Starting phenix.real_space_refine on Mon Aug 25 17:19:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vyf_32203/08_2025/7vyf_32203.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vyf_32203/08_2025/7vyf_32203.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 { model { file = "/net/cci-nas-00/data/ceres_data/7vyf_32203/08_2025/7vyf_32203.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vyf_32203/08_2025/7vyf_32203.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7vyf_32203/08_2025/7vyf_32203.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vyf_32203/08_2025/7vyf_32203.map" } 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 8 5.49 5 Mg 1 5.21 5 S 189 5.16 5 C 18039 2.51 5 N 4952 2.21 5 O 5238 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28456 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3330 Classifications: {'peptide': 433} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 410} 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: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 687 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 81} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "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: 2751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2751 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 22, 'TRANS': 319} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 366 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 3, 'TRANS': 39} 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: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1667 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 195} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 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: 3096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3096 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 364} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {'970': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 128 Unusual residues: {' UQ': 1, 'NDP': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {' UQ:plan-2': 1, ' UQ:plan-3': 1, ' UQ:plan-4': 1, ' UQ:plan-5': 1, ' UQ:plan-6': 1, ' UQ:plan-7': 1} Unresolved non-hydrogen planarities: 30 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: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 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 2718 SG CYS A 382 47.257 48.229 105.077 1.00 15.01 S ATOM 3060 SG CYS A 425 46.622 45.117 110.919 1.00 16.83 S ATOM 2738 SG CYS A 385 44.196 43.832 105.072 1.00 16.21 S ATOM 2699 SG CYS A 379 41.824 48.654 108.944 1.00 17.60 S ATOM 3961 SG CYS B 113 35.464 63.636 70.197 1.00 12.98 S ATOM 3980 SG CYS B 116 40.715 61.482 73.979 1.00 11.73 S ATOM 4003 SG CYS B 119 41.613 64.328 68.624 1.00 12.27 S ATOM 4332 SG CYS B 162 39.351 58.367 69.163 1.00 9.94 S ATOM 4030 SG CYS B 123 47.455 67.267 64.122 1.00 10.95 S ATOM 4256 SG CYS B 152 46.046 65.469 58.105 1.00 5.69 S ATOM 4303 SG CYS B 158 44.113 61.627 63.054 1.00 9.68 S ATOM 4282 SG CYS B 155 50.231 62.277 61.417 1.00 5.92 S ATOM 5724 SG CYS C 166 52.663 65.769 53.890 1.00 9.77 S ATOM 4996 SG CYS C 72 52.908 67.339 47.688 1.00 12.75 S ATOM 4990 SG CYS C 71 58.370 65.648 50.907 1.00 13.76 S ATOM 5494 SG CYS C 136 54.802 70.931 52.810 1.00 11.36 S ATOM 14949 SG CYS M 131 39.747 61.615 86.074 1.00 10.93 S ATOM 14928 SG CYS M 128 43.623 57.082 83.015 1.00 9.94 S ATOM 14989 SG CYS M 137 45.466 60.681 88.228 1.00 11.40 S ATOM 15321 SG CYS M 179 43.708 60.774 99.286 1.00 12.87 S ATOM 15675 SG CYS M 226 40.494 63.364 94.971 1.00 12.78 S ATOM 15345 SG CYS M 182 38.043 63.245 101.059 1.00 13.88 S ATOM 15298 SG CYS M 176 38.192 57.810 97.586 1.00 12.01 S ATOM 14546 SG CYS M 78 55.525 56.872 103.149 1.00 13.43 S ATOM 14647 SG CYS M 92 53.604 58.856 105.392 1.00 15.58 S ATOM 14435 SG CYS M 64 49.165 58.477 103.130 1.00 11.92 S ATOM 14521 SG CYS M 75 50.296 56.594 100.226 1.00 12.13 S ATOM 21484 SG CYS O 135 31.810 30.116 113.050 1.00 38.13 S ATOM 21518 SG CYS O 140 31.110 26.653 113.504 1.00 40.30 S ATOM 21798 SG CYS O 176 35.968 31.438 115.559 1.00 36.59 S ATOM 21821 SG CYS O 180 36.631 28.355 116.257 1.00 43.05 S ATOM 27627 SG CYS T 86 28.723 49.954 77.935 1.00 23.13 S ATOM 27805 SG CYS T 111 29.750 53.383 79.081 1.00 25.69 S Time building chain proxies: 6.34, per 1000 atoms: 0.22 Number of scatterers: 28456 At special positions: 0 Unit cell: (124.607, 142.869, 161.13, 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 189 16.00 P 8 15.00 Mg 1 11.99 O 5238 8.00 N 4952 7.00 C 18039 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=2.05 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.62 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES M 803 " pdb="FE2 FES M 803 " - pdb=" SG CYS M 75 " pdb="FE1 FES M 803 " - pdb=" SG CYS M 78 " 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 135 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 180 " pdb="FE2 FES O 301 " - pdb=" SG CYS O 176 " pdb="FE1 FES O 301 " - pdb=" SG CYS O 140 " 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="FE1 SF4 A 501 " - pdb=" SG CYS A 382 " pdb="FE4 SF4 A 501 " - pdb=" SG CYS A 379 " 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="FE2 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 123 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 158 " pdb=" SF4 C 301 " 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=" SG CYS C 71 " 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="FE4 SF4 M 802 " - pdb=" SG CYS M 176 " pdb="FE1 SF4 M 802 " - pdb=" SG CYS M 179 " pdb="FE3 SF4 M 802 " - pdb=" SG CYS M 182 " pdb="FE2 SF4 M 802 " - pdb=" SG CYS M 226 " 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 " 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6576 Finding SS restraints... Secondary structure from input PDB file: 157 helices and 32 sheets defined 46.0% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 36 through 40 Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 64 through 72 removed outlier: 3.821A pdb=" N GLY A 72 " --> pdb=" O ILE A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 83 Processing helix chain 'A' and resid 94 through 100 Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 125 through 134 removed outlier: 3.905A pdb=" N GLU A 129 " --> pdb=" O CYS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 149 removed outlier: 3.598A 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 203 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 removed outlier: 3.702A pdb=" N SER A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) Proline residue: A 252 - end of helix Processing helix chain 'A' and resid 258 through 264 removed outlier: 3.666A pdb=" N PHE A 262 " --> pdb=" O GLY A 258 " (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 removed outlier: 3.781A pdb=" N GLU A 333 " --> pdb=" O LYS A 329 " (cutoff:3.500A) No H-bonds generated for '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: 4.532A pdb=" N ASP A 390 " --> pdb=" O ARG A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 420 removed outlier: 4.161A pdb=" N ASP A 410 " --> pdb=" O PRO A 406 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER A 411 " --> pdb=" O ALA A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 442 Proline residue: A 434 - end of helix Processing helix chain 'A' and resid 442 through 458 removed outlier: 3.515A pdb=" N LEU A 446 " --> pdb=" O PHE A 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 63 Processing helix chain 'B' and resid 63 through 79 removed outlier: 3.640A pdb=" N PHE B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG B 79 " --> pdb=" O SER B 75 " (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 179 through 182 Processing helix chain 'B' and resid 186 through 207 removed outlier: 5.645A pdb=" N ALA B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N GLU B 200 " --> pdb=" O LYS B 196 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA B 203 " --> pdb=" O ALA B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'C' and resid 42 through 61 Processing helix chain 'C' and resid 70 through 80 removed outlier: 4.129A pdb=" N VAL C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 3.898A 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 96 through 100 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 189 through 196 