: 0.7452 (mp0) REVERT: M 144 MET cc_start: 0.9084 (mmm) cc_final: 0.8727 (mmm) REVERT: M 215 MET cc_start: 0.7739 (OUTLIER) cc_final: 0.7015 (mpt) REVERT: M 544 VAL cc_start: 0.9043 (OUTLIER) cc_final: 0.8763 (t) REVERT: M 677 GLN cc_start: 0.7215 (tt0) cc_final: 0.6928 (tt0) REVERT: N 8 ARG cc_start: 0.6794 (mtm-85) cc_final: 0.6464 (mmt180) REVERT: N 21 ARG cc_start: 0.7673 (mmt180) cc_final: 0.6386 (mpt90) REVERT: N 76 ASP cc_start: 0.8347 (m-30) cc_final: 0.8027 (m-30) REVERT: N 122 GLN cc_start: 0.8281 (mp10) cc_final: 0.7942 (mm-40) REVERT: O 106 GLN cc_start: 0.8994 (OUTLIER) cc_final: 0.8363 (mp10) REVERT: P 83 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8048 (mt-10) REVERT: Q 259 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8554 (mm-30) REVERT: Q 325 ASP cc_start: 0.8950 (p0) cc_final: 0.8726 (p0) REVERT: T 119 ARG cc_start: 0.8463 (ttm-80) cc_final: 0.8222 (ttm170) outliers start: 69 outliers final: 22 residues processed: 487 average time/residue: 0.7716 time to fit residues: 427.9704 Evaluate side-chains 450 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 421 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain I residue 109 ASP Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 544 VAL Chi-restraints excluded: chain M residue 658 ASP Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 203 GLU Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain T residue 105 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 190 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 221 optimal weight: 0.9990 chunk 140 optimal weight: 0.0070 chunk 308 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 255 optimal weight: 5.9990 chunk 129 optimal weight: 6.9990 chunk 176 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 overall best weight: 2.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 HIS E 45 ASN E 99 GLN F 93 ASN H 71 GLN I 9 GLN J 154 GLN ** K 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN M 74 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 460 HIS M 482 GLN ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 678 GLN N 135 GLN O 187 GLN O 189 ASN P 75 GLN Q 270 ASN W 24 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.107701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.085669 restraints weight = 37148.880| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 1.41 r_work: 0.2746 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.342 28715 Z= 0.244 Angle : 0.784 51.514 38928 Z= 0.329 Chirality : 0.048 0.213 4220 Planarity : 0.005 0.059 4997 Dihedral : 9.623 178.956 4091 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.66 % Favored : 96.31 % Rotamer: Outliers : 3.04 % Allowed : 14.23 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.14), residues: 3439 helix: 1.05 (0.14), residues: 1347 sheet: 0.12 (0.25), residues: 383 loop : -0.39 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 62 TYR 0.019 0.002 TYR P 64 PHE 0.024 0.002 PHE Q 204 TRP 0.012 0.002 TRP B 63 HIS 0.009 0.002 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00590 (28676) covalent geometry : angle 0.62347 (38845) SS BOND : bond 0.00751 ( 1) SS BOND : angle 2.60756 ( 2) hydrogen bonds : bond 0.05328 ( 1131) hydrogen bonds : angle 5.07281 ( 3168) metal coordination : bond 0.06003 ( 36) metal coordination : angle 10.44428 ( 81) Misc. bond : bond 0.00208 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 517 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 426 time to evaluate : 1.076 Fit side-chains revert: symmetry clash REVERT: A 102 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.7081 (tmm) REVERT: A 456 GLN cc_start: 0.7598 (mt0) cc_final: 0.7326 (mt0) REVERT: B 208 ASP cc_start: 0.8277 (t70) cc_final: 0.7769 (t0) REVERT: C 65 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8285 (tmm) REVERT: C 126 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8747 (mt-10) REVERT: C 195 ARG cc_start: 0.8542 (mtt-85) cc_final: 0.8213 (mtt90) REVERT: E 25 MET cc_start: 0.8665 (tpt) cc_final: 0.8434 (tpt) REVERT: E 109 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8181 (mt-10) REVERT: F 71 PHE cc_start: 0.8092 (m-10) cc_final: 0.7877 (m-10) REVERT: G 82 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.6726 (mtp180) REVERT: G 92 LYS cc_start: 0.7755 (mttp) cc_final: 0.7513 (mttp) REVERT: G 114 ASP cc_start: 0.8163 (m-30) cc_final: 0.7837 (m-30) REVERT: J 117 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7920 (tmt170) REVERT: J 212 ARG cc_start: 0.8285 (mtt180) cc_final: 0.7724 (mtm-85) REVERT: J 220 MET cc_start: 0.7936 (mtt) cc_final: 0.7684 (mtt) REVERT: K 77 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8060 (mt0) REVERT: M 97 MET cc_start: 0.8464 (mmm) cc_final: 0.8213 (mmm) REVERT: M 144 MET cc_start: 0.9163 (mmm) cc_final: 0.8636 (mmm) REVERT: M 158 ARG cc_start: 0.9119 (OUTLIER) cc_final: 0.8784 (ptt180) REVERT: M 215 MET cc_start: 0.7722 (OUTLIER) cc_final: 0.7154 (mpt) REVERT: M 513 MET cc_start: 0.8759 (OUTLIER) cc_final: 0.7070 (tmm) REVERT: N 8 ARG cc_start: 0.6866 (mtm-85) cc_final: 0.6654 (mtm-85) REVERT: N 21 ARG cc_start: 0.7730 (mmt180) cc_final: 0.6461 (mtt90) REVERT: N 67 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8475 (tm-30) REVERT: N 68 MET cc_start: 0.8504 (tpt) cc_final: 0.8013 (mmt) REVERT: N 76 ASP cc_start: 0.8401 (m-30) cc_final: 0.8075 (m-30) REVERT: O 106 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8343 (mp10) REVERT: P 83 GLU cc_start: 0.8767 (OUTLIER) cc_final: 0.8302 (mt-10) REVERT: T 119 ARG cc_start: 0.8493 (ttm-80) cc_final: 0.8207 (ttm170) outliers start: 91 outliers final: 40 residues processed: 476 average time/residue: 0.8094 time to fit residues: 437.6694 Evaluate side-chains 455 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 403 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 117 ARG Chi-restraints excluded: chain J residue 219 SER Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain K residue 77 GLN Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 148 GLU Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 158 ARG Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 396 GLU Chi-restraints excluded: chain M residue 405 THR Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 67 GLU Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain O residue 203 GLU Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain P residue 85 GLU Chi-restraints excluded: chain Q residue 101 LEU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 105 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 75 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 327 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 222 optimal weight: 0.8980 chunk 302 optimal weight: 0.8980 chunk 218 optimal weight: 0.4980 chunk 272 optimal weight: 0.6980 chunk 130 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 GLN E 45 ASN F 93 ASN G 115 GLN I 9 GLN K 75 ASN L 86 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 677 GLN N 13 GLN N 135 GLN O 187 GLN P 247 GLN Q 270 ASN W 24 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.111071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.089305 restraints weight = 37253.000| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.36 r_work: 0.2823 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.162 28715 Z= 0.115 Angle : 0.726 56.287 38928 Z= 0.276 Chirality : 0.042 0.188 4220 Planarity : 0.005 0.056 4997 Dihedral : 9.104 178.214 4091 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.11 % Favored : 96.86 % Rotamer: Outliers : 2.30 % Allowed : 15.63 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.14), residues: 3439 helix: 1.28 (0.14), residues: 1342 sheet: 0.08 (0.25), residues: 390 loop : -0.31 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 191 TYR 0.013 0.001 TYR P 64 