Starting phenix.real_space_refine on Wed Oct 28 03:46:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lum_0981/10_2026/6lum_0981_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lum_0981/10_2026/6lum_0981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6lum_0981/10_2026/6lum_0981_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lum_0981/10_2026/6lum_0981_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6lum_0981/10_2026/6lum_0981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lum_0981/10_2026/6lum_0981.map" } resolution = 2.84 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= 0.001 sd= 0.056 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: 6 Type Number sf(0) Gaussians Fe 33 7.16 5 P 24 5.49 5 S 192 5.16 5 C 16857 2.51 5 N 4407 2.21 5 O 4678 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 150 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26191 Number of models: 1 Model: "" Number of chains: 28 Chain: "C" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 978 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "D" Number of atoms: 1193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1193 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 137} 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: "E" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 256 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "A" Number of atoms: 4129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4129 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 20, 'TRANS': 518} Chain breaks: 1 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1873 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 221} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 989 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "H" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 991 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 2, 'TRANS': 117} Chain: "I" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 256 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "J" Number of atoms: 4109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 534, 4109 Classifications: {'peptide': 534} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 513} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "K" Number of atoms: 1938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1938 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 19, 'TRANS': 227} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "M" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 990 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 961 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain: "O" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 256 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "P" Number of atoms: 4025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4025 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 20, 'TRANS': 518} Chain breaks: 1 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 9, 'TYR:plan': 2, 'GLU:plan': 8, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 103 Chain: "Q" Number of atoms: 1849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1849 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 16, 'TRANS': 221} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "C" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 85 Unusual residues: {'PEV': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "D" Number of atoms: 262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 262 Unusual residues: {'CDL': 1, 'HEM': 2, 'LPP': 1, 'MQ9': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 70 Planarities with less than four sites: {'MQ9:plan-2': 2, 'MQ9:plan-3': 2, 'MQ9:plan-4': 2, 'MQ9:plan-5': 2, 'MQ9:plan-6': 2, 'MQ9:plan-9': 2, 'MQ9:plan-10': 2} Unresolved non-hydrogen planarities: 68 Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'PIE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {'F3S': 1, 'FES': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'PEV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "H" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 285 Unusual residues: {'CDL': 1, 'HEM': 2, 'LPP': 1, 'MQ9': 1, 'PIE': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'MQ9:plan-2': 1, 'MQ9:plan-3': 1, 'MQ9:plan-4': 1, 'MQ9:plan-5': 1, 'MQ9:plan-6': 1, 'MQ9:plan-9': 1, 'MQ9:plan-10': 1} Unresolved non-hydrogen planarities: 35 Chain: "J" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {'F3S': 1, 'FES': 1, 'PEV': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "M" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 135 Unusual residues: {'HEM': 1, 'PEV': 1, 'PIE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "N" Number of atoms: 241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 241 Unusual residues: {'CDL': 1, 'HEM': 1, 'LPP': 1, 'MQ9': 3} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 99 Planarities with less than four sites: {'MQ9:plan-2': 3, 'MQ9:plan-3': 3, 'MQ9:plan-4': 3, 'MQ9:plan-5': 3, 'MQ9:plan-6': 3, 'MQ9:plan-9': 3, 'MQ9:plan-10': 3} Unresolved non-hydrogen planarities: 104 Chain: "P" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {'F3S': 1, 'FES': 1, 'PEV': 1, 'SF4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7005 SG CYS B 77 99.408 67.715 51.220 1.00 5.32 S ATOM 7037 SG CYS B 82 95.374 66.168 51.476 1.00 9.75 S ATOM 7144 SG CYS B 97 101.425 66.489 56.040 1.00 24.51 S ATOM 7798 SG CYS B 180 87.869 68.988 65.143 1.00 6.28 S ATOM 7781 SG CYS B 177 92.574 67.789 60.331 1.00 5.72 S ATOM 8272 SG CYS B 240 93.389 73.414 63.714 1.00 12.32 S ATOM 7759 SG CYS B 174 87.337 72.421 59.239 1.00 6.05 S ATOM 7824 SG CYS B 184 84.918 66.640 72.367 1.00 24.51 S ATOM 8195 SG CYS B 230 83.610 72.361 74.706 1.00 3.96 S ATOM 8245 SG CYS B 236 88.744 71.671 70.970 1.00 5.76 S ATOM 15288 SG CYS K 77 36.575 41.113 50.382 1.00 9.71 S ATOM 15320 SG CYS K 82 37.190 44.673 50.407 1.00 5.96 S ATOM 15427 SG CYS K 97 34.151 39.513 55.057 1.00 8.82 S ATOM 16081 SG CYS K 180 41.776 50.609 64.475 1.00 3.48 S ATOM 16064 SG CYS K 177 38.921 46.880 59.644 1.00 4.26 S ATOM 16555 SG CYS K 240 43.353 43.719 63.322 1.00 6.63 S ATOM 16042 SG CYS K 174 45.492 49.404 58.761 1.00 5.82 S ATOM 16107 SG CYS K 184 40.538 54.607 71.422 1.00 5.33 S ATOM 16478 SG CYS K 230 45.955 53.196 74.269 1.00 4.91 S ATOM 16528 SG CYS K 236 43.429 48.873 70.473 1.00 6.30 S ATOM 23527 SG CYS Q 97 43.352 113.457 52.931 1.00 13.81 S ATOM 23393 SG CYS Q 77 43.717 110.192 48.516 1.00 19.64 S ATOM 23420 SG CYS Q 82 46.221 107.691 48.440 1.00 11.90 S ATOM 24166 SG CYS Q 180 48.029 100.925 62.877 1.00 6.58 S ATOM 24149 SG CYS Q 177 46.582 105.319 57.675 1.00 7.54 S ATOM 24636 SG CYS Q 240 41.447 103.593 61.300 1.00 10.36 S ATOM 24127 SG CYS Q 174 45.288 98.294 57.087 1.00 12.42 S ATOM 24192 SG CYS Q 184 51.758 99.915 70.042 1.00 6.03 S ATOM 24559 SG CYS Q 230 47.504 96.178 72.709 1.00 10.47 S ATOM 24609 SG CYS Q 236 45.363 100.750 68.765 1.00 12.97 S Time building chain proxies: 5.95, per 1000 atoms: 0.23 Number of scatterers: 26191 At special positions: 0 Unit cell: (136.94, 145.14, 132.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 33 26.01 S 192 16.00 P 24 15.00 O 4678 8.00 N 4407 7.00 C 16857 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=15, symmetry=0 Number of additional bonds: simple=15, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.87 Conformation dependent library (CDL) restraints added in 895.2 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B 303 " pdb="FE1 F3S B 303 " - pdb=" SG CYS B 184 " pdb="FE4 F3S B 303 " - pdb=" SG CYS B 236 " pdb="FE3 F3S B 303 " - pdb=" SG CYS B 230 " pdb=" F3S K 303 " pdb="FE3 F3S K 303 " - pdb=" SG CYS K 230 " pdb="FE4 F3S K 303 " - pdb=" SG CYS K 236 " pdb="FE1 F3S K 303 " - pdb=" SG CYS K 184 " pdb=" F3S Q 303 " pdb="FE1 F3S Q 303 " - pdb=" SG CYS Q 184 " pdb="FE3 F3S Q 303 " - pdb=" SG CYS Q 230 " pdb="FE4 F3S Q 303 " - pdb=" SG CYS Q 236 " pdb=" FES B 301 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 97 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 82 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 77 " pdb=" FES K 301 " pdb="FE2 FES K 301 " - pdb=" SG CYS K 97 " pdb="FE1 FES K 301 " - pdb=" SG CYS K 82 " pdb="FE1 FES K 301 " - pdb=" SG CYS K 77 " pdb=" FES Q 301 " pdb="FE2 FES Q 301 " - pdb=" SG CYS Q 82 " pdb="FE1 FES Q 301 " - pdb=" SG CYS Q 97 " pdb="FE2 FES Q 301 " - pdb=" SG CYS Q 77 " pdb=" SF4 B 302 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 177 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 240 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 180 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 174 " pdb=" SF4 K 302 " pdb="FE1 SF4 K 302 " - pdb=" SG CYS K 180 " pdb="FE2 SF4 K 302 " - pdb=" SG CYS K 177 " pdb="FE3 SF4 K 302 " - pdb=" SG CYS K 240 " pdb="FE4 SF4 K 302 " - pdb=" SG CYS K 174 " pdb=" SF4 Q 302 " pdb="FE2 SF4 Q 302 " - pdb=" SG CYS Q 177 " pdb="FE3 SF4 Q 302 " - pdb=" SG CYS Q 240 " pdb="FE1 SF4 Q 302 " - pdb=" SG CYS Q 180 " pdb="FE4 SF4 Q 302 " - pdb=" SG CYS Q 174 " Number of angles added : 75 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5844 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 25 sheets defined 51.5% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'C' and resid 24 through 53 removed outlier: 3.896A pdb=" N TRP C 28 " --> pdb=" O ASP C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 56 No H-bonds generated for 'chain 'C' and resid 54 through 56' Processing helix chain 'C' and resid 57 through 68 removed outlier: 3.769A pdb=" N TYR C 61 " --> pdb=" O SER C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 100 Processing helix chain 'C' and resid 102 through 107 removed outlier: 3.649A pdb=" N TYR C 106 " --> pdb=" O LYS C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 135 Processing helix chain 'D' and resid 25 through 30 removed outlier: 3.705A pdb=" N HIS D 30 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 71 removed outlier: 3.845A pdb=" N TYR D 46 " --> pdb=" O TYR D 42 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHE D 60 " --> pdb=" O ILE D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 79 Processing helix chain 'D' and resid 80 through 88 Processing helix chain 'D' and resid 90 through 120 Processing helix chain 'D' and resid 122 through 150 Processing