Processing helix chain 'E' and resid 24 through 51 removed outlier: 3.635A 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 69 Processing helix chain 'E' and resid 75 through 95 Processing helix chain 'E' and resid 99 through 105 Processing helix chain 'E' and resid 117 through 125 removed outlier: 3.501A pdb=" N LYS E 121 " --> pdb=" O ASP E 117 " (cutoff:3.500A) 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 40 Processing helix chain 'F' and resid 40 through 48 Processing helix chain 'F' and resid 83 through 96 Processing helix chain 'G' and resid 75 through 89 Processing helix chain 'G' and resid 94 through 98 removed outlier: 3.651A pdb=" N LYS G 97 " --> pdb=" O ASP G 94 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU G 98 " --> pdb=" O PRO G 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 94 through 98' Processing helix chain 'G' and resid 111 through 127 Processing helix chain 'G' and resid 140 through 153 removed outlier: 3.510A pdb=" N ILE G 144 " --> pdb=" O CYS G 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 36 removed outlier: 4.231A pdb=" N ARG H 23 " --> pdb=" O THR H 19 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 61 Processing helix chain 'H' and resid 64 through 73 Processing helix chain 'H' and resid 77 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 77 removed outlier: 4.130A pdb=" N TYR J 68 " --> pdb=" O PHE J 64 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N MET J 76 " --> pdb=" O HIS J 72 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY J 77 " --> pdb=" O LEU J 73 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 98 removed outlier: 5.098A pdb=" N HIS J 93 " --> pdb=" O ASP J 90 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 112 through 120 removed outlier: 3.637A 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 220 through 224 Processing helix chain 'J' and resid 229 through 233 Processing helix chain 'J' and resid 242 through 255 Processing helix chain 'J' and resid 273 through 284 Processing helix chain 'J' and resid 294 through 306 Processing helix chain 'J' and resid 315 through 323 Processing helix chain 'J' and resid 335 through 339 Processing helix chain 'J' and resid 344 through 348 Processing helix chain 'J' and resid 349 through 354 Processing helix chain 'J' and resid 358 through 362 Processing helix chain 'J' and resid 365 through 369 removed outlier: 3.691A pdb=" N ASP J 368 " --> pdb=" O GLU J 365 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL J 369 " --> pdb=" O MET J 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 365 through 369' Processing helix chain 'K' and resid 75 through 80 removed outlier: 4.112A pdb=" N HIS K 78 " --> pdb=" O ASN K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 94 Processing helix chain 'L' and resid 61 through 65 removed outlier: 3.626A pdb=" N THR L 65 " --> pdb=" O THR L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 74 removed outlier: 3.728A pdb=" N THR L 74 " --> pdb=" O GLU L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 95 removed outlier: 4.090A pdb=" N LYS L 95 " --> pdb=" O ASN L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 141 removed outlier: 3.513A pdb=" N ALA L 134 " --> pdb=" O THR L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 165 removed outlier: 3.591A pdb=" N SER L 165 " --> pdb=" O ALA L 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 56 removed outlier: 3.765A pdb=" N VAL M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 123 removed outlier: 4.448A pdb=" N ASN M 123 " --> pdb=" O PHE M 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 131 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 removed outlier: 3.636A pdb=" N ASP M 203 " --> pdb=" O ARG M 200 " (cutoff:3.500A) Processing helix chain 'M' and resid 220 through 226 removed outlier: 4.053A 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 removed outlier: 3.685A pdb=" N ARG M 299 " --> pdb=" O GLY M 296 " (cutoff:3.500A) Processing helix chain 'M' and resid 318 through 333 removed outlier: 3.503A pdb=" N PHE M 333 " --> pdb=" O MET M 329 " (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 361 removed outlier: 3.716A pdb=" N VAL M 361 " --> pdb=" O LEU M 357 " (cutoff:3.500A) Processing helix chain 'M' and resid 381 through 386 removed outlier: 3.598A pdb=" N TYR M 385 " --> pdb=" O ARG M 382 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU M 386 " --> pdb=" O SER M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 391 through 397 Processing helix chain 'M' and resid 406 through 411 Processing helix chain 'M' and resid 411 through 425 Processing helix chain 'M' and resid 449 through 458 removed outlier: 4.115A pdb=" N GLN M 453 " --> pdb=" O PRO M 449 " (cutoff:3.500A) Processing helix chain 'M' and resid 460 through 469 removed outlier: 3.980A pdb=" N GLN M 464 " --> pdb=" O HIS M 460 " (cutoff:3.500A) Processing helix chain 'M' and resid 479 through 483 removed outlier: 4.018A pdb=" N ARG M 483 " --> pdb=" O ALA M 480 " (cutoff:3.500A) 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 556 through 560 Processing helix chain 'M' and resid 588 through 592 removed outlier: 4.073A pdb=" N LYS M 592 " --> pdb=" O TYR M 589 " (cutoff:3.500A) Processing helix chain 'M' and resid 618 through 631 Processing helix chain 'M' and resid 638 through 650 Processing helix chain 'M' and resid 651 through 655 removed outlier: 3.618A pdb=" N ARG M 655 " --> pdb=" O ASN M 652 " (cutoff:3.500A) Processing helix chain 'M' and resid 664 through 673 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 17 removed outlier: 3.641A pdb=" N HIS N 17 " --> pdb=" O GLN N 13 " (cutoff:3.500A) Processing helix chain 'N' and resid 18 through 31 removed outlier: 4.300A pdb=" N GLY N 22 " --> pdb=" O GLY N 18 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 82 removed outlier: 3.673A 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 68 Processing helix chain 'O' and resid 75 through 77 No H-bonds generated for 'chain 'O' and resid 75 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: 3.616A pdb=" N VAL O 112 " --> pdb=" O PRO O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 142 Processing helix chain 'O' and resid 144 through 157 removed outlier: 4.061A pdb=" N ILE O 148 " --> pdb=" O ASN O 144 " (cutoff:3.500A) Processing helix chain 'O' and resid 179 through 183 Processing helix chain 'O' and resid 197 through 210 Processing helix chain 'P' and resid 51 through 69 removed outlier: 3.644A 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: 4.087A pdb=" N TYR P 166 " --> pdb=" O ALA P 162 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG P 168 " --> pdb=" O ASN P 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 242 through 246 Processing helix chain 'Q' and resid 88 through 92 removed outlier: 4.058A pdb=" N HIS Q 92 " --> pdb=" O PRO Q 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 119 through 125 Processing helix chain 'Q' and resid 132 through 140 removed outlier: 4.186A pdb=" N PHE Q 136 " --> pdb=" O ALA Q 132 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP Q 137 " --> pdb=" O LEU Q 133 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP Q 140 " --> pdb=" O PHE Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 160 removed outlier: 3.760A 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: 3.985A pdb=" N PHE Q 201 " --> pdb=" O MET Q 197 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU Q 205 " --> pdb=" O PHE Q 201 " (cutoff:3.500A) removed outlier: 4.430A 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: 3.757A 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 309 through 314 removed outlier: 3.740A pdb=" N ASP Q 312 " --> pdb=" O ASP Q 309 " (cutoff:3.500A) 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: 4.165A pdb=" N ALA Q 430 " --> pdb=" O ALA Q 426 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ASP Q 436 " --> pdb=" O LEU Q 432 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LYS Q 437 " --> pdb=" O ALA Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 443 through 454 Processing helix chain 'Q' and resid 457 through 463 removed outlier: 3.555A pdb=" N VAL Q 461 " --> pdb=" O VAL Q 457 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 56 removed outlier: 3.753A pdb=" N ARG T 52 " --> pdb=" O ASP