Starting phenix.real_space_refine on Sun Sep 13 08:33:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6wu6_21906/09_2026/6wu6_21906.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wu6_21906/09_2026/6wu6_21906.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6wu6_21906/09_2026/6wu6_21906.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6wu6_21906/09_2026/6wu6_21906.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6wu6_21906/09_2026/6wu6_21906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wu6_21906/09_2026/6wu6_21906.map" model { file = "/net/cci-nas-00/data/ceres_data/6wu6_21906/09_2026/6wu6_21906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wu6_21906/09_2026/6wu6_21906.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.099 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 30 7.16 5 P 6 5.49 5 S 183 5.16 5 Na 3 4.78 5 C 13935 2.51 5 N 3783 2.21 5 O 4029 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21969 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 220} Chain: "C" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 881 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "D" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 836 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 103} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TRP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 3621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3621 Classifications: {'peptide': 470} Link IDs: {'PTRANS': 17, 'TRANS': 452} Chain breaks: 2 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: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEM': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' NA': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 456 SG CYS B 55 31.260 67.146 83.685 1.00 26.52 S ATOM 493 SG CYS B 60 35.168 66.107 84.128 1.00 34.02 S ATOM 591 SG CYS B 75 28.122 64.110 80.931 1.00 51.12 S ATOM 1207 SG CYS B 152 36.471 66.545 73.838 1.00 45.97 S ATOM 1224 SG CYS B 155 41.547 67.041 68.097 1.00 52.57 S ATOM 1185 SG CYS B 149 42.733 69.350 74.019 1.00 38.74 S ATOM 1700 SG CYS B 216 36.947 71.735 69.810 1.00 51.94 S ATOM 1674 SG CYS B 212 40.341 69.545 62.515 1.00 53.33 S ATOM 1628 SG CYS B 206 46.713 69.206 58.702 1.00 58.18 S ATOM 1249 SG CYS B 159 43.877 65.005 61.045 1.00 55.83 S Restraints were copied for chains: F, J, G, K, H, L, E, I Time building chain proxies: 5.32, per 1000 atoms: 0.24 Number of scatterers: 21969 At special positions: 0 Unit cell: (130.68, 136.08, 137.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 30 26.01 S 183 16.00 P 6 15.00 Na 3 11.00 O 4029 8.00 N 3783 7.00 C 13935 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B 303 " pdb="FE3 F3S B 303 " - pdb=" SG CYS B 206 " pdb="FE1 F3S B 303 " - pdb=" SG CYS B 212 " pdb="FE4 F3S B 303 " - pdb=" SG CYS B 159 " pdb=" F3S F 303 " pdb="FE3 F3S F 303 " - pdb=" SG CYS F 206 " pdb="FE1 F3S F 303 " - pdb=" SG CYS F 212 " pdb="FE4 F3S F 303 " - pdb=" SG CYS F 159 " pdb=" F3S J 303 " pdb="FE3 F3S J 303 " - pdb=" SG CYS J 206 " pdb="FE1 F3S J 303 " - pdb=" SG CYS J 212 " pdb="FE4 F3S J 303 " - pdb=" SG CYS J 159 " pdb=" FES B 301 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 60 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 75 " pdb=" FES F 301 " pdb="FE1 FES F 301 " - pdb=" SG CYS F 60 " pdb="FE2 FES F 301 " - pdb=" SG CYS F 75 " pdb=" FES J 301 " pdb="FE1 FES J 301 " - pdb=" SG CYS J 60 " pdb="FE2 FES J 301 " - pdb=" SG CYS J 75 " pdb=" SF4 B 302 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 216 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 149 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 155 " pdb=" SF4 F 302 " pdb="FE1 SF4 F 302 " - pdb=" SG CYS F 152 " pdb="FE4 SF4 F 302 " - pdb=" SG CYS F 216 " pdb="FE3 SF4 F 302 " - pdb=" SG CYS F 149 " pdb="FE2 SF4 F 302 " - pdb=" SG CYS F 155 " pdb=" SF4 J 302 " pdb="FE1 SF4 J 302 " - pdb=" SG CYS J 152 " pdb="FE4 SF4 J 302 " - pdb=" SG CYS J 216 " pdb="FE3 SF4 J 302 " - pdb=" SG CYS J 149 " pdb="FE2 SF4 J 302 " - pdb=" SG CYS J 155 " Number of angles added : 72 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5112 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 21 sheets defined 50.7% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'B' and resid 34 through 43 Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 139 through 143 Processing helix chain 'B' and resid 153 through 158 removed outlier: 3.769A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 165 removed outlier: 4.434A pdb=" N TRP B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASN B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 184 removed