helix chain 'E' and resid 2 through 29 Processing helix chain 'A' and resid 15 through 29 Proline residue: A 27 - end of helix Processing helix chain 'A' and resid 38 through 47 removed outlier: 3.851A pdb=" N SER A 42 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS A 43 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N THR A 44 " --> pdb=" O ARG A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 74 removed outlier: 3.905A pdb=" N HIS A 66 " --> pdb=" O ASN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 100 removed outlier: 5.127A pdb=" N ASP A 92 " --> pdb=" O LYS A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 154 removed outlier: 3.824A pdb=" N MET A 142 " --> pdb=" O ARG A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 256 through 261 Processing helix chain 'A' and resid 273 through 278 Processing helix chain 'A' and resid 286 through 300 Processing helix chain 'A' and resid 398 through 422 removed outlier: 4.156A pdb=" N LEU A 402 " --> pdb=" O THR A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 444 Processing helix chain 'A' and resid 450 through 466 Processing helix chain 'A' and resid 471 through 489 Processing helix chain 'A' and resid 502 through 528 removed outlier: 3.759A pdb=" N LEU A 506 " --> pdb=" O ASN A 502 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 513 " --> pdb=" O ILE A 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 66 removed outlier: 3.780A pdb=" N LEU B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 99 Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 133 through 141 Processing helix chain 'B' and resid 164 through 169 removed outlier: 4.361A pdb=" N TYR B 168 " --> pdb=" O ASP B 164 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP B 169 " --> pdb=" O ARG B 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 164 through 169' Processing helix chain 'B' and resid 180 through 183 Processing helix chain 'B' and resid 184 through 189 Processing helix chain 'B' and resid 195 through 207 removed outlier: 3.532A pdb=" N ILE B 199 " --> pdb=" O GLY B 195 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N PHE B 205 " --> pdb=" O ASN B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 221 Processing helix chain 'B' and resid 226 through 230 removed outlier: 4.076A pdb=" N ARG B 229 " --> pdb=" O GLY B 226 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS B 230 " --> pdb=" O VAL B 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 226 through 230' Processing helix chain 'B' and resid 234 through 240 Processing helix chain 'B' and resid 245 through 259 Processing helix chain 'G' and resid 24 through 53 removed outlier: 4.010A pdb=" N TRP G 28 " --> pdb=" O ASP G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 56 No H-bonds generated for 'chain 'G' and resid 54 through 56' Processing helix chain 'G' and resid 57 through 68 Processing helix chain 'G' and resid 70 through 100 Processing helix chain 'G' and resid 103 through 105 No H-bonds generated for 'chain 'G' and resid 103 through 105' Processing helix chain 'G' and resid 106 through 137 Processing helix chain 'H' and resid 42 through 71 removed outlier: 3.702A pdb=" N TYR H 46 " --> pdb=" O TYR H 42 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N PHE H 60 " --> pdb=" O ILE H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 79 Processing helix chain 'H' and resid 80 through 88 Processing helix chain 'H' and resid 90 through 120 Processing helix chain 'H' and resid 122 through 151 Processing helix chain 'I' and resid 2 through 29 Processing helix chain 'J' and resid 15 through 25 Processing helix chain 'J' and resid 42 through 47 Processing helix chain 'J' and resid 62 through 74 removed outlier: 3.830A pdb=" N HIS J 66 " --> pdb=" O ASN J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 79 through 100 removed outlier: 4.353A pdb=" N ASP J 92 " --> pdb=" O LYS J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 154 removed outlier: 3.786A pdb=" N MET J 142 " --> pdb=" O ARG J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 222 through 230 Processing helix chain 'J' and resid 273 through 278 Processing helix chain 'J' and resid 286 through 299 Processing helix chain 'J' and resid 398 through 422 removed outlier: 3.994A pdb=" N LEU J 402 " --> pdb=" O THR J 398 " (cutoff:3.500A) Processing helix chain 'J' and resid 432 through 444 Processing helix chain 'J' and resid 450 through 465 Processing helix chain 'J' and resid 471 through 489 Processing helix chain 'J' and resid 503 through 528 Processing helix chain 'K' and resid 55 through 66 Processing helix chain 'K' and resid 95 through 99 removed outlier: 3.853A pdb=" N VAL K 99 " --> pdb=" O ALA K 96 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 141 Processing helix chain 'K' and resid 161 through 166 removed outlier: 3.764A pdb=" N ALA K 166 " --> pdb=" O PRO K 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 180 through 183 Processing helix chain 'K' and resid 184 through 189 Processing helix chain 'K' and resid 195 through 207 removed outlier: 4.111A pdb=" N PHE K 205 " --> pdb=" O ASN K 201 " (cutoff:3.500A) Processing helix chain 'K' and resid 213 through 222 Processing helix chain 'K' and resid 226 through 230 removed outlier: 3.848A pdb=" N ARG K 229 " --> pdb=" O GLY K 226 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS K 230 " --> pdb=" O VAL K 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 226 through 230' Processing helix chain 'K' and resid 234 through 240 Processing helix chain 'K' and resid 245 through 259 Processing helix chain 'M' and resid 24 through 53 removed outlier: 3.709A pdb=" N TRP M 28 " --> pdb=" O ASP M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 68 removed outlier: 3.735A pdb=" N TYR M 61 " --> pdb=" O SER M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 100 Processing helix chain 'M' and resid 102 through 107 removed outlier: 3.565A pdb=" N TYR M 106 " --> pdb=" O LYS M 102 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 137 removed outlier: 3.857A pdb=" N ALA M 124 " --> pdb=" O VAL M 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 71 removed outlier: 3.702A pdb=" N TYR N 46 " --> pdb=" O TYR N 42 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N PHE N 60 " --> pdb=" O ILE N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 74 through 79 Processing helix chain 'N' and resid 80 through 88 Processing helix chain 'N' and resid 90 through 120 Processing helix chain 'N' and resid 122 through 151 Processing helix chain 'O' and resid 2 through 29 Processing helix chain 'P' and resid 15 through 26 Processing helix chain 'P' and resid 38 through 47 removed outlier: 4.059A pdb=" N SER P 42 " --> pdb=" O PRO P 39 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N HIS P 43 " --> pdb=" O THR P 40 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N THR P 44 " --> pdb=" O ARG P 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 74 removed outlier: 3.523A pdb=" N HIS P 66 " --> pdb=" O ASN P 62 " (cutoff:3.500A) Processing helix chain 'P' and resid 79 through 98 removed outlier: 4.121A pdb=" N ASP P 92 " --> pdb=" O LYS P 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 138 through 154 removed outlier: 4.021A pdb=" N MET P 142 " --> pdb=" O ARG P 138 " (cutoff:3.500A) Processing helix chain 'P' and resid 222 through 229 Processing helix chain 'P' and resid 273 through 278 Processing helix chain 'P' and resid 286 through 301 Processing helix chain 'P' and resid 399 through 422 Processing helix chain 'P' and resid 432 through 444 Processing helix chain 'P' and resid 450 through 466 Processing helix chain 'P' and resid 471 through 489 Processing helix chain 'P' and resid 503 through 528 removed outlier: 3.582A pdb=" N PHE P 513 " --> pdb=" O ILE P 509 " (cutoff:3.500A) Processing helix chain 'P' and resid 544 through 549 Processing helix chain 'Q' and resid 55 through 66 Processing helix chain 'Q' and resid 95 through 99 removed outlier: 3.825A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 104 through 108 removed outlier: 4.446A pdb=" N ASN Q 108 " --> pdb=" O LEU Q 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 133 through 141 Processing helix chain 'Q' and resid 161 through 166 removed outlier: 3.753A pdb=" N ALA Q 166 " --> pdb=" O PRO Q 162 " (cutoff:3.500A) Processing helix chain 'Q' and resid 180 through 183 Processing helix chain 'Q' and resid 184 through 189 Processing helix chain 'Q' and resid 195 through 207 removed outlier: 4.154A pdb=" N PHE Q 205 " --> pdb=" O ASN Q 201 " (cutoff:3.500A) Processing helix chain 'Q' and resid 213 through 222 Processing helix chain 'Q' and resid 226 through 230 removed outlier: 3.831A pdb=" N ARG Q 229 " --> pdb=" O GLY Q 226 " (cutoff:3.500A) Processing helix chain 'Q' and resid 234 through 240 Processing helix chain 'Q' and resid 245 through 259 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 6.515A pdb=" N GLN A 3 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N HIS A 195 " --> pdb=" O GLN A 3 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N HIS A 5 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N THR A 172 " --> pdb=" O PRO A 176 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ALA A 178 " --> pdb=" O THR A 170 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N THR A 170 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY A 180 " --> pdb=" O ALA A 168 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N TYR A 184 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ALA A 164 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 157 through 160 removed outlier: 7.208A pdb=" N THR A 31 " --> pdb=" O GLU A 157 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N PHE A 159 " --> pdb=" O THR A 31 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL A 33 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ILE A 199 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU A 379 " --> pdb=" O VAL A 368 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 52 Processing sheet with id=AA4, first strand: chain 'A' and resid 234 through 235 Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 243 removed outlier: 5.854A pdb=" N HIS A 243 " --> pdb=" O CYS A 353 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N CYS A 353 " --> pdb=" O HIS A 