T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 66 through 73 removed outlier: 3.546A pdb=" N ALA T 72 " --> pdb=" O ILE T 68 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU T 73 " --> pdb=" O ASP T 69 " (cutoff:3.500A) 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: 6.614A pdb=" N LEU A 113 " --> pdb=" O TYR A 155 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N TYR A 157 " --> pdb=" O LEU A 113 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL A 115 " --> pdb=" O TYR A 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 266 through 267 removed outlier: 3.554A 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: 6.361A 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: 6.534A pdb=" N THR B 129 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N TYR B 145 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLU B 131 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG B 141 " --> pdb=" O GLU B 133 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 102 through 106 removed outlier: 6.387A pdb=" N MET C 103 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N MET C 133 " --> pdb=" O MET C 103 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL C 105 " --> pdb=" O MET C 133 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL C 130 " --> pdb=" O ILE C 161 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N VAL C 163 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER C 132 " --> pdb=" O VAL C 163 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 53 through 58 removed outlier: 8.437A pdb=" N LEU F 54 " --> pdb=" O ARG F 17 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE F 19 " --> pdb=" O LEU F 54 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ARG F 56 " --> pdb=" O ILE F 19 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE F 21 " --> pdb=" O ARG F 56 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N CYS F 58 " --> pdb=" O ILE F 21 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU F 23 " --> pdb=" O CYS F 58 " (cutoff:3.500A) removed outlier: 3.599A 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 68 removed outlier: 6.543A pdb=" N PHE P 87 " --> pdb=" O GLN P 74 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N VAL P 76 " --> pdb=" O GLU P 85 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU P 85 " --> pdb=" O VAL P 76 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU P 84 " --> pdb=" O ARG P 142 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LYS P 144 " --> pdb=" O LEU P 84 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE P 86 " --> pdb=" O LYS P 144 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N TYR P 146 " --> pdb=" O ILE P 86 " (cutoff:3.500A) removed outlier: 8.860A pdb=" N ILE P 88 " --> pdb=" O TYR P 146 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP P 113 " --> pdb=" O ASN P 131 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LEU P 133 " --> pdb=" O LEU P 111 " (cutoff:3.500A) removed outlier: 5.335A 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 107 removed outlier: 6.409A pdb=" N ALA J 56 " --> pdb=" O ILE J 81 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL J 58 " --> pdb=" O PRO J 83 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL J 126 " --> pdb=" O ILE J 165 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE J 167 " --> pdb=" O VAL J 126 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ASN J 128 " --> pdb=" O ILE J 167 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N LEU J 164 " --> pdb=" O THR J 199 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ILE J 201 " --> pdb=" O LEU J 164 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N HIS J 166 " --> pdb=" O ILE J 201 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ILE J 200 " --> pdb=" O PHE J 263 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N PHE J 265 " --> pdb=" O ILE J 200 " (cutoff:3.500A) removed outlier: 6.477A 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 226 through 228 Processing sheet with id=AB4, first strand: chain 'J' and resid 236 through 237 Processing sheet with id=AB5, first strand: chain 'L' and resid 125 through 128 Processing sheet with id=AB6, first strand: chain 'L' and resid 106 through 108 Processing sheet with id=AB7, first strand: chain 'M' and resid 39 through 43 removed outlier: 9.185A pdb=" N ILE M 102 " --> pdb=" O GLU M 33 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N PHE M 35 " --> pdb=" O ILE M 102 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLU M 81 " --> pdb=" O LEU M 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 169 through 171 Processing sheet with id=AB9, first strand: chain 'M' and resid 196 through 198 Processing sheet with id=AC1, first strand: chain 'M' and resid 246 through 251 removed outlier: 7.586A pdb=" N ASN M 260 " --> pdb=" O PRO M 275 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL M 262 " --> pdb=" O ILE M 273 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE M 273 " --> pdb=" O VAL M 262 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N SER M 264 " --> pdb=" O MET M 271 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'M' and resid 306 through 308 Processing sheet with id=AC3, first strand: chain 'M' and resid 366 through 367 removed outlier: 6.925A pdb=" N ILE M 566 " --> pdb=" O VAL M 582 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N LEU M 584 " --> pdb=" O ILE M 566 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N TYR M 568 " --> pdb=" O LEU M 584 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'M' and resid 443 through 444 removed outlier: 6.906A pdb=" N VAL M 429 " --> pdb=" O ASP M 443 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE M 400 " --> pdb=" O ALA M 430 " (cutoff:3.500A) removed outlier: 7.947A pdb=" N ILE M 432 " --> pdb=" O ILE M 400 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU M 402 " --> pdb=" O ILE M 432 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL M 399 " --> pdb=" O MET M 473 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL M 475 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU M 401 " --> pdb=" O VAL M 475 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLY M 477 " --> pdb=" O LEU M 401 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N VAL M 403 " --> pdb=" O GLY M 477 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'M' and resid 595 through 597 Processing sheet with id=AC6, first strand: chain 'N' and resid 37 through 41 removed outlier: 5.885A pdb=" N LEU N 38 " --> pdb=" O GLU N 50 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N GLU N 50 " --> pdb=" O LEU N 38 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'O' and resid 169 through 174 removed outlier: 6.397A pdb=" N TYR O 130 " --> pdb=" O THR O 170 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ILE O 172 " --> pdb=" O TYR O 130 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ILE O 132 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL O 174 " --> pdb=" O ILE O 132 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N VAL O 134 " --> pdb=" O VAL O 174 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N TYR O 192 " --> pdb=" O GLY O 217 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 153 through 154 removed outlier: 6.450A pdb=" N ILE P 153 " --> pdb=" O ALA P 179 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'P' and resid 208 through 213 Processing sheet with id=AD1, first strand: chain 'Q' and resid 80 through 84 removed outlier: 6.636A pdb=" N ARG Q 96 " --> pdb=" O PRO Q 111 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL Q 98 " --> pdb=" O CYS Q 109 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N CYS Q 109 " --> pdb=" O VAL Q 98 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLU Q 100 " --> pdb=" O ARG Q 107 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'Q' and resid 227 through 228 Processing sheet with id=AD3, first strand: chain 'Q' and resid 394 through 402 Processing sheet with id=AD4, first strand: chain 'T' and resid 77 through 78 removed outlier: 6.070A pdb=" N SER T 77 " --> pdb=" O ARG T 119 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'T' and resid 83 through 86 1137 hydrogen bonds defined for protein. 3096 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: 5.26 Time building geometry restraints manager: 3.