PHE 0.012 0.001 PHE A 101 TRP 0.010 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00255 (28676) covalent geometry : angle 0.52092 (38845) SS BOND : bond 0.00555 ( 1) SS BOND : angle 2.25652 ( 2) hydrogen bonds : bond 0.03914 ( 1131) hydrogen bonds : angle 4.82535 ( 3168) metal coordination : bond 0.02879 ( 36) metal coordination : angle 11.09818 ( 81) Misc. bond : bond 0.00262 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 421 time to evaluate : 1.106 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8162 (tp) REVERT: A 149 MET cc_start: 0.9064 (mtm) cc_final: 0.8827 (ptp) REVERT: A 456 GLN cc_start: 0.7484 (mt0) cc_final: 0.7227 (mt0) REVERT: B 208 ASP cc_start: 0.8228 (t70) cc_final: 0.7730 (t0) REVERT: C 47 VAL cc_start: 0.8697 (t) cc_final: 0.8335 (p) REVERT: C 49 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8380 (mmtm) REVERT: C 65 MET cc_start: 0.8898 (OUTLIER) cc_final: 0.8300 (tmm) REVERT: C 86 MET cc_start: 0.8882 (ptt) cc_final: 0.8406 (ptt) REVERT: C 126 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8712 (mt-10) REVERT: C 195 ARG cc_start: 0.8448 (mtt-85) cc_final: 0.8104 (mtt90) REVERT: E 25 MET cc_start: 0.8623 (tpt) cc_final: 0.8250 (mmt) REVERT: E 109 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8128 (mt-10) REVERT: F 38 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7616 (pt0) REVERT: F 71 PHE cc_start: 0.7863 (m-10) cc_final: 0.7589 (m-10) REVERT: G 80 LYS cc_start: 0.8117 (tttt) cc_final: 0.7849 (ttpp) REVERT: G 82 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.6678 (mtp180) REVERT: I 109 ASP cc_start: 0.8357 (t70) cc_final: 0.8118 (t0) REVERT: J 212 ARG cc_start: 0.8279 (mtt180) cc_final: 0.7725 (mtm-85) REVERT: J 322 VAL cc_start: 0.9128 (p) cc_final: 0.8795 (m) REVERT: M 44 GLU cc_start: 0.7856 (mp0) cc_final: 0.7627 (mp0) REVERT: M 97 MET cc_start: 0.8449 (mmm) cc_final: 0.8193 (mmm) REVERT: M 144 MET cc_start: 0.9111 (mmm) cc_final: 0.8514 (mmm) REVERT: M 173 MET cc_start: 0.9169 (mmm) cc_final: 0.8960 (mmm) REVERT: M 215 MET cc_start: 0.7800 (OUTLIER) cc_final: 0.7051 (mpt) REVERT: M 513 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.6917 (tmm) REVERT: N 21 ARG cc_start: 0.7688 (mmt180) cc_final: 0.6416 (mtt90) REVERT: N 76 ASP cc_start: 0.8439 (m-30) cc_final: 0.8112 (m-30) REVERT: O 106 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8338 (mp10) REVERT: P 83 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8181 (mt-10) REVERT: T 119 ARG cc_start: 0.8453 (ttm-80) cc_final: 0.8206 (ttm170) outliers start: 69 outliers final: 27 residues processed: 451 average time/residue: 0.7909 time to fit residues: 405.3455 Evaluate side-chains 442 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 405 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain O residue 203 GLU Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 303 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 85 optimal weight: 0.0570 chunk 44 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 184 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 252 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 GLN E 99 GLN H 71 GLN I 9 GLN K 75 ASN L 86 ASN M 74 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 677 GLN N 135 GLN O 187 GLN Q 270 ASN W 24 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.109109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.087227 restraints weight = 37240.083| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 1.43 r_work: 0.2774 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.246 28715 Z= 0.176 Angle : 0.735 52.047 38928 Z= 0.295 Chirality : 0.045 0.198 4220 Planarity : 0.005 0.057 4997 Dihedral : 9.068 179.773 4091 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.52 % Favored : 96.45 % Rotamer: Outliers : 2.57 % Allowed : 16.33 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.14), residues: 3439 helix: 1.22 (0.14), residues: 