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 360 through 361 removed outlier: 5.856A pdb=" N ILE A 360 " --> pdb=" O CYS A 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 43 through 48 Processing sheet with id=AA8, first strand: chain 'B' and resid 125 through 127 removed outlier: 6.714A pdb=" N VAL B 130 " --> pdb=" O GLU B 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 4 through 6 removed outlier: 6.489A pdb=" N HIS J 5 " --> pdb=" O HIS J 195 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA J 168 " --> pdb=" O THR J 179 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N VAL J 181 " --> pdb=" O ASP J 166 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASP J 166 " --> pdb=" O VAL J 181 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ALA J 183 " --> pdb=" O ALA J 164 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA J 164 " --> pdb=" O ALA J 183 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU J 185 " --> pdb=" O PHE J 162 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N PHE J 162 " --> pdb=" O GLU J 185 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 157 through 159 removed outlier: 6.584A pdb=" N VAL J 33 " --> pdb=" O PHE J 159 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ILE J 11 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ILE J 199 " --> pdb=" O TYR J 380 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 51 through 52 Processing sheet with id=AB3, first strand: chain 'J' and resid 234 through 235 Processing sheet with id=AB4, first strand: chain 'J' and resid 240 through 243 removed outlier: 6.571A pdb=" N GLN J 241 " --> pdb=" O HIS J 354 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 266 through 267 Processing sheet with id=AB6, first strand: chain 'J' and resid 360 through 361 removed outlier: 5.946A pdb=" N ILE J 360 " --> pdb=" O CYS J 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'K' and resid 42 through 47 removed outlier: 6.641A pdb=" N THR K 27 " --> pdb=" O ILE K 115 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N ILE K 117 " --> pdb=" O THR K 27 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LYS K 29 " --> pdb=" O ILE K 117 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL K 92 " --> pdb=" O ILE K 89 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 125 through 127 removed outlier: 6.869A pdb=" N VAL K 130 " --> pdb=" O GLU K 126 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'P' and resid 3 through 6 removed outlier: 6.313A pdb=" N THR P 172 " --> pdb=" O PRO P 176 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ALA P 178 " --> pdb=" O THR P 170 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N THR P 170 " --> pdb=" O ALA P 178 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLY P 180 " --> pdb=" O ALA P 168 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP P 166 " --> pdb=" O ILE P 182 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N TYR P 184 " --> pdb=" O ALA P 164 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ALA P 164 " --> pdb=" O TYR P 184 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 158 through 159 removed outlier: 6.607A pdb=" N VAL P 33 " --> pdb=" O PHE P 159 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N VAL P 10 " --> pdb=" O VAL P 200 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE P 199 " --> pdb=" O TYR P 380 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'P' and resid 51 through 52 Processing sheet with id=AC3, first strand: chain 'P' and resid 233 through 235 Processing sheet with id=AC4, first strand: chain 'P' and resid 240 through 243 removed outlier: 3.628A pdb=" N TYR P 355 " --> pdb=" O GLN P 241 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N HIS P 243 " --> pdb=" O CYS P 353 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N CYS P 353 " --> pdb=" O HIS P 243 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 360 through 361 removed outlier: 6.171A pdb=" N ILE P 360 " --> pdb=" O CYS P 387 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'Q' and resid 42 through 48 Processing sheet with id=AC7, first strand: chain 'Q' and resid 125 through 127 removed outlier: 7.099A pdb=" N VAL Q 130 " --> pdb=" O GLU Q 126 " (cutoff:3.500A) 1279 hydrogen bonds defined for protein. 3675 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.53 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.78: 26521 1.78 - 2.38: 302 2.38 - 2.99: 0 2.99 - 3.60: 0 3.60 - 4.20: 9 Bond restraints: 26832 Sorted by residual: bond pdb=" S4 F3S B 303 " pdb="FE1 F3S B 303 " ideal model delta sigma weight residual 2.233 4.205 -1.972 2.00e-02 2.50e+03 9.72e+03 bond pdb=" S4 F3S Q 303 " pdb="FE1 F3S Q 303 " ideal model delta sigma weight residual 2.233 4.203 -1.970 2.00e-02 2.50e+03 9.70e+03 bond pdb=" S4 F3S K 303 " pdb="FE1 F3S K 303 " ideal model delta sigma weight residual 2.233 4.181 -1.948 2.00e-02 2.50e+03 9.48e+03 bond pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " ideal model delta sigma weight residual 2.258 4.183 -1.925 2.00e-02 2.50e+03 9.26e+03 bond pdb=" S1 F3S Q 303 " pdb="FE4 F3S Q 303 " ideal model delta sigma weight residual 2.258 4.175 -1.917 2.00e-02 2.50e+03 9.19e+03 ... (remaining 26827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.62: 36310 14.62 - 29.24: 97 29.24 - 43.86: 20 43.86 - 58.48: 3 58.48 - 73.10: 6 Bond angle restraints: 36436 Sorted by residual: angle pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " pdb=" S3 F3S B 303 " ideal model delta sigma weight residual 114.75 41.65 73.10 3.00e+00 1.11e-01 5.94e+02 angle pdb=" S1 F3S K 303 " pdb="FE4 F3S K 303 " pdb=" S3 F3S K 303 " ideal model delta sigma weight residual 114.75 41.82 72.93 3.00e+00 1.11e-01 5.91e+02 angle pdb=" S1 F3S Q 303 " pdb="FE4 F3S Q 303 " pdb=" S3 F3S Q 303 " ideal model delta sigma weight residual 114.75 41.84 72.91 3.00e+00 1.11e-01 5.91e+02 angle pdb=" S3 F3S B 303 " pdb="FE1 F3S B 303 " pdb=" S4 F3S B 303 " ideal model delta sigma weight residual 112.59 42.45 70.14 3.00e+00 1.11e-01 5.47e+02 angle pdb=" S3 F3S Q 303 " pdb="FE1 F3S Q 303 " pdb=" S4 F3S Q 303 " ideal model delta sigma weight residual 112.59 43.09 69.50 3.00e+00 1.11e-01 5.37e+02 ... (remaining 36431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.87: 15359 34.87 - 69.74: 634 69.74 - 104.61: 27 104.61 - 139.49: 1 139.49 - 174.36: 2 Dihedral angle restraints: 16023 sinusoidal: 6907 harmonic: 9116 Sorted by residual: dihedral pdb=" CA ASN K 37 " pdb=" C ASN K 37 " pdb=" N PRO K 38 " pdb=" CA PRO K 38 " ideal model delta harmonic sigma weight residual 180.00 149.08 30.92 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CA GLY K 80 " pdb=" C GLY K 80 " pdb=" N VAL K 81 " pdb=" CA VAL K 81 " ideal model delta harmonic sigma weight residual -180.00 -149.26 -30.74 0 5.00e+00 4.00e-02 3.78e+01 dihedral pdb=" CA GLY B 80 " pdb=" C GLY B 80 " pdb=" N VAL B 81 " pdb=" CA VAL B 81 " ideal model delta harmonic sigma weight residual -180.00 -152.25 -27.75 0 5.00e+00 4.00e-02 3.08e+01 ... (remaining 16020 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.335: 3930 1.335 - 2.669: 0 2.669 - 4.003: 0 4.003 - 5.338: 0 5.338 - 6.672: 3 Chirality restraints: 3933 Sorted by residual: chirality pdb=" S2 F3S Q 303 " pdb="FE1 F3S Q 303 " pdb="FE3 F3S Q 303 " pdb="FE4 F3S Q 303 " both_signs ideal model delta sigma weight residual False 10.77 4.10 6.67 2.00e-01 2.50e+01 1.11e+03 chirality pdb=" S2 F3S K 303 " pdb="FE1 F3S K 303 " pdb="FE3 F3S K 303 " pdb="FE4 F3S K 303 " both_signs ideal model delta sigma weight residual False 10.77 4.65 6.11 2.00e-01 2.50e+01 9.34e+02 chirality pdb=" S2 F3S B 303 " pdb="FE1 F3S B 303 " pdb="FE3 F3S B 303 " pdb="FE4 F3S B 303 " both_signs ideal model delta sigma weight residual False 10.77 4.73 6.04 2.00e-01 2.50e+01 9.11e+02 ... (remaining 3930 not shown) Planarity restraints: 4540 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 MQ9 N 203 " -0.367 2.00e-02 2.50e+03 5.12e-01 3.28e+03 pdb=" C11 MQ9 N 203 " -0.275 2.00e-02 2.50e+03 pdb=" C7 MQ9 N 203 " -0.572 2.00e-02 2.50e+03 pdb=" C8 MQ9 N 203 " 0.746 2.00e-02 2.50e+03 pdb=" C9 MQ9 N 203 " 0.467 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 MQ9 H 204 " -0.282 2.00e-02 2.50e+03 3.17e-01 1.26e+03 pdb=" C13 MQ9 H 204 " 0.578 2.00e-02 2.50e+03 pdb=" C14 MQ9 H 204 " -0.296 2.00e-02 2.50e+03 pdb=" C15 MQ9 H 204 " 0.022 2.00e-02 2.50e+03 pdb=" C16 MQ9 H 204 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 MQ9 D 205 " -0.280 2.00e-02 2.50e+03 3.16e-01 1.25e+03 pdb=" C13 MQ9 D 205 " 0.571 2.00e-02 2.50e+03 pdb=" C14 MQ9 D 205 " -0.303 2.00e-02 2.50e+03 pdb=" C15 MQ9 D 205 " -0.041 2.00e-02 2.50e+03 pdb=" C16 MQ9 D 205 " 0.053 2.00e-02 2.50e+03 ... (remaining 4537 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 347 2.63 - 3.20: 23336 3.20 - 3.76: 38946 3.76 - 4.33: 57369 4.33 - 4.90: 97392 Nonbonded interactions: 217390 Sorted by model distance: nonbonded pdb=" O THR K 233 " pdb=" S4 F3S K 303 " model vdw 2.061 3.400 nonbonded pdb=" O ILE D 68 " pdb=" NH2 ARG D 78 " model vdw 2.086 3.120 nonbonded pdb=" OH TYR P 501 " pdb=" OE1 GLU Q 126 " model vdw 2.087 3.040 nonbonded pdb=" O PHE H 50 " pdb=" OG SER H 54 " model vdw 2.087 3.040 nonbonded pdb=" O PHE N 50 " pdb=" OG SER N 54 " model vdw 2.088 3.040 ... (remaining 217385 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 5 or (resid 6 through 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 through 108 or (resid 109 and (name \ N or name CA or name C or name O or name CB )) or resid 110 through 121 or (resi \ d 122 and (name N or name CA or name C or name O or name CB )) or resid 123 thro \ ugh 130 or (resid 131 through 132 and (name N or name CA or name C or name O or \ name CB )) or resid 133 through 137 or (resid 138 and (name N or name CA or name \ C or name O or name CB )) or resid 139 through 170 or (resid 171 and (name N or \ name CA or name C or name O or name CB )) or resid 172 through 255 or (resid 25 \ 6 through 257 and (name N or name CA or name C or name O or name CB )) or resid \ 258 through 260 or (resid 261 and (name N or name CA or name C or name O or name \ CB )) or resid 262 through 268 or (resid 269 and (name N or name CA or name C o \ r name O or name CB )) or resid 270 through 275 or (resid 276 through 278 and (n \ ame N or name CA or name C or name O or name CB )) or resid 279 through 