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.40: 11760 1.40 - 1.62: 17020 1.62 - 1.84: 272 1.84 - 2.06: 1 2.06 - 2.28: 80 Bond restraints: 29133 Sorted by residual: bond pdb=" C18 UQ J 403 " pdb=" C19 UQ J 403 " ideal model delta sigma weight residual 1.336 1.556 -0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C13 UQ J 403 " pdb=" C14 UQ J 403 " ideal model delta sigma weight residual 1.335 1.548 -0.213 2.00e-02 2.50e+03 1.14e+02 bond pdb=" C17 970 C 302 " pdb=" O16 970 C 302 " ideal model delta sigma weight residual 1.355 1.568 -0.213 2.00e-02 2.50e+03 1.13e+02 bond pdb=" C23 UQ J 403 " pdb=" C24 UQ J 403 " ideal model delta sigma weight residual 1.335 1.545 -0.210 2.00e-02 2.50e+03 1.10e+02 bond pdb=" C8 UQ J 403 " pdb=" C9 UQ J 403 " ideal model delta sigma weight residual 1.334 1.536 -0.202 2.00e-02 2.50e+03 1.02e+02 ... (remaining 29128 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 39251 3.41 - 6.82: 177 6.82 - 10.23: 36 10.23 - 13.64: 18 13.64 - 17.05: 8 Bond angle restraints: 39490 Sorted by residual: angle pdb=" PA NDP J 402 " pdb=" O3 NDP J 402 " pdb=" PN NDP J 402 " ideal model delta sigma weight residual 107.74 124.79 -17.05 1.95e+00 2.62e-01 7.62e+01 angle pdb=" C11 CDL N 201 " pdb=" CA5 CDL N 201 " pdb=" OA6 CDL N 201 " ideal model delta sigma weight residual 111.33 120.73 -9.40 1.32e+00 5.72e-01 5.05e+01 angle pdb=" C5B NDP J 402 " pdb=" O5B NDP J 402 " pdb=" PA NDP J 402 " ideal model delta sigma weight residual 103.84 117.35 -13.51 1.91e+00 2.73e-01 4.98e+01 angle pdb=" C51 CDL N 201 " pdb=" CB5 CDL N 201 " pdb=" OB6 CDL N 201 " ideal model delta sigma weight residual 111.33 120.47 -9.14 1.32e+00 5.72e-01 4.78e+01 angle pdb=" O1X NDP J 402 " pdb=" P2B NDP J 402 " pdb=" O3X NDP J 402 " ideal model delta sigma weight residual 117.46 109.44 8.02 1.17e+00 7.36e-01 4.73e+01 ... (remaining 39485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.06: 17204 33.06 - 66.12: 359 66.12 - 99.19: 44 99.19 - 132.25: 4 132.25 - 165.31: 9 Dihedral angle restraints: 17620 sinusoidal: 7391 harmonic: 10229 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 93.00 40.93 52.07 1 1.00e+01 1.00e-02 3.70e+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 180.00 154.68 25.32 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" CA CYS F 24 " pdb=" C CYS F 24 " pdb=" N GLN F 25 " pdb=" CA GLN F 25 " ideal model delta harmonic sigma weight residual -180.00 -155.35 -24.65 0 5.00e+00 4.00e-02 2.43e+01 ... (remaining 17617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3860 0.077 - 0.153: 400 0.153 - 0.230: 11 0.230 - 0.306: 3 0.306 - 0.383: 1 Chirality restraints: 4275 Sorted by residual: chirality pdb=" C3B NDP J 402 " pdb=" C2B NDP J 402 " pdb=" C4B NDP J 402 " pdb=" O3B NDP J 402 " both_signs ideal model delta sigma weight residual False -2.75 -2.36 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CA PHE B 78 " pdb=" N PHE B 78 " pdb=" C PHE B 78 " pdb=" CB PHE B 78 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" C3D NDP J 402 " pdb=" C2D NDP J 402 " pdb=" C4D NDP J 402 " pdb=" O3D NDP J 402 " both_signs ideal model delta sigma weight residual False -2.71 -2.44 -0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 4272 not shown) Planarity restraints: 5092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 UQ J 403 " -0.109 2.00e-02 2.50e+03 2.60e-01 8.44e+02 pdb=" C11 UQ J 403 " 0.061 2.00e-02 2.50e+03 pdb=" C7 UQ J 403 " 0.236 2.00e-02 2.50e+03 pdb=" C8 UQ J 403 " -0.446 2.00e-02 2.50e+03 pdb=" C9 UQ J 403 " 0.259 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 UQ J 403 " -0.201 2.00e-02 2.50e+03 2.27e-01 6.44e+02 pdb=" C13 UQ J 403 " 0.142 2.00e-02 2.50e+03 pdb=" C14 UQ J 403 " 0.356 2.00e-02 2.50e+03 pdb=" C15 UQ J 403 " -0.034 2.00e-02 2.50e+03 pdb=" C16 UQ J 403 " -0.263 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2N NDP J 402 " 0.068 2.00e-02 2.50e+03 2.26e-01 6.39e+02 pdb=" C3N NDP J 402 " 0.403 2.00e-02 2.50e+03 pdb=" C4N NDP J 402 " -0.071 2.00e-02 2.50e+03 pdb=" C7N NDP J 402 " -0.245 2.00e-02 2.50e+03 pdb=" N1N NDP J 402 " -0.154 2.00e-02 2.50e+03 ... (remaining 5089 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 352 2.64 - 3.21: 25279 3.21 - 3.77: 44719 3.77 - 4.34: 66436 4.34 - 4.90: 106340 Nonbonded interactions: 243126 Sorted by model distance: nonbonded pdb=" N1 FMN A 502 " pdb=" O3' FMN A 502 " model vdw 2.078 3.120 nonbonded pdb=" NH2 ARG A 152 " pdb=" O PRO K 99 " model vdw 2.207 3.120 nonbonded pdb=" O THR M 389 " pdb=" OG1 THR M 390 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR N 127 " pdb=" O GLU T 61 " model vdw 2.216 3.040 nonbonded pdb=" OG1 THR J 199 " pdb=" O ALA J 258 " model vdw 2.217 3.040 ... (remaining 243121 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: 2.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.530 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 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 : 0.007 0.315 29170 Z= 0.344 Angle : 0.841 20.916 39573 Z= 0.388 Chirality : 0.046 0.383 4275 Planarity : 0.010 0.260 5092 Dihedral : 14.527 165.310 11041 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.94 % Favored : 96.00 % Rotamer: Outliers : 0.03 % Allowed : 0.26 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: -0.15 (0.14), residues: 3502 helix: 0.67 (0.14), residues: 1345 sheet: -0.07 (0.25), residues: 397 loop : -0.66 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 191 TYR 0.046 0.002 TYR C 142 PHE 0.026 0.002 PHE Q 211 TRP 0.078 0.002 TRP J 108 HIS 0.008 0.001 HIS M 460 Details of bonding type rmsd covalent geometry : bond 0.00737 (29133) covalent geometry : angle 0.75989 (39490) SS BOND : bond 0.01693 ( 1) SS BOND : angle 8.44321 ( 2) hydrogen bonds : bond 0.14877 ( 1137) hydrogen bonds : angle 6.26617 ( 3096) metal coordination : bond 0.01368 ( 35) metal coordination : angle 7.90975 ( 81) Misc. bond : bond 0.17893 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 459 time to evaluate : 1.349 Fit side-chains REVERT: A 298 GLU cc_start: 0.7735 (tt0) cc_final: 0.7472 (tt0) REVERT: A 367 ILE cc_start: 0.8914 (mm) cc_final: 0.8487 (mm) REVERT: A 396 MET cc_start: 0.8984 (mmm) cc_final: 0.8749 (mmt) REVERT: C 79 MET cc_start: 0.8779 (ttp) cc_final: 0.8476 (ttp) REVERT: F 46 LYS cc_start: 0.8413 (mttt) cc_final: 0.8038 (mtpt) REVERT: G 80 LYS cc_start: 0.8062 (tttm) cc_final: 0.7817 (tppt) REVERT: G 90 TYR cc_start: 0.8110 (t80) cc_final: 0.7611 (t80) REVERT: J 368 ASP cc_start: 0.8085 (t70) cc_final: 0.7452 (t0) REVERT: L 99 MET cc_start: 0.9024 (ttm) cc_final: 0.8763 (ttp) REVERT: M 271 MET cc_start: 0.8917 (mmp) cc_final: 0.8628 (mmm) REVERT: M 666 GLN cc_start: 0.7557 (pp30) cc_final: 0.7159 (pp30) REVERT: N 51 ASP cc_start: 0.8698 (t70) cc_final: 0.8413 (t70) REVERT: O 50 ASP cc_start: 0.8090 (m-30) cc_final: 0.7786 (m-30) REVERT: P 113 ASP cc_start: 0.7878 (t0) cc_final: 0.7637 (t70) outliers start: 1 outliers final: 1 residues processed: 460 average time/residue: 0.7559 time to fit residues: 394.1558 Evaluate side-chains 382 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 381 time to evaluate : 0.726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN A 418 GLN B 59 GLN F 93 ASN H 83 GLN ** J 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN M 464 GLN N 116 ASN O 69 ASN O 123 ASN O 187 GLN P 247 GLN Q 92 HIS T 43 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.110995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.087688 restraints weight = 35934.392| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 1.48 r_work: 0.2729 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.0940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 29170 Z= 0.203 Angle : 0.716 24.390 39573 Z= 0.318 Chirality : 0.046 0.151 4275 Planarity : 0.005 0.055 5092 Dihedral : 10.441 174.953 4083 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.60 % Favored : 96.37 % Rotamer: Outliers : 1.61 % Allowed : 7.07 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: -0.02 (0.14), residues: 3502 helix: 0.87 (0.14), residues: 1358 sheet: 0.04 (0.26), residues: 386 loop : -0.68 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 98 TYR 0.033 0.002 TYR C 142 PHE 0.021 0.002 PHE Q 204 TRP 0.013 0.001 TRP M 422 HIS 0.009 0.001 HIS J 323 Details of bonding type rmsd covalent geometry : bond 0.00494 (29133) covalent geometry : angle 0.61053 (39490) SS BOND : bond 0.00717 ( 1) SS BOND : angle 4.64688 ( 2) hydrogen bonds : bond 0.04975 ( 1137) hydrogen bonds : angle 5.03018 ( 3096) metal coordination : bond 0.01526 ( 35) metal coordination : angle 8.25920 ( 81) Misc. bond : bond 0.00224 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 385 time to evaluate : 1.218 Fit side-chains REVERT: A 298 GLU cc_start: 0.8301 (tt0) cc_final: 0.7984 (tt0) REVERT: A 367 ILE cc_start: 0.9043 (mm) cc_final: 0.8674 (mm) REVERT: B 39 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.9053 (ptpp) REVERT: B 65 GLU cc_start: 0.8194 (pm20) cc_final: 0.7963 (pm20) REVERT: B 146 ASP cc_start: 0.8892 (m-30) cc_final: 0.8684 (m-30) REVERT: C 79 MET cc_start: 0.9290 (ttp) cc_final: 0.8925 (ttp) REVERT: E 101 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8692 (p) REVERT: F 46 LYS cc_start: 0.8472 (mttt) cc_final: 0.8067 (mtpt) REVERT: F 89 ARG cc_start: 0.7871 (mmm-85) cc_final: 0.7604 (tpp80) REVERT: G 90 TYR cc_start: 0.8194 (t80) cc_final: 0.7853 (t80) REVERT: G 97 LYS cc_start: 0.8077 (tppt) cc_final: 0.7653 (ttmp) REVERT: H 18 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7888 (pt0) REVERT: H 40 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7811 (tppt) REVERT: H 67 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8419 (mmtp) REVERT: I 105 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8198 (mm-30) REVERT: J 368 ASP cc_start: 0.8526 (t70) cc_final: 0.7573 (t0) REVERT: L 99 MET cc_start: 0.9417 (ttm) cc_final: 0.9161 (ttp) REVERT: M 688 GLN cc_start: 0.8953 (OUTLIER) cc_final: 0.7941 (mm-40) REVERT: N 51 ASP cc_start: 0.8975 (t70) cc_final: 0.8675 (t70) REVERT: O 50 ASP cc_start: 0.8559 (m-30) cc_final: 0.8208 (m-30) REVERT: O 236 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7411 (mm-30) REVERT: P 232 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8688 (ttmm) REVERT: Q 281 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: T 52 ARG cc_start: 0.8648 (mtm-85) cc_final: 0.8433 (mtm-85) outliers start: 49 outliers final: 14 residues processed: 410 average time/residue: 0.7984 time to fit residues: 371.9058 Evaluate side-chains 389 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 367 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 67 LYS Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain M residue 688 GLN Chi-restraints excluded: chain M residue 697 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 128 SER Chi-restraints excluded: chain P residue 156 SER Chi-restraints excluded: chain P residue 232 LYS Chi-restraints excluded: chain Q residue 281 GLU Chi-restraints excluded: chain T residue 79 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 304 optimal weight: 1.9990 chunk 255 optimal weight: 0.8980 chunk 340 optimal weight: 0.3980 chunk 158 optimal weight: 4.9990 chunk 258 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 333 optimal weight: 0.7980 chunk 257 optimal weight: 0.5980 chunk 306 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN F 93 ASN ** J 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 ASN M 464 GLN M 598 ASN M 663 ASN M 666 GLN N 116 ASN O 99 ASN O 187 GLN P 247 GLN Q 92 HIS Q 431 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.113785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.091708 restraints weight = 35870.513| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.30 r_work: 0.2798 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29170 Z= 0.112 Angle : 0.626 21.572 39573 Z= 0.270 Chirality : 0.042 0.145 4275 Planarity : 0.004 0.051 5092 Dihedral : 9.731 177.538 4082 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % Rotamer: Outliers : 1.45 % Allowed : 9.38 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 0.18 (0.14), residues: 3502 helix: 1.14 (0.14), residues: 1361 sheet: -0.03 (0.25), residues: 405 loop : -0.62 (0.15), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 191 TYR 0.016 0.001 TYR J 180 PHE 0.014 0.001 PHE Q 458 TRP 0.012 0.001 TRP M 422 HIS 0.007 0.001 HIS J 323 Details of bonding type rmsd covalent geometry : bond 0.00257 (29133) covalent geometry : angle 0.51564 (39490) SS BOND : bond 0.02435 ( 1) SS BOND : angle 4.46516 ( 2) hydrogen bonds : bond 0.03834 ( 1137) hydrogen bonds : angle 4.69348 ( 3096) metal coordination : bond 0.00927 ( 35) metal coordination : angle 7.82043 ( 81) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 397 time to evaluate : 1.218 Fit side-chains REVERT: A 298 GLU cc_start: 0.8232 (tt0) cc_final: 0.7952 (tt0) REVERT: A 367 ILE cc_start: 0.8969 (mm) cc_final: 0.8599 (mm) REVERT: B 39 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.9066 (ptpp) REVERT: C 79 MET cc_start: 0.9246 (ttp) cc_final: 0.8914 (ttp) REVERT: F 46 LYS cc_start: 0.8505 (mttt) cc_final: 0.8112 (mtpt) REVERT: G 114 ASP cc_start: 0.8648 (m-30) cc_final: 0.8380 (m-30) REVERT: H 18 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7780 (pt0) REVERT: H 40 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.7811 (tppt) REVERT: H 70 GLU cc_start: 0.8139 (tp30) cc_final: 0.7823 (tp30) REVERT: I 103 ARG cc_start: 0.8040 (ttp80) cc_final: 0.7747 (ttp80) REVERT: I 105 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8214 (mm-30) REVERT: J 272 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8883 (mt) REVERT: J 368 ASP cc_start: 0.8355 (t70) cc_final: 0.7439 (t0) REVERT: L 99 MET cc_start: 0.9325 (ttm) cc_final: 0.9093 (ttp) REVERT: M 54 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.6849 (tt0) REVERT: M 696 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8613 (mtt) REVERT: N 51 ASP cc_start: 0.8944 (t70) cc_final: 0.8639 (t70) REVERT: O 50 ASP cc_start: 0.8504 (m-30) cc_final: 0.8181 (m-30) REVERT: O 121 MET cc_start: 0.9092 (mtp) cc_final: 0.8891 (mtp) REVERT: O 146 ASP cc_start: 0.8368 (t0) cc_final: 0.7806 (t0) REVERT: O 150 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.6851 (mp0) REVERT: O 236 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7330 (mm-30) outliers start: 44 outliers final: 10 residues processed: 418 average time/residue: 0.8955 time to fit residues: 426.8374 Evaluate side-chains 391 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 374 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain P residue 156 SER Chi-restraints excluded: chain T residue 79 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 100 optimal weight: 0.0470 chunk 98 optimal weight: 0.6980 chunk 134 optimal weight: 4.9990 chunk 340 optimal weight: 0.5980 chunk 320 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 245 optimal weight: 2.9990 chunk 173 optimal weight: 0.0980 chunk 312 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 overall best weight: 0.4078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN F 76 ASN F 93 ASN H 71 GLN J 37 HIS L 86 ASN L 109 ASN M 663 ASN M 666 GLN N 116 ASN N 135 GLN O 87 GLN P 247 GLN Q 147 ASN ** Q 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.116289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.093100 restraints weight = 35830.448| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.34 r_work: 0.2826 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 29170 Z= 0.097 Angle : 0.597 22.057 39573 Z= 0.256 Chirality : 0.041 0.142 4275 Planarity : 0.004 0.048 5092 Dihedral : 9.005 178.692 4082 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % Rotamer: Outliers : 1.51 % Allowed : 10.59 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 0.39 (0.14), residues: 3502 helix: 1.39 (0.14), residues: 1359 sheet: 0.02 (0.25), residues: 406 loop : -0.55 (0.15), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 191 TYR 0.014 0.001 TYR J 180 PHE 0.012 0.001 PHE Q 458 TRP 0.011 0.001 TRP M 422 HIS 0.005 0.001 HIS J 323 Details of bonding type rmsd covalent geometry : bond 0.00215 (29133) covalent geometry : angle 0.49057 (39490) SS BOND : bond 0.01416 ( 1) SS BOND : angle 3.67519 ( 2) hydrogen bonds : bond 0.03362 ( 1137) hydrogen bonds : angle 4.50233 ( 3096) metal coordination : bond 0.00789 ( 35) metal coordination : angle 7.50584 ( 81) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 405 time to evaluate : 1.230 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8332 (mp) REVERT: A 298 GLU cc_start: 0.8227 (tt0) cc_final: 0.7901 (tt0) REVERT: A 367 ILE cc_start: 0.8845 (mm) cc_final: 0.8508 (mm) REVERT: B 