1349 sheet: 0.04 (0.25), residues: 392 loop : -0.34 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 191 TYR 0.015 0.002 TYR Q 214 PHE 0.016 0.002 PHE Q 458 TRP 0.010 0.001 TRP M 422 HIS 0.009 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00422 (28676) covalent geometry : angle 0.56048 (38845) SS BOND : bond 0.00658 ( 1) SS BOND : angle 2.43353 ( 2) hydrogen bonds : bond 0.04486 ( 1131) hydrogen bonds : angle 4.88960 ( 3168) metal coordination : bond 0.04332 ( 36) metal coordination : angle 10.42470 ( 81) Misc. bond : bond 0.00096 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 407 time to evaluate : 1.134 Fit side-chains revert: symmetry clash REVERT: A 102 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.7004 (tmm) REVERT: A 296 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9047 (tt) REVERT: A 456 GLN cc_start: 0.7515 (mt0) cc_final: 0.7238 (mt0) REVERT: B 208 ASP cc_start: 0.8281 (t70) cc_final: 0.7762 (t0) REVERT: C 49 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8379 (mmtm) REVERT: C 65 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8389 (tmm) REVERT: C 126 GLU cc_start: 0.8944 (mt-10) cc_final: 0.8734 (mt-10) REVERT: C 195 ARG cc_start: 0.8465 (mtt-85) cc_final: 0.8166 (mtt90) REVERT: E 25 MET cc_start: 0.8635 (tpt) cc_final: 0.8366 (tpt) REVERT: E 109 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8183 (mt-10) REVERT: G 80 LYS cc_start: 0.8075 (tttt) cc_final: 0.7835 (ttpp) REVERT: G 82 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.6592 (mtp180) REVERT: I 109 ASP cc_start: 0.8426 (t70) cc_final: 0.8215 (t0) REVERT: J 212 ARG cc_start: 0.8315 (mtt180) cc_final: 0.7783 (mtm-85) REVERT: L 105 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8495 (tt0) REVERT: M 97 MET cc_start: 0.8492 (mmm) cc_final: 0.8243 (mmm) REVERT: M 117 MET cc_start: 0.9230 (tpp) cc_final: 0.9002 (tpp) REVERT: M 144 MET cc_start: 0.9106 (mmm) cc_final: 0.8574 (mmm) REVERT: M 215 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7380 (mpt) REVERT: M 513 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.6987 (tmm) REVERT: N 8 ARG cc_start: 0.6909 (mtm-85) cc_final: 0.6563 (mmt180) REVERT: N 21 ARG cc_start: 0.7664 (mmt180) cc_final: 0.6405 (mtt90) REVERT: N 67 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8494 (tm-30) REVERT: N 76 ASP cc_start: 0.8441 (m-30) cc_final: 0.8091 (m-30) REVERT: N 144 TYR cc_start: 0.7699 (OUTLIER) cc_final: 0.7250 (p90) REVERT: O 106 GLN cc_start: 0.9006 (OUTLIER) cc_final: 0.8341 (mp10) REVERT: O 168 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8423 (tp) REVERT: P 83 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8280 (mt-10) REVERT: T 119 ARG cc_start: 0.8522 (ttm-80) cc_final: 0.8239 (ttm170) outliers start: 77 outliers final: 42 residues processed: 440 average time/residue: 0.7995 time to fit residues: 399.5502 Evaluate side-chains 458 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 402 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 43 MET Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 219 SER Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 67 GLU Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 144 TYR Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain O residue 168 LEU Chi-restraints excluded: chain O residue 203 GLU Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 142 optimal weight: 0.9980 chunk 216 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 281 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 248 optimal weight: 1.9990 chunk 223 optimal weight: 0.9980 chunk 251 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 GLN E 45 ASN I 9 GLN K 75 ASN L 86 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 677 GLN N 135 GLN O 187 GLN Q 270 ASN W 24 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.109989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.088195 restraints weight = 