280 or ( \ resid 281 and (name N or name CA or name C or name O or name CB )) or resid 282 \ through 286 or (resid 287 and (name N or name CA or name C or name O or name CB \ )) or resid 288 through 296 or (resid 297 and (name N or name CA or name C or na \ me O or name CB )) or resid 298 through 300 or resid 347 through 426 or (resid 4 \ 27 and (name N or name CA or name C or name O or name CB )) or resid 428 through \ 429 or (resid 430 and (name N or name CA or name C or name O or name CB )) or r \ esid 431 through 440 or (resid 441 and (name N or name CA or name C or name O or \ name CB )) or resid 442 through 448 or (resid 449 and (name N or name CA or nam \ e C or name O or name CB )) or resid 450 through 468 or (resid 469 and (name N o \ r name CA or name C or name O or name CB )) or resid 470 through 531 or (resid 5 \ 32 and (name N or name CA or name C or name O or name CB )) or resid 533 through \ 569 or (resid 570 and (name N or name CA or name C or name O or name CB )) or r \ esid 571 through 577 or (resid 578 and (name N or name CA or name C or name O or \ name CB )) or resid 579 through 700)) selection = (chain 'J' and (resid 2 through 5 or (resid 6 through 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 through 108 or (resid 109 and (name \ N or name CA or name C or name O or name CB )) or resid 110 through 121 or (resi \ d 122 and (name N or name CA or name C or name O or name CB )) or resid 123 thro \ ugh 125 or (resid 126 through 127 and (name N or name CA or name C or name O or \ name CB )) or resid 128 through 130 or (resid 131 through 132 and (name N or nam \ e CA or name C or name O or name CB )) or resid 133 through 137 or (resid 138 an \ d (name N or name CA or name C or name O or name CB )) or resid 139 through 156 \ or (resid 157 and (name N or name CA or name C or name O or name CB )) or resid \ 158 through 170 or (resid 171 and (name N or name CA or name C or name O or name \ CB )) or resid 172 through 260 or (resid 261 and (name N or name CA or name C o \ r name O or name CB )) or resid 262 through 275 or (resid 276 through 278 and (n \ ame N or name CA or name C or name O or name CB )) or resid 279 through 280 or ( \ resid 281 and (name N or name CA or name C or name O or name CB )) or resid 282 \ through 286 or (resid 287 and (name N or name CA or name C or name O or name CB \ )) or resid 288 through 296 or (resid 297 and (name N or name CA or name C or na \ me O or name CB )) or resid 298 through 426 or (resid 427 and (name N or name CA \ or name C or name O or name CB )) or resid 428 or (resid 429 through 430 and (n \ ame N or name CA or name C or name O or name CB )) or resid 431 through 432 or ( \ resid 433 and (name N or name CA or name C or name O or name CB )) or resid 434 \ through 440 or (resid 441 and (name N or name CA or name C or name O or name CB \ )) or resid 442 through 448 or (resid 449 and (name N or name CA or name C or na \ me O or name CB )) or resid 450 through 468 or (resid 469 and (name N or name CA \ or name C or name O or name CB )) or resid 470 through 531 or (resid 532 and (n \ ame N or name CA or name C or name O or name CB )) or resid 533 through 569 or ( \ resid 570 and (name N or name CA or name C or name O or name CB )) or resid 571 \ through 577 or (resid 578 and (name N or name CA or name C or name O or name CB \ )) or resid 579 through 700)) selection = (chain 'P' and (resid 2 through 156 or (resid 157 and (name N or name CA or name \ C or name O or name CB )) or resid 158 through 268 or (resid 269 and (name N or \ name CA or name C or name O or name CB )) or resid 270 through 300 or resid 347 \ through 432 or (resid 433 and (name N or name CA or name C or name O or name CB \ )) or resid 434 through 700)) } ncs_group { reference = (chain 'B' and (resid 23 through 78 or (resid 79 and (name N or name CA or name \ C or name O or name CB )) or resid 80 through 107 or (resid 108 and (name N or n \ ame CA or name C or name O or name CB )) or resid 109 through 111 or (resid 112 \ and (name N or name CA or name C or name O or name CB )) or resid 113 through 15 \ 6 or (resid 157 and (name N or name CA or name C or name O or name CB )) or resi \ d 158 through 159 or (resid 160 and (name N or name CA or name C or name O or na \ me CB )) or resid 161 through 211 or (resid 212 through 215 and (name N or name \ CA or name C or name O or name CB )) or resid 216 through 303)) selection = (chain 'K' and (resid 23 through 78 or (resid 79 and (name N or name CA or name \ C or name O or name CB )) or resid 80 through 107 or (resid 108 and (name N or n \ ame CA or name C or name O or name CB )) or resid 109 through 111 or (resid 112 \ and (name N or name CA or name C or name O or name CB )) or resid 113 through 15 \ 6 or (resid 157 and (name N or name CA or name C or name O or name CB )) or resi \ d 158 through 159 or (resid 160 and (name N or name CA or name C or name O or na \ me CB )) or resid 161 through 211 or (resid 212 through 215 and (name N or name \ CA or name C or name O or name CB )) or resid 216 through 303)) selection = (chain 'Q' and resid 23 through 303) } ncs_group { reference = (chain 'C' and (resid 16 through 136 or resid 202)) selection = (chain 'G' and (resid 16 through 136 or resid 201)) selection = (chain 'M' and (resid 16 through 136 or resid 203)) } ncs_group { reference = (chain 'E' and resid 1 through 31) selection = chain 'I' selection = chain 'O' } ncs_group { reference = (chain 'H' and (resid 41 through 156 or resid 202 or resid 204)) selection = (chain 'N' and (resid 41 through 156 or resid 202 or resid 204)) } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.360 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: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.930 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 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 : 0.040 1.972 26877 Z= 1.945 Angle : 2.059 73.100 36511 Z= 0.866 Chirality : 0.188 6.672 3933 Planarity : 0.016 0.512 4540 Dihedral : 17.288 174.358 10179 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.77 % Favored : 90.07 % Rotamer: Outliers : 1.72 % Allowed : 5.38 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.41 (0.13), residues: 3142 helix: -0.95 (0.12), residues: 1515 sheet: -2.05 (0.30), residues: 231 loop : -3.92 (0.12), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 204 TYR 0.021 0.002 TYR M 68 PHE 0.023 0.002 PHE O 5 TRP 0.022 0.002 TRP D 102 HIS 0.008 0.001 HIS C 47 Details of bonding type rmsd/Z covalent geometry : bond 0.03858 / 1.90 (26832) covalent geometry : angle 1.97684 / 0.86 (36436) hydrogen bonds : bond 0.08613 / 5.84 ( 1279) hydrogen bonds : angle 5.17576 / 3.86 ( 3675) metal coordination : bond 0.31383 / 19.16 ( 30) metal coordination : angle 12.86017 / 7.95 ( 75) Misc. bond : bond 0.19349 / 10.73 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 428 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 27 MET cc_start: 0.8548 (ttt) cc_final: 0.8205 (ttt) REVERT: A 137 ASP cc_start: 0.7065 (t0) cc_final: 0.6765 (t0) REVERT: A 287 ARG cc_start: 0.6825 (mmt180) cc_final: 0.6499 (mpt-90) REVERT: J 448 ASN cc_start: 0.7023 (p0) cc_final: 0.6631 (p0) REVERT: K 47 ARG cc_start: 0.7378 (ttm-80) cc_final: 0.7129 (mtm180) REVERT: P 410 ARG cc_start: 0.7261 (mtp85) cc_final: 0.6750 (mtm-85) REVERT: Q 47 ARG cc_start: 0.7319 (ttm110) cc_final: 0.6950 (pmt170) REVERT: Q 87 MET cc_start: 0.7841 (mtt) cc_final: 0.7636 (mtt) REVERT: Q 104 MET cc_start: 0.3783 (mtm) cc_final: 0.2896 (ppp) outliers start: 44 outliers final: 4 residues processed: 464 average time/residue: 0.6390 time to fit residues: 344.1382 Evaluate side-chains 352 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 348 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain N residue 54 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 33 HIS C 87 HIS D 30 HIS A 57 ASN A 105 ASN A 114 GLN A 141 HIS A 195 HIS A 374 ASN A 421 ASN A 459 GLN A 465 ASN B 79 HIS B 160 GLN G 33 HIS G 47 HIS G 87 HIS G 109 GLN H 110 ASN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 365 ASN J 459 GLN J 460 GLN J 464 ASN J 477 GLN J 557 GLN K 90 ASN K 132 ASN K 245 GLN M 33 HIS M 87 HIS M 132 HIS N 110 ASN N 123 ASN P 62 ASN P 114 GLN P 241 GLN P 405 ASN P 459 GLN P 465 ASN P 527 ASN P 557 GLN Q 37 ASN Q 132 ASN Q 245 GLN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.170818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.123565 restraints weight = 28293.680| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.98 r_work: 0.3206 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 26877 Z= 0.167 Angle : 1.524 88.225 36511 Z= 0.464 Chirality : 0.049 1.047 3933 Planarity : 0.005 0.051 4540 Dihedral : 15.249 166.126 4577 Min Nonbonded Distance : 1.566 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.77 % Allowed : 12.60 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.14), residues: 3142 helix: 0.53 (0.13), residues: 1528 sheet: -1.61 (0.30), residues: 233 loop : -3.39 (0.14), residues: 1381 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 105 TYR 0.019 0.001 TYR J 569 PHE 0.013 0.001 PHE M 86 TRP 0.018 0.001 TRP D 48 HIS 0.007 0.001 HIS P 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.17 (26832) covalent geometry : angle 1.17387 / 0.46 (36436) hydrogen bonds : bond 0.05159 / 3.51 ( 1279) hydrogen bonds : angle 4.46079 / 3.33 ( 3675) metal coordination : bond 0.01434 / 1.05 ( 30) metal coordination : angle 21.46015 / 13.58 ( 75) Misc. bond : bond 0.02137 / 0.76 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 386 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 105 ARG cc_start: 0.8390 (mtp-110) cc_final: 0.8119 (ttm110) REVERT: D 71 MET cc_start: 0.8825 (mtp) cc_final: 0.8312 (mtt) REVERT: A 137 ASP cc_start: 0.7597 (t0) cc_final: 0.6979 (t0) REVERT: A 281 ILE cc_start: 0.6506 (OUTLIER) cc_final: 0.6272 (pp) REVERT: A 302 ARG cc_start: 0.8467 (ttm-80) cc_final: 0.8250 (ttp-110) REVERT: B 25 MET cc_start: 0.7959 (mmm) cc_final: 0.7649 (mmm) REVERT: H 74 ASP cc_start: 0.7935 (m-30) cc_final: 0.7668 (m-30) REVERT: I 30 ASP cc_start: 0.7942 (OUTLIER) cc_final: 0.7551 (m-30) REVERT: J 130 ARG cc_start: 0.6735 (mtt90) cc_final: 0.6335 (mtp85) REVERT: J 427 MET cc_start: 0.7266 (pmm) cc_final: 0.6864 (tpt) REVERT: J 448 ASN cc_start: 0.6926 (p0) cc_final: 0.6424 (p0) REVERT: J 487 GLU cc_start: 0.8438 (pp20) cc_final: 0.8173 (pp20) REVERT: J 540 TYR cc_start: 0.7820 (m-10) cc_final: 0.7592 (m-10) REVERT: J 580 MET cc_start: 0.6434 (ptm) cc_final: 0.5958 (pmm) REVERT: K 25 MET cc_start: 0.8223 (mmm) cc_final: 0.8006 (mmm) REVERT: K 29 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8223 (ttmt) REVERT: K 47 ARG cc_start: 0.8352 (ttm-80) cc_final: 0.7310 (mtm110) REVERT: M 131 MET cc_start: 0.8088 (ttp) cc_final: 0.7434 (ptm) REVERT: O 1 MET cc_start: 0.6792 (OUTLIER) cc_final: 0.6146 (tmt) REVERT: P 410 ARG cc_start: 0.6567 (mtp85) cc_final: 0.5808 (mtm-85) REVERT: P 434 MET cc_start: 0.7642 (ttt) cc_final: 0.7349 (tmm) REVERT: P 462 MET cc_start: 0.7386 (mmm) cc_final: 0.7142 (mmp) REVERT: Q 51 LEU cc_start: 0.8194 (mm) cc_final: 0.7830 (tm) REVERT: Q 100 LEU cc_start: 0.7391 (tt) cc_final: 0.7129 (pt) REVERT: Q 104 MET cc_start: 0.3501 (mtm) cc_final: 0.2523 (ppp) REVERT: Q 223 GLU cc_start: 0.7950 (tm-30) cc_final: 0.7629 (tm-30) REVERT: Q 225 ASP cc_start: 0.7818 (p0) cc_final: 0.7518 (p0) outliers start: 71 outliers final: 26 residues processed: 424 average time/residue: 0.6301 time to fit residues: 311.3515 Evaluate side-chains 369 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 339 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 30 ASP Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain J residue 474 THR Chi-restraints excluded: chain J residue 493 THR Chi-restraints excluded: chain K residue 29 LYS Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 463 ASP Chi-restraints excluded: chain P residue 539 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: [63, 84, 65, 1, 147, 283, 156, 94, 12, 74, 56] chunk 63 optimal weight: 0.3980 chunk 84 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 147 optimal weight: 0.7980 chunk 283 optimal weight: 5.9990 chunk 156 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 56 optimal weight: 0.0060 overall best weight: 1.0398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 34 ASN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 354 HIS J 367 GLN J 423 ASN J 465 ASN ** J 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 132 ASN P 267 ASN P 354 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.170510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.123653 restraints weight = 28404.671| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.01 r_work: 0.3198 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.165 26877 Z= 0.172 Angle : 1.325 84.080 36511 Z= 0.442 Chirality : 0.054 1.409 3933 Planarity : 0.005 0.055 4540 Dihedral : 14.018 164.801 4575 Min Nonbonded Distance : 1.555 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 3.00 % Allowed : 15.53 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.15), residues: 3142 helix: 1.05 (0.13), residues: 1536 sheet: -1.25 (0.33), residues: 219 loop : -3.07 (0.14), residues: 1387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 22 TYR 0.014 0.001 TYR M 68 PHE 0.014 0.001 PHE C 43 TRP 0.015 0.001 TRP N 48 HIS 0.006 0.001 HIS P 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (26832) covalent geometry : angle 1.12419 / 0.44 (36436) hydrogen bonds : bond 0.05059 / 3.42 ( 1279) hydrogen bonds : angle 4.28739 / 3.20 ( 3675) metal coordination : bond 0.00561 / 0.39 ( 30) metal coordination : angle 15.51297 / 10.28 ( 75) Misc. bond : bond 0.01687 / 0.60 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 378 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 105 ARG cc_start: 0.8367 (mtp-110) cc_final: 0.8136 (ttm110) REVERT: C 131 MET cc_start: 0.8348 (ttp) cc_final: 0.8031 (ptm) REVERT: D 71 MET cc_start: 0.8828 (mtp) cc_final: 0.8416 (mtt) REVERT: D 86 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: A 6 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7936 (ttm110) REVERT: A 137 ASP cc_start: 0.7589 (t0) cc_final: 0.6944 (t0) REVERT: A 142 MET cc_start: 0.8682 (mmm) cc_final: 0.8377 (mmp) REVERT: A 276 ARG cc_start: 0.7238 (ptt180) cc_final: 0.6987 (tmm-80) REVERT: A 281 ILE cc_start: 0.6459 (OUTLIER) cc_final: 0.6236 (pp) REVERT: J 69 ASP cc_start: 0.7265 (m-30) cc_final: 0.7036 (m-30) REVERT: J 130 ARG cc_start: 0.6713 (mtt90) cc_final: 0.6303 (mtp85) REVERT: J 448 ASN cc_start: 0.6940 (p0) cc_final: 0.6464 (p0) REVERT: J 487 GLU cc_start: 0.8439 (pp20) cc_final: 0.8211 (pp20) REVERT: J 580 MET cc_start: 0.6262 (ptm) cc_final: 0.5893 (pmm) REVERT: K 29 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8189 (ttmt) REVERT: K 47 ARG cc_start: 0.8368 (ttm-80) cc_final: 0.7162 (mtm180) REVERT: K 94 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7422 (mmp80) REVERT: K 134 GLU cc_start: 0.8306 (mm-30) cc_final: 0.8087 (mm-30) REVERT: K 238 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8262 (tm-30) REVERT: M 131 MET cc_start: 0.8083 (ttp) cc_final: 0.7437 (ptm) REVERT: O 1 MET cc_start: 0.6739 (OUTLIER) cc_final: 0.6095 (tmt) REVERT: P 9 VAL cc_start: 0.6907 (OUTLIER) cc_final: 0.6594 (m) REVERT: P 77 LEU cc_start: 0.6360 (OUTLIER) cc_final: 0.6045 (tt) REVERT: P 100 MET cc_start: 0.7287 (mtp) cc_final: 0.6884 (mpp) REVERT: P 264 ARG cc_start: 0.7100 (ptm160) cc_final: 0.6733 (ptm160) REVERT: P 410 ARG cc_start: 0.6598 (mtp85) cc_final: 0.5806 (mtm-85) REVERT: P 434 MET cc_start: 0.7554 (ttt) cc_final: 0.7292 (tmm) REVERT: P 462 MET cc_start: 0.7330 (mmm) cc_final: 0.7094 (mmp) REVERT: Q 51 LEU cc_start: 0.8256 (mm) cc_final: 0.7810 (tm) REVERT: Q 104 MET cc_start: 0.3000 (mtm) cc_final: 0.2345 (ppp) outliers start: 77 outliers final: 29 residues processed: 429 average time/residue: 0.6084 time to fit residues: 305.6373 Evaluate side-chains 380 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 343 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 388 VAL Chi-restraints excluded: chain J residue 403 ASP Chi-restraints excluded: chain J residue 493 THR Chi-restraints excluded: chain K residue 29 LYS Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 299 LEU Chi-restraints excluded: chain Q residue 95 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: [105, 164, 265, 17, 131, 256, 161, 162, 91, 76, 83] chunk 105 optimal weight: 7.9990 chunk 164 optimal weight: 0.5980 chunk 265 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 131 optimal weight: 4.9990 chunk 256 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 162 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 423 ASN ** J 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 132 ASN P 114 GLN P 372 ASN P 527 ASN P 551 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.172190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.124369 restraints weight = 28251.049| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.02 r_work: 0.3222 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 26877 Z= 0.154 Angle : 1.229 83.453 36511 Z= 0.417 Chirality : 0.057 1.483 3933 Planarity : 0.004 0.056 4540 Dihedral : 13.480 164.061 4575 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.97 % Allowed : 17.09 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.15), residues: 3142 helix: 1.37 (0.13), residues: 1532 sheet: -0.98 (0.34), residues: 219 loop : -2.90 (0.14), residues: 1391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG Q 47 TYR 0.014 0.001 TYR J 540 PHE 0.016 0.001 PHE J 407 TRP 0.016 0.001 TRP H 48 HIS 0.006 0.001 HIS K 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (26832) covalent geometry : angle 1.05420 / 0.41 (36436) hydrogen bonds : bond 0.04722 / 3.19 ( 1279) hydrogen bonds : angle 4.16453 / 3.11 ( 3675) metal coordination : bond 0.00540 / 0.39 ( 30) metal coordination : angle 13.96950 / 9.20 ( 75) Misc. bond : bond 0.02290 / 0.78 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 377 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 105 ARG cc_start: 0.8368 (mtp-110) cc_final: 0.8133 (ttm110) REVERT: C 131 MET cc_start: 0.8364 (ttp) cc_final: 0.8060 (ptm) REVERT: D 71 MET cc_start: 0.8818 (mtp) cc_final: 0.8362 (mtt) REVERT: A 6 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7879 (ttm110) REVERT: A 137 ASP cc_start: 0.7600 (t0) cc_final: 0.6956 (t0) REVERT: A 142 MET cc_start: 0.8623 (mmm) cc_final: 0.8345 (mmp) REVERT: A 276 ARG cc_start: 0.7156 (ptt180) cc_final: 0.6953 (tmm-80) REVERT: A 281 ILE cc_start: 0.6475 (OUTLIER) cc_final: 0.6243 (pp) REVERT: A 302 ARG cc_start: 0.8438 (ttm-80) cc_final: 0.7854 (mtm110) REVERT: B 98 LYS cc_start: 0.8451 (mttm) cc_final: 0.8249 (mtpp) REVERT: B 164 ASP cc_start: 0.8071 (t0) cc_final: 0.7808 (t0) REVERT: J 69 ASP cc_start: 0.7283 (m-30) cc_final: 0.7038 (m-30) REVERT: J 92 ASP cc_start: 0.7004 (t0) cc_final: 0.6544 (m-30) REVERT: J 130 ARG cc_start: 0.6656 (mtt90) cc_final: 0.6279 (mtp85) REVERT: J 448 ASN cc_start: 0.6914 (p0) cc_final: 0.6475 (p0) REVERT: J 487 GLU cc_start: 0.8447 (pp20) cc_final: 0.8239 (pp20) REVERT: J 580 MET cc_start: 0.6210 (ptm) cc_final: 0.5859 (pmm) REVERT: K 25 MET cc_start: 0.8237 (mmm) cc_final: 0.7991 (mmm) REVERT: K 29 LYS cc_start: 0.8514 (OUTLIER) cc_final: 0.8171 (ttmt) REVERT: K 47 ARG cc_start: 0.8338 (ttm-80) cc_final: 0.7212 (mtm180) REVERT: K 94 ARG cc_start: 0.7665 (OUTLIER) cc_final: 0.7429 (mmp80) REVERT: M 131 MET cc_start: 0.8041 (ttp) cc_final: 0.7396 (ptm) REVERT: O 1 MET cc_start: 0.6739 (OUTLIER) cc_final: 0.6121 (tmt) REVERT: P 9 VAL cc_start: 0.6741 (OUTLIER) cc_final: 0.6501 (m) REVERT: P 77 LEU cc_start: 0.6283 (OUTLIER) cc_final: 0.6018 (tt) REVERT: P 116 ARG cc_start: 0.7529 (ptp-110) cc_final: 0.7274 (ptp-110) REVERT: P 264 ARG cc_start: 0.7052 (ptm160) cc_final: 0.6666 (ptm160) REVERT: P 410 ARG cc_start: 0.6543 (mtp85) cc_final: 0.5831 (mmm-85) REVERT: P 434 MET cc_start: 0.7612 (ttt) cc_final: 0.7361 (tmm) REVERT: P 443 LEU cc_start: 0.7970 (mp) cc_final: 0.7698 (mp) REVERT: P 462 MET cc_start: 0.7266 (mmm) cc_final: 0.7048 (mmp) REVERT: Q 104 MET cc_start: 0.2675 (mtm) cc_final: 0.2164 (ppp) REVERT: Q 223 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7624 (tm-30) REVERT: Q 225 ASP cc_start: 0.7564 (p0) cc_final: 0.7353 (p0) outliers start: 76 outliers final: 34 residues processed: 430 average time/residue: 0.5932 time to fit residues: 299.5567 Evaluate side-chains 400 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 358 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 282 VAL Chi-restraints excluded: chain J residue 474 THR Chi-restraints excluded: chain K residue 29 LYS Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 463 ASP Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain Q residue 100 LEU Chi-restraints excluded: chain Q residue 223 GLU Chi-restraints excluded: chain Q residue 244 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: [266, 191, 98, 202, 40, 77, 4, 208, 296, 116, 219] chunk 266 optimal weight: 9.9990 chunk 191 optimal weight: 4.9990 chunk 98 optimal weight: 0.7980 chunk 202 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 208 optimal weight: 0.9990 chunk 296 optimal weight: 0.0770 chunk 116 optimal weight: 4.9990 chunk 219 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 34 ASN J 57 ASN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 215 ASN J 423 ASN ** J 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 132 ASN P 114 GLN P 527 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.173711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.126373 restraints weight = 28257.378| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.98 r_work: 0.3241 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 26877 Z= 0.147 Angle : 1.155 83.632 36511 Z= 0.409 Chirality : 0.057 1.479 3933 Planarity : 0.004 0.057 4540 Dihedral : 13.021 163.484 4575 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.04 % Allowed : 17.79 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.15), residues: 3142 helix: 1.57 (0.13), residues: 1528 sheet: -0.83 (0.34), residues: 219 loop : -2.76 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG Q 47 TYR 0.017 0.001 TYR J 540 PHE 0.017 0.001 PHE P 407 TRP 0.017 0.001 TRP H 48 HIS 0.006 0.001 HIS K 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 (26832) covalent geometry : angle 1.04237 / 0.41 (36436) hydrogen bonds : bond 0.04444 / 3.00 ( 1279) hydrogen bonds : angle 4.06653 / 3.04 ( 3675) metal coordination : bond 0.00417 / 0.29 ( 30) metal coordination : angle 11.02232 / 7.32 ( 75) Misc. bond : bond 0.02831 / 0.97 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 379 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 131 MET cc_start: 0.8399 (ttp) cc_final: 0.8126 (ptm) REVERT: D 32 ARG cc_start: 0.7451 (mtp85) cc_final: 0.7245 (mtp-110) REVERT: A 137 ASP cc_start: 0.7549 (t0) cc_final: 0.6957 (t0) REVERT: A 142 MET cc_start: 0.8599 (mmm) cc_final: 0.8351 (mmt) REVERT: A 281 ILE cc_start: 0.6477 (OUTLIER) cc_final: 0.6244 (pp) REVERT: A 302 ARG cc_start: 0.8396 (ttm-80) cc_final: 0.7849 (mtm110) REVERT: A 471 THR cc_start: 0.7844 (OUTLIER) cc_final: 0.7369 (p) REVERT: B 47 ARG cc_start: 0.8322 (mtp180) cc_final: 0.7284 (mtm180) REVERT: B 164 ASP cc_start: 0.8160 (t0) cc_final: 0.7901 (t0) REVERT: J 69 ASP cc_start: 0.7313 (m-30) cc_final: 0.7069 (m-30) REVERT: J 92 ASP cc_start: 0.7053 (t0) cc_final: 0.6588 (m-30) REVERT: J 130 ARG cc_start: 0.6595 (mtt90) cc_final: 0.6227 (mtp85) REVERT: J 448 ASN cc_start: 0.6929 (p0) cc_final: 0.6490 (p0) REVERT: J 580 MET cc_start: 0.6165 (ptm) cc_final: 0.5889 (pmm) REVERT: K 29 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8213 (ttmt) REVERT: K 47 ARG cc_start: 0.8381 (ttm-80) cc_final: 0.7172 (mtm110) REVERT: K 79 HIS cc_start: 0.5583 (OUTLIER) cc_final: 0.5045 (m90) REVERT: K 98 LYS cc_start: 0.8620 (mttp) cc_final: 0.8347 (mttt) REVERT: K 133 MET cc_start: 0.9001 (mmm) cc_final: 0.8708 (mmm) REVERT: K 238 GLU cc_start: 0.8466 (tm-30) cc_final: 0.8180 (tm-30) REVERT: K 247 THR cc_start: 0.8803 (t) cc_final: 0.8427 (m) REVERT: M 106 TYR cc_start: 0.8117 (m-80) cc_final: 0.7844 (m-80) REVERT: O 1 MET cc_start: 0.6869 (OUTLIER) cc_final: 0.6247 (tmt) REVERT: P 9 VAL cc_start: 0.6682 (OUTLIER) cc_final: 0.6414 (m) REVERT: P 116 ARG cc_start: 0.7526 (ptp-110) cc_final: 0.7300 (ptp-110) REVERT: P 384 GLU cc_start: 0.5879 (tt0) cc_final: 0.5572 (tt0) REVERT: P 410 ARG cc_start: 0.6640 (mtp85) cc_final: 0.5905 (mmm-85) REVERT: P 462 MET cc_start: 0.7327 (mmm) cc_final: 0.7097 (mmp) REVERT: Q 51 LEU cc_start: 0.8220 (mm) cc_final: 0.7815 (tm) REVERT: Q 104 MET cc_start: 0.2401 (mtm) cc_final: 0.2025 (ppp) REVERT: Q 223 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7672 (tm-30) outliers start: 78 outliers final: 37 residues processed: 429 average time/residue: 0.5913 time to fit residues: 297.9473 Evaluate side-chains 402 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 358 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 403 ASP Chi-restraints excluded: chain J residue 474 THR Chi-restraints excluded: chain K residue 29 LYS Chi-restraints excluded: chain K residue 79 HIS Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 220 THR Chi-restraints excluded: chain P residue 453 ASP Chi-restraints excluded: chain P residue 463 ASP Chi-restraints excluded: chain P residue 539 ASP Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 95 LEU Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 223 GLU Chi-restraints excluded: chain Q residue 244 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: [233, 284, 18, 257, 6, 173, 185, 166, 305, 102, 16] chunk 233 optimal weight: 0.9990 chunk 284 optimal weight: 20.0000 chunk 18 optimal weight: 1.9990 chunk 257 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 173 optimal weight: 5.9990 chunk 185 optimal weight: 7.9990 chunk 166 optimal weight: 8.9990 chunk 305 optimal weight: 0.5980 chunk 102 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 132 ASN P 114 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.172001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.124460 restraints weight = 28286.091| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.95 r_work: 0.3199 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 26877 Z= 0.165 Angle : 1.182 83.863 36511 Z= 0.418 Chirality : 0.058 1.494 3933 Planarity : 0.005 0.065 4540 Dihedral : 12.864 163.061 4573 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 3.00 % Allowed : 19.16 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.15), residues: 3142 helix: 1.55 (0.13), residues: 1528 sheet: -0.75 (0.34), residues: 219 loop : -2.70 (0.15), residues: 1395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG C 105 TYR 0.020 0.001 TYR J 540 PHE 0.018 0.001 PHE J 407 TRP 0.015 0.001 TRP H 48 HIS 0.006 0.001 HIS K 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.16 (26832) covalent geometry : angle 1.05796 / 0.42 (36436) hydrogen bonds : bond 0.04809 / 3.24 ( 1279) hydrogen bonds : angle 4.11750 / 3.08 ( 3675) metal coordination : bond 0.00535 / 0.38 ( 30) metal coordination : angle 11.65919 / 7.69 ( 75) Misc. bond : bond 0.02784 / 0.95 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 369 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 131 MET cc_start: 0.8422 (ttp) cc_final: 0.8150 (ptm) REVERT: A 137 ASP cc_start: 0.7537 (t0) cc_final: 0.6927 (t0) REVERT: A 142 MET cc_start: 0.8649 (mmm) cc_final: 0.8397 (mmt) REVERT: A 281 ILE cc_start: 0.6480 (OUTLIER) cc_final: 0.6258 (pp) REVERT: A 471 THR cc_start: 0.7893 (OUTLIER) cc_final: 0.7430 (p) REVERT: B 47 ARG cc_start: 0.8300 (mtp180) cc_final: 0.7366 (mtm180) REVERT: B 164 ASP cc_start: 0.8186 (t0) cc_final: 0.7904 (t0) REVERT: G 107 GLN cc_start: 0.8371 (OUTLIER) cc_final: 0.8089 (pp30) REVERT: J 69 ASP cc_start: 0.7320 (m-30) cc_final: 0.7069 (m-30) REVERT: J 130 ARG cc_start: 0.6701 (mtt90) cc_final: 0.6281 (mtp85) REVERT: J 448 ASN cc_start: 0.6925 (p0) cc_final: 0.6493 (p0) REVERT: J 578 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7951 (mm-30) REVERT: J 580 MET cc_start: 0.6181 (ptm) cc_final: 0.5928 (pmm) REVERT: K 29 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8160 (ttmt) REVERT: K 47 ARG cc_start: 0.8379 (ttm-80) cc_final: 0.7207 (mtm110) REVERT: K 133 MET cc_start: 0.9025 (mmm) cc_final: 0.8702 (mmm) REVERT: M 102 LYS cc_start: 0.7015 (ttpt) cc_final: 0.6646 (ttmm) REVERT: M 106 TYR cc_start: 0.8140 (m-80) cc_final: 0.7826 (m-80) REVERT: O 1 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.6182 (tmt) REVERT: P 9 VAL cc_start: 0.6715 (OUTLIER) cc_final: 0.6442 (m) REVERT: P 77 LEU cc_start: 0.6365 (OUTLIER) cc_final: 0.6097 (tt) REVERT: P 116 ARG cc_start: 0.7497 (ptp-110) cc_final: 0.7275 (ptp-110) REVERT: P 264 ARG cc_start: 0.6787 (ptm-80) cc_final: 0.6574 (ptm160) REVERT: P 384 GLU cc_start: 0.5886 (tt0) cc_final: 0.5630 (tt0) REVERT: P 410 ARG cc_start: 0.6625 (mtp85) cc_final: 0.5879 (mmm-85) REVERT: P 462 MET cc_start: 0.7326 (mmm) cc_final: 0.7122 (mmp) REVERT: Q 104 MET cc_start: 0.2440 (mtm) cc_final: 0.2050 (ppp) REVERT: Q 223 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7661 (tm-30) REVERT: Q 225 ASP cc_start: 0.7662 (p0) cc_final: 0.7358 (p0) outliers start: 77 outliers final: 44 residues processed: 422 average time/residue: 0.6045 time to fit residues: 298.8664 Evaluate side-chains 408 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 355 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 471 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 219 LEU Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 474 THR Chi-restraints excluded: chain J residue 493 THR Chi-restraints excluded: chain J residue 578 GLU Chi-restraints excluded: chain K residue 29 LYS Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 114 GLN Chi-restraints excluded: chain P residue 220 THR Chi-restraints excluded: chain P residue 453 ASP Chi-restraints excluded: chain P residue 463 ASP Chi-restraints excluded: chain P residue 539 ASP Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 209 SER Chi-restraints excluded: chain Q residue 223 GLU Chi-restraints excluded: chain Q residue 244 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: [39, 9, 136, 23, 215, 172, 271, 275, 156, 43, 300] chunk 39 optimal weight: 6.9990 chunk 9 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 271 optimal weight: 0.9980 chunk 275 optimal weight: 9.9990 chunk 156 optimal weight: 7.9990 chunk 43 optimal weight: 0.5980 chunk 300 optimal weight: 0.9980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 34 ASN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 574 GLN K 132 ASN P 57 ASN P 114 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.169597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.121685 restraints weight = 28178.091| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 1.95 