39 LYS cc_start: 0.9291 (OUTLIER) cc_final: 0.9029 (ptpp) REVERT: E 101 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8652 (p) REVERT: F 46 LYS cc_start: 0.8468 (mttt) cc_final: 0.8046 (mtpt) REVERT: F 89 ARG cc_start: 0.7865 (mmm-85) cc_final: 0.7660 (tpp80) REVERT: G 80 LYS cc_start: 0.8178 (tmtt) cc_final: 0.7532 (ttmp) REVERT: G 114 ASP cc_start: 0.8635 (m-30) cc_final: 0.8409 (m-30) REVERT: H 18 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7747 (pt0) REVERT: H 40 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7843 (tppt) REVERT: I 105 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8141 (mm-30) REVERT: J 272 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8873 (mt) REVERT: J 368 ASP cc_start: 0.8300 (t70) cc_final: 0.7424 (t0) REVERT: K 98 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7524 (mtp) REVERT: L 99 MET cc_start: 0.9346 (ttm) cc_final: 0.9097 (ttp) REVERT: M 678 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.6549 (tp-100) REVERT: M 696 MET cc_start: 0.8912 (OUTLIER) cc_final: 0.8590 (mtt) REVERT: N 51 ASP cc_start: 0.8917 (t70) cc_final: 0.8605 (t70) REVERT: O 50 ASP cc_start: 0.8471 (m-30) cc_final: 0.8125 (m-30) REVERT: O 87 GLN cc_start: 0.9292 (OUTLIER) cc_final: 0.9038 (tt0) REVERT: O 146 ASP cc_start: 0.8230 (t0) cc_final: 0.7631 (t0) REVERT: O 150 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.6683 (mp0) REVERT: Q 409 VAL cc_start: 0.9453 (OUTLIER) cc_final: 0.9222 (t) REVERT: T 103 ASP cc_start: 0.8587 (m-30) cc_final: 0.8336 (m-30) REVERT: W 5 LYS cc_start: 0.6722 (OUTLIER) cc_final: 0.6374 (ptpt) outliers start: 46 outliers final: 13 residues processed: 430 average time/residue: 0.8954 time to fit residues: 438.2701 Evaluate side-chains 413 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 387 time to evaluate : 1.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain M residue 678 GLN Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain O residue 87 GLN Chi-restraints excluded: chain O residue 140 CYS Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain P residue 156 SER Chi-restraints excluded: chain Q residue 409 VAL Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain W residue 5 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 336 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 163 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 287 optimal weight: 0.3980 chunk 70 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 197 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN F 76 ASN F 93 ASN H 71 GLN L 86 ASN M 663 ASN M 666 GLN N 116 ASN N 122 GLN O 87 GLN P 247 GLN Q 92 HIS Q 147 ASN Q 454 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.113120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.091114 restraints weight = 35473.105| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 1.35 r_work: 0.2756 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 29170 Z= 0.202 Angle : 0.683 23.989 39573 Z= 0.302 Chirality : 0.046 0.156 4275 Planarity : 0.005 0.052 5092 Dihedral : 9.166 178.941 4082 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.63 % Favored : 96.34 % Rotamer: Outliers : 1.97 % Allowed : 10.86 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 0.23 (0.14), residues: 3502 helix: 1.19 (0.14), residues: 1354 sheet: 0.11 (0.26), residues: 391 loop : -0.63 (0.15), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 98 TYR 0.020 0.002 TYR J 180 PHE 0.023 0.002 PHE M 462 TRP 0.012 0.002 TRP M 510 HIS 0.006 0.001 HIS J 37 Details of bonding type rmsd covalent geometry : bond 0.00495 (29133) covalent geometry : angle 0.58069 (39490) SS BOND : bond 0.01377 ( 1) SS BOND : angle 4.36670 ( 2) hydrogen bonds : bond 0.04585 ( 1137) hydrogen bonds : angle 4.70980 ( 3096) metal coordination : bond 0.01424 ( 35) metal coordination : angle 7.92989 ( 81) Misc. bond : bond 0.00084 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 386 time to evaluate : 1.370 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8458 (mp) REVERT: A 121 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8340 (tp30) REVERT: A 298 GLU cc_start: 0.8266 (tt0) cc_final: 0.7944 (tt0) REVERT: A 367 ILE cc_start: 0.8986 (mm) cc_final: 0.8637 (mm) REVERT: B 39 LYS cc_start: 0.9311 (OUTLIER) cc_final: 0.9068 (ptpp) REVERT: B 65 GLU cc_start: 0.8193 (pm20) cc_final: 0.7939 (pm20) REVERT: C 79 MET cc_start: 0.9320 (ttp) cc_final: 0.8982 (ttp) REVERT: E 92 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8207 (tt0) REVERT: E 101 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8729 (p) REVERT: F 89 ARG cc_start: 0.7934 (mmm-85) cc_final: 0.7690 (tpp80) REVERT: G 80 LYS cc_start: 0.8259 (tmtt) cc_final: 0.7615 (ttmp) REVERT: G 92 LYS cc_start: 0.8568 (OUTLIER) cc_final: 0.8279 (mttp) REVERT: G 114 ASP cc_start: 0.8694 (m-30) cc_final: 0.8477 (m-30) REVERT: H 18 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7873 (pt0) REVERT: H 40 LYS cc_start: 0.8269 (OUTLIER) cc_final: 0.7862 (tppt) REVERT: I 105 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8254 (mm-30) REVERT: J 272 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8955 (mt) REVERT: J 368 ASP cc_start: 0.8423 (t70) cc_final: 0.7523 (t0) REVERT: K 98 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.7695 (mtp) REVERT: L 99 MET cc_start: 0.9352 (ttm) cc_final: 0.9115 (ttp) REVERT: M 54 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7066 (tt0) REVERT: M 678 GLN cc_start: 0.7237 (OUTLIER) cc_final: 0.6673 (tp-100) REVERT: M 696 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8778 (mtt) REVERT: N 51 ASP cc_start: 0.8990 (t70) cc_final: 0.8681 (t70) REVERT: O 50 ASP cc_start: 0.8524 (m-30) cc_final: 0.8179 (m-30) REVERT: O 87 GLN cc_start: 0.9267 (OUTLIER) cc_final: 0.9062 (tt0) REVERT: O 150 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.6913 (mp0) REVERT: Q 281 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8102 (mp0) REVERT: T 119 ARG cc_start: 0.8464 (ptp90) cc_final: 0.8107 (ptp-170) outliers start: 60 outliers final: 26 residues processed: 415 average time/residue: 0.8834 time to fit residues: 416.9195 Evaluate side-chains 414 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 372 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 203 ASP Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain M residue 678 GLN Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain M residue 697 THR Chi-restraints excluded: chain O residue 87 GLN Chi-restraints excluded: chain O residue 140 CYS Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain P residue 156 SER Chi-restraints excluded: chain Q residue 147 ASN Chi-restraints excluded: chain Q residue 281 GLU Chi-restraints excluded: chain Q residue 444 LEU Chi-restraints excluded: chain T residue 79 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 183 optimal weight: 0.5980 chunk 320 optimal weight: 0.8980 chunk 114 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 150 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 312 optimal weight: 0.5980 chunk 309 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN F 93 ASN H 71 GLN L 86 ASN M 540 ASN M 663 ASN M 666 GLN N 122 GLN O 87 GLN P 247 GLN Q 92 HIS Q 147 ASN T 43 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.115103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.093025 restraints weight = 35610.843| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.38 r_work: 0.2790 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29170 Z= 0.112 Angle : 0.618 21.652 39573 Z= 0.268 Chirality : 0.042 0.144 4275 Planarity : 0.004 0.051 5092 Dihedral : 8.780 179.325 4082 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.26 % Favored : 96.72 % Rotamer: Outliers : 1.58 % Allowed : 11.91 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 0.34 (0.14), residues: 3502 helix: 1.30 (0.14), residues: 1363 sheet: 0.04 (0.25), residues: 406 loop : -0.56 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 195 TYR 0.016 0.001 TYR J 180 PHE 0.015 0.001 PHE M 462 TRP 0.011 0.001 TRP M 422 HIS 0.006 0.001 HIS J 323 Details of bonding type rmsd covalent geometry : bond 0.00255 (29133) covalent geometry : angle 0.51166 (39490) SS BOND : bond 0.01137 ( 1) SS BOND : angle 3.23503 ( 2) hydrogen bonds : bond 0.03683 ( 1137) hydrogen bonds : angle 4.55026 ( 3096) metal coordination : bond 0.00891 ( 