37189.384| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 1.36 r_work: 0.2791 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2688 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.200 28715 Z= 0.146 Angle : 0.725 53.945 38928 Z= 0.284 Chirality : 0.044 0.191 4220 Planarity : 0.005 0.056 4997 Dihedral : 8.819 179.362 4091 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.23 % Favored : 96.74 % Rotamer: Outliers : 2.37 % Allowed : 16.60 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.14), residues: 3439 helix: 1.26 (0.14), residues: 1342 sheet: 0.05 (0.25), residues: 390 loop : -0.33 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 191 TYR 0.013 0.001 TYR P 64 PHE 0.013 0.001 PHE Q 458 TRP 0.010 0.001 TRP M 422 HIS 0.008 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00343 (28676) covalent geometry : angle 0.54064 (38845) SS BOND : bond 0.00601 ( 1) SS BOND : angle 2.37601 ( 2) hydrogen bonds : bond 0.04174 ( 1131) hydrogen bonds : angle 4.83226 ( 3168) metal coordination : bond 0.03557 ( 36) metal coordination : angle 10.60956 ( 81) Misc. bond : bond 0.00081 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 422 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.6947 (tmm) REVERT: A 296 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9057 (tt) REVERT: A 456 GLN cc_start: 0.7466 (mt0) cc_final: 0.7230 (mt0) REVERT: B 208 ASP cc_start: 0.8262 (t70) cc_final: 0.7745 (t0) REVERT: C 47 VAL cc_start: 0.8638 (t) cc_final: 0.8294 (p) REVERT: C 49 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8400 (mmtm) REVERT: C 65 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8362 (tmm) REVERT: C 86 MET cc_start: 0.8894 (ptt) cc_final: 0.8417 (ptt) REVERT: C 126 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8711 (mt-10) REVERT: C 195 ARG cc_start: 0.8458 (mtt-85) cc_final: 0.8152 (mtt90) REVERT: E 25 MET cc_start: 0.8637 (tpt) cc_final: 0.8278 (mmt) REVERT: E 109 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: F 38 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7694 (pt0) REVERT: G 80 LYS cc_start: 0.8101 (tttt) cc_final: 0.7862 (ttpp) REVERT: G 82 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.6621 (mtp180) REVERT: I 109 ASP cc_start: 0.8407 (t70) cc_final: 0.8196 (t0) REVERT: J 212 ARG cc_start: 0.8295 (mtt180) cc_final: 0.7794 (mtm-85) REVERT: L 105 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8475 (tt0) REVERT: M 44 GLU cc_start: 0.7871 (mp0) cc_final: 0.7646 (mp0) REVERT: M 97 MET cc_start: 0.8483 (mmm) cc_final: 0.8204 (mmm) REVERT: M 117 MET cc_start: 0.9166 (tpp) cc_final: 0.8958 (tpp) REVERT: M 144 MET cc_start: 0.9064 (mmm) cc_final: 0.8553 (mmm) REVERT: M 215 MET cc_start: 0.7927 (OUTLIER) cc_final: 0.7388 (mpt) REVERT: M 513 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.6921 (tmm) REVERT: N 8 ARG cc_start: 0.6994 (mtm-85) cc_final: 0.6674 (mmt180) REVERT: N 9 ARG cc_start: 0.7293 (mtp180) cc_final: 0.7044 (mtm-85) REVERT: N 21 ARG cc_start: 0.7690 (mmt180) cc_final: 0.6434 (mtt90) REVERT: N 25 ARG cc_start: 0.7935 (ttt90) cc_final: 0.7663 (ttt180) REVERT: N 76 ASP cc_start: 0.8479 (m-30) cc_final: 0.8103 (m-30) REVERT: O 106 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8344 (mp10) REVERT: P 83 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8267 (mt-10) REVERT: Q 108 LYS cc_start: 0.8596 (tttp) cc_final: 0.8373 (tmtp) REVERT: T 119 ARG cc_start: 0.8514 (ttm-80) cc_final: 0.8094 (ttm170) outliers start: 71 outliers final: 42 residues processed: 455 average time/residue: 0.7926 time to fit residues: 410.5000 Evaluate side-chains 460 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 406 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 65 MET Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 219 SER Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 70 GLU Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 396 