r_work: 0.3174 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 26877 Z= 0.201 Angle : 1.227 83.897 36511 Z= 0.434 Chirality : 0.059 1.492 3933 Planarity : 0.005 0.057 4540 Dihedral : 12.937 163.287 4573 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 3.43 % Allowed : 19.47 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.15), residues: 3142 helix: 1.47 (0.13), residues: 1519 sheet: -0.75 (0.33), residues: 219 loop : -2.66 (0.15), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG Q 47 TYR 0.025 0.002 TYR J 540 PHE 0.016 0.002 PHE I 5 TRP 0.013 0.001 TRP H 48 HIS 0.007 0.001 HIS K 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.20 (26832) covalent geometry : angle 1.08492 / 0.43 (36436) hydrogen bonds : bond 0.05429 / 3.66 ( 1279) hydrogen bonds : angle 4.20966 / 3.14 ( 3675) metal coordination : bond 0.00780 / 0.56 ( 30) metal coordination : angle 12.70177 / 8.23 ( 75) Misc. bond : bond 0.02604 / 0.92 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 359 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 131 MET cc_start: 0.8444 (ttp) cc_final: 0.8155 (ptm) REVERT: A 137 ASP cc_start: 0.7600 (t0) cc_final: 0.6977 (t0) REVERT: A 142 MET cc_start: 0.8629 (mmm) cc_final: 0.8377 (mmp) REVERT: A 302 ARG cc_start: 0.8430 (ttm-80) cc_final: 0.7769 (mtm110) REVERT: B 164 ASP cc_start: 0.8225 (t0) cc_final: 0.7927 (t0) REVERT: G 107 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8196 (pp30) REVERT: J 69 ASP cc_start: 0.7393 (m-30) cc_final: 0.7141 (m-30) REVERT: J 92 ASP cc_start: 0.7114 (t0) cc_final: 0.6674 (m-30) REVERT: J 130 ARG cc_start: 0.6822 (mtt90) cc_final: 0.6426 (mtp85) REVERT: J 448 ASN cc_start: 0.6924 (p0) cc_final: 0.6483 (p0) REVERT: J 574 GLN cc_start: 0.7898 (OUTLIER) cc_final: 0.7438 (tp40) REVERT: J 578 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.8003 (mm-30) REVERT: J 580 MET cc_start: 0.6259 (ptm) cc_final: 0.5967 (pmm) REVERT: K 29 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8164 (ttmt) REVERT: K 47 ARG cc_start: 0.8373 (ttm-80) cc_final: 0.7220 (mtm180) REVERT: M 102 LYS cc_start: 0.6964 (ttpt) cc_final: 0.6724 (ttmm) REVERT: M 106 TYR cc_start: 0.8259 (m-80) cc_final: 0.8047 (m-80) REVERT: O 1 MET cc_start: 0.6802 (OUTLIER) cc_final: 0.6157 (tmt) REVERT: P 9 VAL cc_start: 0.6851 (OUTLIER) cc_final: 0.6543 (m) REVERT: P 77 LEU cc_start: 0.6481 (OUTLIER) cc_final: 0.6151 (tt) REVERT: P 264 ARG cc_start: 0.6790 (ptm-80) cc_final: 0.6558 (ptm160) REVERT: P 410 ARG cc_start: 0.6671 (mtp85) cc_final: 0.5947 (mmm-85) REVERT: P 462 MET cc_start: 0.7377 (mmm) cc_final: 0.7137 (mmp) REVERT: Q 51 LEU cc_start: 0.8182 (mm) cc_final: 0.7777 (tm) REVERT: Q 104 MET cc_start: 0.2536 (mtm) cc_final: 0.2111 (ppp) REVERT: Q 223 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7612 (tm-30) REVERT: Q 225 ASP cc_start: 0.7599 (p0) cc_final: 0.7352 (p0) outliers start: 88 outliers final: 51 residues processed: 422 average time/residue: 0.5940 time to fit residues: 294.2373 Evaluate side-chains 417 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 358 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 580 MET Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain H residue 76 VAL Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 219 LEU Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 474 THR Chi-restraints excluded: chain J residue 493 THR Chi-restraints excluded: chain J residue 562 LEU Chi-restraints excluded: chain J residue 574 GLN Chi-restraints excluded: chain J residue 578 GLU Chi-restraints excluded: chain K residue 29 LYS Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 94 ARG Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 220 THR Chi-restraints excluded: chain P residue 299 LEU Chi-restraints excluded: chain P residue 463 ASP Chi-restraints excluded: chain P residue 539 ASP Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 223 GLU Chi-restraints excluded: chain Q residue 236 CYS Chi-restraints excluded: chain Q residue 244 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: [135, 103, 212, 296, 144, 71, 109, 189, 79, 124, 186] chunk 135 optimal weight: 0.0670 chunk 103 optimal weight: 1.9990 chunk 212 optimal weight: 0.9980 chunk 296 optimal weight: 9.9990 chunk 144 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 574 GLN K 132 ASN P 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.171831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.124621 restraints weight = 28325.751| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 2.00 r_work: 0.3208 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3072 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.109 26877 Z= 0.160 Angle : 1.194 83.533 36511 Z= 0.420 Chirality : 0.058 1.502 3933 Planarity : 0.005 0.056 4540 Dihedral : 12.678 161.339 4573 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 2.73 % Allowed : 20.25 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.15), residues: 3142 helix: 1.64 (0.13), residues: 1514 sheet: -0.65 (0.34), residues: 219 loop : -2.61 (0.15), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Q 47 TYR 0.027 0.001 TYR J 540 PHE 0.015 0.001 PHE P 407 TRP 0.017 0.001 TRP H 48 HIS 0.006 0.001 HIS K 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (26832) covalent geometry : angle 1.05957 / 0.42 (36436) hydrogen bonds : bond 0.04787 / 3.23 ( 1279) hydrogen bonds : angle 4.13056 / 3.08 ( 3675) metal coordination : bond 0.00554 / 0.39 ( 30) metal coordination : angle 12.18185 / 7.94 ( 75) Misc. bond : bond 0.02745 / 0.93 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 370 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 131 MET cc_start: 0.8438 (ttp) cc_final: 0.8150 (ptm) REVERT: A 88 LYS cc_start: 0.7517 (mtpp) cc_final: 0.7164 (mttt) REVERT: A 137 ASP cc_start: 0.7550 (t0) cc_final: 0.6947 (t0) REVERT: A 302 ARG cc_start: 0.8420 (ttm-80) cc_final: 0.7848 (mtm110) REVERT: A 384 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7683 (tt0) REVERT: B 47 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.8006 (ttm-80) REVERT: B 164 ASP cc_start: 0.8233 (t0) cc_final: 0.7967 (t0) REVERT: G 107 GLN cc_start: 0.8413 (OUTLIER) cc_final: 0.8060 (pp30) REVERT: J 69 ASP cc_start: 0.7408 (m-30) cc_final: 0.7150 (m-30) REVERT: J 92 ASP cc_start: 0.7027 (t0) cc_final: 0.6541 (m-30) REVERT: J 130 ARG cc_start: 0.6794 (mtt90) cc_final: 0.6466 (mtp85) REVERT: J 427 MET cc_start: 0.7405 (pmm) cc_final: 0.6815 (mmt) REVERT: J 448 ASN cc_start: 0.6928 (p0) cc_final: 0.6496 (p0) REVERT: J 580 MET cc_start: 0.6230 (ptm) cc_final: 0.5979 (pmm) REVERT: K 29 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8139 (ttmt) REVERT: K 47 ARG cc_start: 0.8341 (ttm-80) cc_final: 0.7225 (mtm110) REVERT: K 79 HIS cc_start: 0.5716 (OUTLIER) cc_final: 0.5285 (m90) REVERT: M 22 ARG cc_start: 0.8171 (ttm110) cc_final: 0.7906 (ttp-110) REVERT: M 106 TYR cc_start: 0.8252 (m-80) cc_final: 0.7882 (m-80) REVERT: O 1 MET cc_start: 0.6872 (OUTLIER) cc_final: 0.6216 (tmt) REVERT: P 9 VAL cc_start: 0.6647 (OUTLIER) cc_final: 0.6397 (m) REVERT: P 77 LEU cc_start: 0.6462 (OUTLIER) cc_final: 0.6172 (tt) REVERT: P 264 ARG cc_start: 0.6720 (ptm-80) cc_final: 0.6365 (ptm160) REVERT: P 384 GLU cc_start: 0.5958 (tt0) cc_final: 0.5719 (tt0) REVERT: P 410 ARG cc_start: 0.6657 (mtp85) cc_final: 0.5915 (mmm-85) REVERT: P 462 MET cc_start: 0.7390 (mmm) cc_final: 0.7189 (mmp) REVERT: Q 32 ARG cc_start: 0.7313 (mmm160) cc_final: 0.7096 (mmm160) REVERT: Q 51 LEU cc_start: 0.8161 (mm) cc_final: 0.7745 (tm) REVERT: Q 104 MET cc_start: 0.2263 (mtm) cc_final: 0.1925 (ppp) REVERT: Q 223 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7649 (tm-30) outliers start: 70 outliers final: 47 residues processed: 416 average time/residue: 0.6137 time to fit residues: 298.6834 Evaluate side-chains 414 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 358 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 281 ILE Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain B residue 47 ARG Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 88 ARG Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain G residue 27 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain I residue 28 VAL Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 474 THR Chi-restraints excluded: chain J residue 493 THR Chi-restraints excluded: chain K residue 29 LYS Chi-restraints excluded: chain K residue 79 HIS Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 128 ASP Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 114 GLN Chi-restraints excluded: chain P residue 208 ARG Chi-restraints excluded: chain P residue 220 THR Chi-restraints excluded: chain P residue 463 ASP Chi-restraints excluded: chain P residue 539 ASP Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 223 GLU Chi-restraints excluded: chain Q residue 236 CYS Chi-restraints excluded: chain Q residue 244 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: [241, 85, 184, 12, 171, 252, 297, 202, 46, 69, 235] chunk 241 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 chunk 184 optimal weight: 7.9990 chunk 12 optimal weight: 6.9990 chunk 171 optimal weight: 0.0670 chunk 252 optimal weight: 5.9990 chunk 297 optimal weight: 0.8980 chunk 202 optimal weight: 0.5980 chunk 46 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 235 optimal weight: 6.