35) metal coordination : angle 7.67173 ( 81) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 392 time to evaluate : 1.355 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8441 (mp) REVERT: A 298 GLU cc_start: 0.8268 (tt0) cc_final: 0.7963 (tt0) REVERT: A 367 ILE cc_start: 0.8941 (mm) cc_final: 0.8583 (mm) REVERT: B 39 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.9063 (ptpp) REVERT: B 48 MET cc_start: 0.8552 (mmp) cc_final: 0.8342 (tpp) REVERT: B 65 GLU cc_start: 0.8082 (pm20) cc_final: 0.7867 (pm20) REVERT: C 79 MET cc_start: 0.9313 (ttp) cc_final: 0.8940 (ttp) REVERT: E 101 THR cc_start: 0.8966 (OUTLIER) cc_final: 0.8676 (p) REVERT: G 80 LYS cc_start: 0.8229 (tmtt) cc_final: 0.7621 (ttmp) REVERT: G 92 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8199 (mttp) REVERT: G 114 ASP cc_start: 0.8652 (m-30) cc_final: 0.8421 (m-30) REVERT: H 18 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7831 (pt0) REVERT: H 40 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7870 (tppt) REVERT: I 105 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8258 (mm-30) REVERT: J 37 HIS cc_start: 0.0619 (OUTLIER) cc_final: -0.1446 (m170) REVERT: J 272 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8935 (mt) REVERT: J 368 ASP cc_start: 0.8353 (t70) cc_final: 0.7429 (t0) REVERT: K 98 MET cc_start: 0.8557 (OUTLIER) cc_final: 0.7640 (mtp) REVERT: L 99 MET cc_start: 0.9336 (ttm) cc_final: 0.9111 (ttp) REVERT: M 678 GLN cc_start: 0.7255 (OUTLIER) cc_final: 0.6692 (tp-100) REVERT: M 696 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8575 (mtt) REVERT: N 51 ASP cc_start: 0.8966 (t70) cc_final: 0.8671 (t70) REVERT: O 50 ASP cc_start: 0.8517 (m-30) cc_final: 0.8175 (m-30) REVERT: O 87 GLN cc_start: 0.9261 (OUTLIER) cc_final: 0.8974 (tt0) REVERT: O 146 ASP cc_start: 0.8235 (t0) cc_final: 0.7673 (t0) REVERT: O 150 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.6772 (mp0) REVERT: Q 281 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8073 (mp0) REVERT: T 103 ASP cc_start: 0.8697 (m-30) cc_final: 0.8380 (m-30) outliers start: 48 outliers final: 17 residues processed: 419 average time/residue: 0.8819 time to fit residues: 420.9638 Evaluate side-chains 413 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 382 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain J residue 37 HIS Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain M residue 678 GLN Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain O residue 87 GLN Chi-restraints excluded: chain O residue 140 CYS Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain P residue 153 ILE Chi-restraints excluded: chain P residue 156 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 281 GLU Chi-restraints excluded: chain T residue 79 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 281 optimal weight: 4.9990 chunk 208 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 324 optimal weight: 0.0670 chunk 97 optimal weight: 8.9990 chunk 95 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 144 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 227 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN E 70 ASN F 93 ASN L 86 ASN M 663 ASN M 666 GLN N 116 ASN N 122 GLN N 135 GLN O 87 GLN P 247 GLN Q 92 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.113942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.091987 restraints weight = 35506.673| |-----------------------------------------------------------------------------| r_work (start): 0.2902 rms_B_bonded: 1.34 r_work: 0.2788 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 29170 Z= 0.150 Angle : 0.642 22.333 39573 Z= 0.280 Chirality : 0.043 0.146 4275 Planarity : 0.005 0.050 5092 Dihedral : 8.723 179.236 4082 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.57 % Favored : 96.40 % Rotamer: Outliers : 2.01 % Allowed : 11.81 % Favored : 86.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 0.33 (0.14), residues: 3502 helix: 1.29 (0.14), residues: 1355 sheet: 0.18 (0.26), residues: 387 loop : -0.59 (0.15), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 195 TYR 0.017 0.001 TYR J 180 PHE 0.024 0.001 PHE M 462 TRP 0.011 0.001 TRP M 422 HIS 0.005 0.001 HIS J 323 Details of bonding type rmsd covalent geometry : bond 0.00363 (29133) covalent geometry : angle 0.53850 (39490) SS BOND : bond 0.01057 ( 1) SS BOND : angle 3.69183 ( 2) hydrogen bonds : bond 0.04022 ( 1137) hydrogen bonds : angle 4.59656 ( 3096) metal coordination : bond 0.01102 ( 35) metal coordination : angle 7.73938 ( 81) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 382 time to evaluate : 1.200 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8465 (mp) REVERT: A 121 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8272 (tp30) REVERT: A 298 GLU cc_start: 0.8258 (tt0) cc_final: 0.7953 (tt0) REVERT: A 367 ILE cc_start: 0.8950 (mm) cc_final: 0.8606 (mm) REVERT: B 39 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.9067 (ptpp) REVERT: B 48 MET cc_start: 0.8568 (mmp) cc_final: 0.8359 (tpp) REVERT: B 65 GLU cc_start: 0.8123 (pm20) cc_final: 0.7920 (pm20) REVERT: C 79 MET cc_start: 0.9318 (ttp) cc_final: 0.8978 (ttp) REVERT: C 126 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.8317 (mt-10) REVERT: E 92 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8243 (tt0) REVERT: E 101 THR cc_start: 0.9042 (OUTLIER) cc_final: 0.8715 (p) REVERT: F 25 GLN cc_start: 0.7524 (tp-100) cc_final: 0.7243 (mm-40) REVERT: G 80 LYS cc_start: 0.8240 (tmtt) cc_final: 0.8006 (tmtt) REVERT: G 92 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8188 (mttp) REVERT: G 114 ASP cc_start: 0.8690 (m-30) cc_final: 0.8460 (m-30) REVERT: H 18 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7848 (pt0) REVERT: H 40 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7875 (tppt) REVERT: H 49 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7994 (tt0) REVERT: H 67 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8372 (mmtp) REVERT: I 105 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8268 (mm-30) REVERT: J 37 HIS cc_start: 0.0742 (OUTLIER) cc_final: -0.1060 (m170) REVERT: J 272 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8961 (mt) REVERT: J 368 ASP cc_start: 0.8351 (t70) cc_final: 0.7450 (t0) REVERT: K 98 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.7661 (mtp) REVERT: L 99 MET cc_start: 0.9332 (ttm) cc_final: 0.9114 (ttp) REVERT: M 54 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.7035 (tt0) REVERT: M 678 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.6711 (tp-100) REVERT: M 696 MET cc_start: 0.8973 (OUTLIER) cc_final: 0.8719 (mtt) REVERT: N 51 ASP cc_start: 0.8982 (t70) cc_final: 0.8684 (t70) REVERT: O 50 ASP cc_start: 0.8504 (m-30) cc_final: 0.8169 (m-30) REVERT: O 87 GLN cc_start: 0.9275 (OUTLIER) cc_final: 0.9036 (tt0) REVERT: O 150 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.6870 (mp0) REVERT: Q 281 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8108 (mp0) REVERT: T 119 ARG cc_start: 0.8449 (ptp90) cc_final: 0.8080 (ptp-170) REVERT: W 5 LYS cc_start: 0.6791 (OUTLIER) cc_final: 0.6443 (ptpt) outliers start: 61 outliers final: 25 residues processed: 416 average time/residue: 0.8988 time to fit residues: 426.4902 Evaluate side-chains 417 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 371 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 101 ASP Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain E residue 92 GLU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 40 ARG Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain H residue 49 GLU Chi-restraints excluded: chain H residue 67 LYS Chi-restraints excluded: chain J residue 37 HIS Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain L residue 157 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 171 THR Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain M residue 678 GLN Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain O residue 87 GLN Chi-restraints excluded: chain O residue 140 CYS Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain P residue 156 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 281 GLU Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain W residue 5 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 345 random chunks: chunk 213 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 269 