GLU Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 513 MET Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain O residue 203 GLU Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain Q residue 147 ASN Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 337 optimal weight: 0.0570 chunk 311 optimal weight: 4.9990 chunk 292 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 240 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 117 optimal weight: 0.0070 chunk 60 optimal weight: 0.5980 chunk 213 optimal weight: 0.9990 chunk 319 optimal weight: 0.9980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 GLN E 45 ASN I 9 GLN K 75 ASN K 78 HIS L 86 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 482 GLN ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 677 GLN N 135 GLN Q 270 ASN W 24 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.111821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.090095 restraints weight = 37197.997| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.38 r_work: 0.2841 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.149 28715 Z= 0.108 Angle : 0.707 54.045 38928 Z= 0.270 Chirality : 0.042 0.183 4220 Planarity : 0.004 0.054 4997 Dihedral : 8.573 179.798 4091 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.29 % Favored : 96.69 % Rotamer: Outliers : 1.84 % Allowed : 17.47 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.14), residues: 3439 helix: 1.37 (0.14), residues: 1345 sheet: 0.10 (0.25), residues: 390 loop : -0.30 (0.15), residues: 1704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 191 TYR 0.011 0.001 TYR P 64 PHE 0.012 0.001 PHE Q 458 TRP 0.010 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00237 (28676) covalent geometry : angle 0.51190 (38845) SS BOND : bond 0.00532 ( 1) SS BOND : angle 2.28109 ( 2) hydrogen bonds : bond 0.03693 ( 1131) hydrogen bonds : angle 4.72873 ( 3168) metal coordination : bond 0.02646 ( 36) metal coordination : angle 10.68346 ( 81) Misc. bond : bond 0.00031 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 424 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.6938 (tmm) REVERT: A 456 GLN cc_start: 0.7480 (mt0) cc_final: 0.7244 (mt0) REVERT: B 208 ASP cc_start: 0.8217 (t70) cc_final: 0.7708 (t0) REVERT: C 47 VAL cc_start: 0.8634 (t) cc_final: 0.8281 (p) REVERT: C 49 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8389 (mmtm) REVERT: C 86 MET cc_start: 0.8874 (ptt) cc_final: 0.8388 (ptt) REVERT: C 126 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8693 (mt-10) REVERT: C 195 ARG cc_start: 0.8408 (mtt-85) cc_final: 0.8139 (mtt90) REVERT: E 23 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7421 (mtp-110) REVERT: E 25 MET cc_start: 0.8598 (tpt) cc_final: 0.8235 (mmt) REVERT: E 109 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8115 (mt-10) REVERT: E 110 THR cc_start: 0.8846 (p) cc_final: 0.8517 (m) REVERT: F 38 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7641 (pt0) REVERT: G 80 LYS cc_start: 0.8105 (tttt) cc_final: 0.7864 (ttpp) REVERT: G 82 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6618 (mtp180) REVERT: I 109 ASP cc_start: 0.8348 (t70) cc_final: 0.8121 (OUTLIER) REVERT: J 212 ARG cc_start: 0.8260 (mtt180) cc_final: 0.7770 (mtm-85) REVERT: J 322 VAL cc_start: 0.9147 (p) cc_final: 0.8812 (m) REVERT: K 75 ASN cc_start: 0.8153 (t0) cc_final: 0.7645 (t0) REVERT: L 105 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8434 (tt0) REVERT: M 44 GLU cc_start: 0.7951 (mp0) cc_final: 0.7720 (mp0) REVERT: M 97 MET cc_start: 0.8497 (mmm) cc_final: 0.8220 (mmm) REVERT: M 144 MET cc_start: 0.9037 (mmm) cc_final: 0.8512 (mmm) REVERT: M 215 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.6992 (mpt) REVERT: N 8 ARG cc_start: 0.6936 (mtm-85) cc_final: 0.6616 (mmt180) REVERT: N 9 ARG cc_start: 0.7252 (mtp180) cc_final: 0.6993 (mtm-85) REVERT: N 21 ARG cc_start: 0.7820 (mmt180) cc_final: 0.6587 (mtt90) REVERT: N 25 ARG cc_start: 