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 34 ASN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 132 ASN P 57 ASN P 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.173477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.126400 restraints weight = 28429.752| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.04 r_work: 0.3231 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 26877 Z= 0.150 Angle : 1.182 83.552 36511 Z= 0.417 Chirality : 0.058 1.506 3933 Planarity : 0.004 0.056 4540 Dihedral : 12.453 159.397 4573 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 2.58 % Allowed : 20.64 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.37 (0.15), residues: 3142 helix: 1.72 (0.13), residues: 1514 sheet: -0.57 (0.34), residues: 219 loop : -2.57 (0.15), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG Q 47 TYR 0.026 0.001 TYR J 540 PHE 0.016 0.001 PHE P 407 TRP 0.019 0.001 TRP H 48 HIS 0.006 0.001 HIS K 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (26832) covalent geometry : angle 1.05524 / 0.41 (36436) hydrogen bonds : bond 0.04516 / 3.06 ( 1279) hydrogen bonds : angle 4.08335 / 3.03 ( 3675) metal coordination : bond 0.00479 / 0.34 ( 30) metal coordination : angle 11.81656 / 7.76 ( 75) Misc. bond : bond 0.02908 / 0.98 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 367 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 131 MET cc_start: 0.8453 (ttp) cc_final: 0.8169 (ptm) REVERT: A 88 LYS cc_start: 0.7463 (mtpp) cc_final: 0.7129 (mttt) REVERT: A 137 ASP cc_start: 0.7596 (t0) cc_final: 0.7026 (t0) REVERT: A 302 ARG cc_start: 0.8404 (ttm-80) cc_final: 0.7832 (mtm110) REVERT: G 107 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8067 (pp30) REVERT: J 69 ASP cc_start: 0.7418 (m-30) cc_final: 0.7169 (m-30) REVERT: J 92 ASP cc_start: 0.7012 (t0) cc_final: 0.6577 (m-30) REVERT: J 130 ARG cc_start: 0.6730 (mtt90) cc_final: 0.6427 (mtp85) REVERT: J 427 MET cc_start: 0.7411 (pmm) cc_final: 0.6845 (mmt) REVERT: J 448 ASN cc_start: 0.6902 (p0) cc_final: 0.6467 (p0) REVERT: J 580 MET cc_start: 0.6201 (ptm) cc_final: 0.5959 (pmm) REVERT: K 29 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8171 (ttmt) REVERT: K 79 HIS cc_start: 0.5549 (OUTLIER) cc_final: 0.5088 (m90) REVERT: M 22 ARG cc_start: 0.8106 (ttm110) cc_final: 0.7867 (ttp-110) REVERT: O 1 MET cc_start: 0.6804 (OUTLIER) cc_final: 0.6173 (tmt) REVERT: P 9 VAL cc_start: 0.6553 (OUTLIER) cc_final: 0.6325 (m) REVERT: P 77 LEU cc_start: 0.6445 (OUTLIER) cc_final: 0.6127 (tt) REVERT: P 264 ARG cc_start: 0.6752 (ptm-80) cc_final: 0.6300 (ptm160) REVERT: P 384 GLU cc_start: 0.5948 (tt0) cc_final: 0.5716 (tt0) REVERT: P 410 ARG cc_start: 0.6644 (mtp85) cc_final: 0.5894 (mmm-85) REVERT: P 462 MET cc_start: 0.7360 (mmm) cc_final: 0.7158 (mmp) REVERT: P 553 MET cc_start: 0.6699 (ttt) cc_final: 0.6249 (tpp) REVERT: Q 51 LEU cc_start: 0.8206 (mm) cc_final: 0.7771 (tm) REVERT: Q 104 MET cc_start: 0.2168 (mtm) cc_final: 0.1878 (ppp) REVERT: Q 223 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7710 (tm-30) REVERT: Q 225 ASP cc_start: 0.7650 (p0) cc_final: 0.7243 (p0) outliers start: 66 outliers final: 43 residues processed: 411 average time/residue: 0.5890 time to fit residues: 283.9999 Evaluate side-chains 412 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 362 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 225 ASP Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain H residue 112 MET Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 95 LEU Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 219 LEU Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 474 THR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 29 LYS Chi-restraints excluded: chain K residue 79 HIS Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 114 GLN Chi-restraints excluded: chain P residue 208 ARG Chi-restraints excluded: chain P residue 220 THR Chi-restraints excluded: chain P residue 453 ASP Chi-restraints excluded: chain P residue 463 ASP Chi-restraints excluded: chain P residue 539 ASP Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 223 GLU Chi-restraints excluded: chain Q residue 244 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: [255, 227, 105, 72, 243, 38, 191, 103, 241, 270, 58] chunk 255 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 chunk 105 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 243 optimal weight: 3.9990 chunk 38 optimal weight: 0.0970 chunk 191 optimal weight: 0.0570 chunk 103 optimal weight: 0.8980 chunk 241 optimal weight: 5.9990 chunk 270 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 overall best weight: 1.2100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 132 ASN P 57 ASN P 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.171594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.124230 restraints weight = 28246.335| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.98 r_work: 0.3204 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 26877 Z= 0.174 Angle : 1.211 83.963 36511 Z= 0.428 Chirality : 0.058 1.502 3933 Planarity : 0.005 0.061 4540 Dihedral : 12.481 158.718 4571 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.26 % Allowed : 21.11 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.15), residues: 3142 helix: 1.60 (0.13), residues: 1527 sheet: -0.51 (0.34), residues: 219 loop : -2.56 (0.15), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG Q 47 TYR 0.028 0.001 TYR J 540 PHE 0.015 0.001 PHE P 407 TRP 0.015 0.001 TRP H 48 HIS 0.006 0.001 HIS K 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.17 (26832) covalent geometry : angle 1.07293 / 0.43 (36436) hydrogen bonds : bond 0.04926 / 3.33 ( 1279) hydrogen bonds : angle 4.13067 / 3.07 ( 3675) metal coordination : bond 0.00625 / 0.45 ( 30) metal coordination : angle 12.44928 / 8.08 ( 75) Misc. bond : bond 0.02934 / 1.00 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6284 Ramachandran restraints generated. 3142 Oldfield, 0 Emsley, 3142 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 363 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 LYS cc_start: 0.7525 (mtpp) cc_final: 0.7186 (mttt) REVERT: A 137 ASP cc_start: 0.7647 (t0) cc_final: 0.7076 (t0) REVERT: A 302 ARG cc_start: 0.8360 (ttm-80) cc_final: 0.7774 (mtm110) REVERT: G 107 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8123 (pp30) REVERT: J 69 ASP cc_start: 0.7425 (m-30) cc_final: 0.7170 (m-30) REVERT: J 92 ASP cc_start: 0.7071 (t0) cc_final: 0.6635 (m-30) REVERT: J 130 ARG cc_start: 0.6840 (mtt90) cc_final: 0.6538 (mtp85) REVERT: J 427 MET cc_start: 0.7393 (pmm) cc_final: 0.6843 (mmt) REVERT: J 448 ASN cc_start: 0.6876 (p0) cc_final: 0.6436 (p0) REVERT: J 580 MET cc_start: 0.6244 (ptm) cc_final: 0.6009 (pmm) REVERT: K 29 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8145 (ttmt) REVERT: K 47 ARG cc_start: 0.8406 (tpp80) cc_final: 0.7023 (mpt180) REVERT: K 157 GLU cc_start: 0.7934 (pp20) cc_final: 0.7669 (pp20) REVERT: M 22 ARG cc_start: 0.8178 (ttm110) cc_final: 0.7917 (ttp-110) REVERT: O 1 MET cc_start: 0.6786 (OUTLIER) cc_final: 0.6167 (tmt) REVERT: P 9 VAL cc_start: 0.6644 (OUTLIER) cc_final: 0.6380 (m) REVERT: P 77 LEU cc_start: 0.6504 (OUTLIER) cc_final: 0.6216 (tt) REVERT: P 264 ARG cc_start: 0.6758 (ptm-80) cc_final: 0.6304 (ptm160) REVERT: P 384 GLU cc_start: 0.6000 (tt0) cc_final: 0.5753 (tt0) REVERT: P 410 ARG cc_start: 0.6666 (mtp85) cc_final: 0.5914 (mmm-85) REVERT: P 445 GLU cc_start: 0.5995 (tp30) cc_final: 0.5560 (tm-30) REVERT: P 462 MET cc_start: 0.7379 (mmm) cc_final: 0.7147 (mmp) REVERT: Q 32 ARG cc_start: 0.7294 (mmm160) cc_final: 0.7030 (mmm160) REVERT: Q 51 LEU cc_start: 0.8194 (mm) cc_final: 0.7770 (tm) REVERT: Q 104 MET cc_start: 0.2285 (mtm) cc_final: 0.1962 (ppp) REVERT: Q 223 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: Q 225 ASP cc_start: 0.7683 (p0) cc_final: 0.7287 (p0) outliers start: 58 outliers final: 43 residues processed: 403 average time/residue: 0.5801 time to fit residues: 274.8357 Evaluate side-chains 405 residues out of total 2607 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 356 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 154 ASN Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 244 ILE Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain I residue 7 ILE Chi-restraints excluded: chain J residue 9 VAL Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 51 MET Chi-restraints excluded: chain J residue 107 THR Chi-restraints excluded: chain J residue 112 ILE Chi-restraints excluded: chain J residue 219 LEU Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain J residue 474 THR Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 29 LYS Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 244 ILE Chi-restraints excluded: chain M residue 54 VAL Chi-restraints excluded: chain M residue 67 THR Chi-restraints excluded: chain M residue 111 LEU Chi-restraints excluded: chain N residue 124 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 77 LEU Chi-restraints excluded: chain P residue 91 ILE Chi-restraints excluded: chain P residue 220 THR Chi-restraints excluded: chain P residue 453 ASP Chi-restraints excluded: chain P residue 463 ASP Chi-restraints excluded: chain P residue 539 ASP Chi-restraints excluded: chain Q residue 27 THR Chi-restraints excluded: chain Q residue 81 VAL Chi-restraints excluded: chain Q residue 116 THR Chi-restraints excluded: chain Q residue 223 GLU Chi-restraints excluded: chain Q residue 236 CYS Chi-restraints excluded: chain Q residue 244 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: [185, 310, 7, 165, 168, 166, 189, 75, 118, 113, 294] chunk 185 optimal weight: 0.9990 chunk 310 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 165 optimal weight: 5.9990 chunk 168 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 189 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 113 optimal weight: 0.0970 chunk 294 optimal weight: 0.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 34 ASN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 132 ASN P 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.174528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.128273 restraints weight = 28222.965| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.08 r_work: 0.3241 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 26877 Z= 0.150 Angle : 1.180 83.686 36511 Z= 0.417 Chirality : 0.058 1.510 3933 Planarity : 0.004 0.057 4540 Dihedral : 12.178 154.967 4571 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.91 % Allowed : 21.69 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.15), residues: 3142 helix: 1.71 (0.13), residues: 1529 sheet: -0.18 (0.37), residues: 199 loop : -2.52 (0.15), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG Q 47 TYR 0.025 0.001 TYR J 540 PHE 0.016 0.001 PHE P 407 TRP 0.020 0.001 TRP H 48 HIS 0.006 0.001 HIS K 203 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (26832) covalent geometry : angle 1.05449 / 0.41 (36436) hydrogen bonds : bond 0.04384 / 2.97 ( 1279) hydrogen bonds : angle 4.05375 / 3.01 ( 3675) metal coordination : bond 0.00484 / 0.34 ( 30) metal coordination : angle 11.73053 / 7.72 ( 75) Misc. bond : bond 0.02889 / 0.98 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9950.43 seconds wall clock time: 169 minutes 30.61 seconds (10170.61 seconds total)