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 166 optimal weight: 0.5980 chunk 201 optimal weight: 7.9990 chunk 341 optimal weight: 0.9980 chunk 156 optimal weight: 8.9990 chunk 143 optimal weight: 0.6980 chunk 205 optimal weight: 0.4980 chunk 241 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN F 76 ASN H 71 GLN L 86 ASN M 663 ASN M 666 GLN N 87 HIS N 122 GLN O 87 GLN O 153 GLN P 63 GLN P 247 GLN Q 92 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.114662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.091606 restraints weight = 35821.715| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 1.48 r_work: 0.2773 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 29170 Z= 0.110 Angle : 0.615 21.102 39573 Z= 0.265 Chirality : 0.042 0.145 4275 Planarity : 0.004 0.049 5092 Dihedral : 8.455 179.407 4082 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.46 % Favored : 96.52 % Rotamer: Outliers : 1.74 % Allowed : 12.04 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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 aren not related in a simple way. whole: 0.43 (0.14), residues: 3502 helix: 1.40 (0.14), residues: 1352 sheet: 0.11 (0.26), residues: 404 loop : -0.53 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 195 TYR 0.016 0.001 TYR J 180 PHE 0.017 0.001 PHE M 462 TRP 0.011 0.001 TRP M 422 HIS 0.006 0.001 HIS J 323 Details of bonding type rmsd covalent geometry : bond 0.00253 (29133) covalent geometry : angle 0.50953 (39490) SS BOND : bond 0.00966 ( 1) SS BOND : angle 3.08546 ( 2) hydrogen bonds : bond 0.03600 ( 1137) hydrogen bonds : angle 4.51108 ( 3096) metal coordination : bond 0.00915 ( 35) metal coordination : angle 7.59993 ( 81) Misc. bond : bond 0.00024 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7004 Ramachandran restraints generated. 3502 Oldfield, 0 Emsley, 3502 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 388 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: A 97 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8419 (mp) REVERT: A 298 GLU cc_start: 0.8312 (tt0) cc_final: 0.7994 (tt0) REVERT: A 367 ILE cc_start: 0.8916 (mm) cc_final: 0.8575 (mm) REVERT: B 39 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.9054 (ptpp) REVERT: B 65 GLU cc_start: 0.8137 (pm20) cc_final: 0.7919 (pm20) REVERT: C 76 MET cc_start: 0.9264 (ttp) cc_final: 0.9052 (ttp) REVERT: C 79 MET cc_start: 0.9334 (ttp) cc_final: 0.8976 (ttp) REVERT: E 101 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8688 (p) REVERT: F 25 GLN cc_start: 0.7616 (tp-100) cc_final: 0.7362 (mm-40) REVERT: G 80 LYS cc_start: 0.8178 (tmtt) cc_final: 0.7959 (tmtt) REVERT: G 92 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8167 (mttp) REVERT: G 114 ASP cc_start: 0.8670 (m-30) cc_final: 0.8449 (m-30) REVERT: H 18 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7838 (pt0) REVERT: H 40 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7862 (tppt) REVERT: I 105 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8269 (mm-30) REVERT: J 37 HIS cc_start: 0.0785 (OUTLIER) cc_final: -0.1215 (m170) REVERT: J 272 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8929 (mt) REVERT: J 368 ASP cc_start: 0.8330 (t70) cc_final: 0.7414 (t0) REVERT: K 98 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7651 (mtp) REVERT: L 99 MET cc_start: 0.9338 (ttm) cc_final: 0.9117 (ttp) REVERT: M 54 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7047 (tt0) REVERT: M 678 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.6622 (tp-100) REVERT: M 696 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8582 (mtt) REVERT: N 51 ASP cc_start: 0.8967 (t70) cc_final: 0.8656 (t70) REVERT: O 50 ASP cc_start: 0.8577 (m-30) cc_final: 0.8237 (m-30) REVERT: O 146 ASP cc_start: 0.8266 (t0) cc_final: 0.7756 (t0) REVERT: O 150 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.6843 (mp0) REVERT: Q 281 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: T 119 ARG cc_start: 0.8413 (ptp90) cc_final: 0.8041 (ptp-170) REVERT: W 5 LYS cc_start: 0.6768 (OUTLIER) cc_final: 0.6416 (ptpt) outliers start: 53 outliers final: 21 residues processed: 416 average time/residue: 0.8901 time to fit residues: 421.8169 Evaluate side-chains 415 residues out of total 3048 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 379 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 71 CYS Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain F residue 24 CYS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 92 LYS Chi-restraints excluded: chain G residue 138 LEU Chi-restraints excluded: chain H residue 18 GLU Chi-restraints excluded: chain H residue 40 LYS Chi-restraints excluded: chain J residue 37 HIS Chi-restraints excluded: chain J residue 140 ASP Chi-restraints excluded: chain J residue 272 LEU Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain K residue 102 SER Chi-restraints excluded: chain M residue 41 VAL Chi-restraints excluded: chain M residue 54 GLU Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 457 SER Chi-restraints excluded: chain M residue 632 MET Chi-restraints excluded: chain M residue 659 VAL Chi-restraints excluded: chain M residue 674 LEU Chi-restraints excluded: chain M residue 678 GLN Chi-restraints excluded: chain M residue 682 ASP Chi-restraints excluded: chain M residue 696 MET Chi-restraints excluded: chain O residue 140 CYS Chi-restraints excluded: chain O residue 150 GLU Chi-restraints excluded: chain P residue 153 ILE Chi-restraints excluded: chain P residue 156 SER Chi-restraints excluded: chain Q residue 217 VAL Chi-restraints excluded: chain Q residue 281 GLU Chi-restraints excluded: chain T residue 79 VAL Chi-restraints excluded: chain W residue 5 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.2938 > 50: distance: 94 - 98: 4.729 distance: 98 - 99: 9.547 distance: 99 - 100: 17.692 distance: 99 - 102: 7.002 distance: 100 - 101: 12.262 distance: 100 - 110: 6.932 distance: 102 - 103: 10.616 distance: 103 - 104: 7.755 distance: 103 - 105: 8.120 distance: 104 - 106: 10.982 distance: 105 - 107: 6.309 distance: 106 - 108: 6.447 distance: 107 - 108: 4.966 distance: 108 - 109: 3.374 distance: 110 - 111: 11.507 distance: 111 - 112: 9.604 distance: 111 - 114: 12.053 distance: 112 - 113: 9.288 distance: 112 - 118: 8.620 distance: 114 - 115: 4.038 distance: 115 - 116: 10.083 distance: 115 - 117: 4.963 distance: 118 - 119: 27.396 distance: 119 - 120: 6.846 distance: 119 - 122: 7.847 distance: 120 - 121: 30.920 distance: 120 - 129: 37.214 distance: 122 - 123: 13.164 distance: 123 - 124: 20.809 distance: 124 - 125: 5.521 distance: 125 - 126: 7.792 distance: 126 - 127: 9.890 distance: 126 - 128: 7.847 distance: 129 - 130: 11.589 distance: 130 - 131: 40.091 distance: 130 - 133: 29.722 distance: 131 - 132: 19.073 distance: 131 - 138: 38.635 distance: 133 - 134: 28.050 distance: 134 - 135: 7.208 distance: 135 - 136: 22.285 distance: 136 - 137: 15.424 distance: 138 - 139: 33.114 distance: 138 - 144: 27.561 distance: 139 - 140: 29.471 distance: 139 - 142: 9.042 distance: 140 - 141: 29.330 distance: 140 - 145: 13.792 distance: 142 - 143: 21.719 distance: 143 - 144: 22.663 distance: 145 - 146: 16.736 distance: 146 - 147: 23.155 distance: 146 - 149: 16.027 distance: 147 - 148: 11.055 distance: 147 - 152: 17.484 distance: 149 - 150: 9.220 distance: 149 - 151: 17.831 distance: 152 - 153: 31.375 distance: 153 - 154: 26.714 distance: 154 - 155: 24.400 distance: 154 - 156: 33.630 distance: 156 - 157: 12.042 distance: 157 - 158: 33.095 distance: 157 - 160: 14.802 distance: 158 - 159: 27.218 distance: 158 - 165: 21.463 distance: 160 - 161: 37.704 distance: 161 - 162: 11.800 distance: 162 - 163: 18.134 distance: 163 - 164: 25.381 distance: 165 - 166: 9.402 distance: 166 - 167: 14.021 distance: 166 - 169: 17.167 distance: 167 - 168: 19.221 distance: 167 - 177: 9.678 distance: 169 - 170: 19.680 distance: 170 - 171: 7.715 distance: 170 - 172: 13.020 distance: 171 - 173: 6.081 distance: 172 - 174: 14.412 distance: 173 - 175: 10.915 distance: 174 - 175: 14.924 distance: 175 - 176: 16.953 distance: 177 - 178: 32.491 distance: 178 - 179: 6.671 distance: 178 - 181: 16.087 distance: 179 - 180: 13.222 distance: 179 - 187: 21.917 distance: 181 - 182: 30.316 distance: 182 - 183: 15.768 distance: 182 - 184: 37.178 distance: 183 - 185: 30.499 distance: 184 - 186: 29.575 distance: 185 - 186: 21.552