0.7955 (ttt90) cc_final: 0.7690 (ttt180) REVERT: N 76 ASP cc_start: 0.8465 (m-30) cc_final: 0.8116 (m-30) REVERT: O 106 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8310 (mp10) REVERT: P 83 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8167 (mt-10) REVERT: Q 108 LYS cc_start: 0.8591 (tttp) cc_final: 0.8372 (tmtp) REVERT: T 119 ARG cc_start: 0.8473 (ttm-80) cc_final: 0.8105 (ttm170) outliers start: 55 outliers final: 35 residues processed: 453 average time/residue: 0.7919 time to fit residues: 409.1122 Evaluate side-chains 449 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 405 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 23 ARG Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 203 GLU Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 48 optimal weight: 0.9980 chunk 322 optimal weight: 0.8980 chunk 175 optimal weight: 0.9980 chunk 199 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 327 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 GLN E 45 ASN I 9 GLN L 86 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 677 GLN N 135 GLN O 187 GLN P 77 GLN Q 270 ASN Q 454 GLN W 24 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.111206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.089395 restraints weight = 37080.202| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 1.37 r_work: 0.2818 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.182 28715 Z= 0.127 Angle : 0.713 51.962 38928 Z= 0.278 Chirality : 0.043 0.186 4220 Planarity : 0.005 0.054 4997 Dihedral : 8.515 178.839 4091 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.26 % Favored : 96.71 % Rotamer: Outliers : 1.80 % Allowed : 17.60 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.14), residues: 3439 helix: 1.34 (0.14), residues: 1351 sheet: 0.06 (0.25), residues: 402 loop : -0.28 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 191 TYR 0.012 0.001 TYR C 84 PHE 0.015 0.001 PHE Q 458 TRP 0.009 0.001 TRP M 422 HIS 0.007 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00293 (28676) covalent geometry : angle 0.53182 (38845) SS BOND : bond 0.00570 ( 1) SS BOND : angle 2.30102 ( 2) hydrogen bonds : bond 0.03902 ( 1131) hydrogen bonds : angle 4.73168 ( 3168) metal coordination : bond 0.03212 ( 36) metal coordination : angle 10.40434 ( 81) Misc. bond : bond 0.00072 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6878 Ramachandran restraints generated. 3439 Oldfield, 0 Emsley, 3439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 418 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.6944 (tmm) REVERT: A 456 GLN cc_start: 0.7515 (mt0) cc_final: 0.7269 (mt0) REVERT: B 208 ASP cc_start: 0.8245 (t70) cc_final: 0.7731 (t0) REVERT: C 47 VAL cc_start: 0.8625 (t) cc_final: 0.8278 (p) REVERT: C 49 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8391 (mmtm) REVERT: C 86 MET cc_start: 0.8890 (ptt) cc_final: 0.8419 (ptt) REVERT: C 126 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8702 (mt-10) REVERT: C 195 ARG cc_start: 0.8400 (mtt-85) cc_final: 0.8134 (mtt90) REVERT: E 25 MET cc_start: 0.8599 (tpt) cc_final: 0.8241 (mmt) REVERT: E 109 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: E 110 THR cc_start: 0.8845 (p) cc_final: 0.8511 (m) REVERT: F 38 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7599 (pt0) REVERT: G 80 LYS cc_start: 0.8096 (tttt) cc_final: 0.7863 (ttpp) REVERT: G 82 ARG cc_start: 0.7624 (OUTLIER) cc_final: 0.6727 (mtp180) REVERT: I 109 ASP cc_start: 0.8422 (t70) cc_final: 0.8197 (t0) REVERT: J 212 ARG cc_start: 0.8267 (mtt180) cc_final: 0.7770 (mtm-85) REVERT: L 105 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8427 (tt0) REVERT: M 44 GLU cc_start: 0.7906 (mp0) cc_final: 0.7667 (mp0) REVERT: M 77 MET cc_start: 0.8778 (tpt) cc_final: 0.8306 (tpt) REVERT: M 97 MET cc_start: 0.8507 (mmm) cc_final: 0.8234 (mmm) REVERT: M 144 MET cc_start: 0.9026 (mmm) cc_final: 0.8503 (mmm) REVERT: M 215 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7023 (mpt) REVERT: N 8 ARG cc_start: 0.6910 (mtm-85) cc_final: 0.6641 (mmt180) REVERT: N 9 ARG cc_start: 0.7238 (mtp180) cc_final: 0.6973 (mtm-85) REVERT: N 21 ARG cc_start: 0.7709 (mmt180) cc_final: 0.6466 (mtt90) REVERT: N 76 ASP cc_start: 0.8468 (m-30) cc_final: 0.8094 (m-30) REVERT: O 106 GLN cc_start: 0.8992 (OUTLIER) cc_final: 0.8260 (mp10) REVERT: P 83 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8189 (mt-10) REVERT: Q 108 LYS cc_start: 0.8596 (tttp) cc_final: 0.8386 (tmtp) REVERT: T 119 ARG cc_start: 0.8479 (ttm-80) cc_final: 0.8117 (ttm170) outliers start: 54 outliers final: 38 residues processed: 445 average time/residue: 0.8108 time to fit residues: 411.2596 Evaluate side-chains 458 residues out of total 3000 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 411 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain C residue 49 LYS Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 19 ILE Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 91 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 92 MET Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 236 VAL Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain M residue 56 VAL Chi-restraints excluded: chain M residue 204 MET Chi-restraints excluded: chain M residue 215 MET Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 689 LEU Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain O residue 106 GLN Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 203 GLU Chi-restraints excluded: chain P residue 80 CYS Chi-restraints excluded: chain P residue 83 GLU Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 308 TYR Chi-restraints excluded: chain Q residue 457 VAL Chi-restraints excluded: chain T residue 31 THR Chi-restraints excluded: chain T residue 105 GLU Chi-restraints excluded: chain W residue 31 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 339 random chunks: chunk 69 optimal weight: 3.9990 chunk 253 optimal weight: 2.9990 chunk 209 optimal weight: 2.9990 chunk 100 optimal weight: 0.0040 chunk 13 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 204 optimal weight: 0.9990 chunk 231 optimal weight: 2.9990 chunk 221 optimal weight: 7.9990 chunk 164 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 123 GLN E 45 ASN H 71 GLN H 83 GLN I 9 GLN K 75 ASN L 86 ASN M 74 ASN ** M 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 604 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 677 GLN M 678 GLN N 135 GLN O 187 GLN P 236 ASN Q 147 ASN Q 270 ASN Q 454 GLN W 24 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.109328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.087427 restraints weight = 37076.236| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.43 r_work: 0.2779 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.246 28715 Z= 0.187 Angle : 0.739 50.636 38928 Z= 0.300 Chirality : 0.045 0.192 4220 Planarity : 0.005 0.055 4997 Dihedral : 8.629 177.315 4091 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.46 % Favored : 96.51 % Rotamer: Outliers : 2.10 % Allowed : 17.37 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.14), residues: 3439 helix: 1.23 (0.14), residues: 1356 sheet: 0.03 (0.25), residues: 402 loop : -0.33 (0.15), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 71 TYR 0.016 0.002 TYR Q 214 PHE 0.017 0.002 PHE Q 458 TRP 0.008 0.001 TRP M 422 HIS 0.009 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00451 (28676) covalent geometry : angle 0.57304 (38845) SS BOND : bond 0.00637 ( 1) SS BOND : angle 2.38130 ( 2) hydrogen bonds : bond 0.04462 ( 1131) hydrogen bonds : angle 4.83952 ( 3168) metal coordination : bond 0.04374 ( 36) metal coordination : angle 10.22227 ( 81) Misc. bond : bond 0.00103 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10258.80 seconds wall clock time: 174 minutes 55.20 seconds (10495.20 seconds total)