outlier: 3.782A pdb=" N ALA B 178 " --> pdb=" O GLY B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 200 removed outlier: 3.960A pdb=" N ARG B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP B 199 " --> pdb=" O ASP B 195 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA B 200 " --> pdb=" O GLY B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 216 removed outlier: 4.489A pdb=" N SER B 214 " --> pdb=" O MET B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 238 removed outlier: 3.915A pdb=" N ALA B 225 " --> pdb=" O ASN B 221 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B 230 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 53 removed outlier: 3.747A pdb=" N ALA C 26 " --> pdb=" O ILE C 22 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG C 31 " --> pdb=" O SER C 27 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL C 39 " --> pdb=" O VAL C 35 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY C 42 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER C 53 " --> pdb=" O GLY C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 65 removed outlier: 3.899A pdb=" N GLU C 59 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 96 Processing helix chain 'C' and resid 102 through 129 Processing helix chain 'D' and resid 12 through 39 Processing helix chain 'D' and resid 44 through 53 Processing helix chain 'D' and resid 54 through 83 removed outlier: 3.650A pdb=" N LYS D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE D 74 " --> pdb=" O ILE D 70 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 113 Processing helix chain 'F' and resid 34 through 43 Processing helix chain 'F' and resid 107 through 116 Processing helix chain 'F' and resid 139 through 143 Processing helix chain 'F' and resid 153 through 158 removed outlier: 3.770A pdb=" N THR F 157 " --> pdb=" O ALA F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 165 removed outlier: 4.434A pdb=" N TRP F 164 " --> pdb=" O PRO F 160 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASN F 165 " --> pdb=" O SER F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 184 removed outlier: 3.783A pdb=" N ALA F 178 " --> pdb=" O GLY F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 200 removed outlier: 3.961A pdb=" N ARG F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP F 199 " --> pdb=" O ASP F 195 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA F 200 " --> pdb=" O GLY F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 210 through 216 removed outlier: 4.490A pdb=" N SER F 214 " --> pdb=" O MET F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 221 through 238 removed outlier: 3.916A pdb=" N ALA F 225 " --> pdb=" O ASN F 221 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS F 230 " --> pdb=" O ILE F 226 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 53 removed outlier: 3.747A pdb=" N ALA G 26 " --> pdb=" O ILE G 22 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N HIS G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG G 31 " --> pdb=" O SER G 27 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL G 39 " --> pdb=" O VAL G 35 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLY G 42 " --> pdb=" O PHE G 38 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER G 53 " --> pdb=" O GLY G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 65 removed outlier: 3.899A pdb=" N GLU G 59 " --> pdb=" O PRO G 55 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN G 60 " --> pdb=" O GLU G 56 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 96 Processing helix chain 'G' and resid 102 through 129 Processing helix chain 'H' and resid 12 through 39 Processing helix chain 'H' and resid 44 through 53 Processing helix chain 'H' and resid 54 through 83 removed outlier: 3.650A pdb=" N LYS H 58 " --> pdb=" O SER H 54 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE H 74 " --> pdb=" O ILE H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 113 Processing helix chain 'J' and resid 34 through 43 Processing helix chain 'J' and resid 107 through 116 Processing helix chain 'J' and resid 139 through 143 Processing helix chain 'J' and resid 153 through 158 removed outlier: 3.769A pdb=" N THR J 157 " --> pdb=" O ALA J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 165 removed outlier: 4.434A pdb=" N TRP J 164 " --> pdb=" O PRO J 160 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ASN J 165 " --> pdb=" O SER J 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 172 through 184 removed outlier: 3.782A pdb=" N ALA J 178 " --> pdb=" O GLY J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 200 removed outlier: 3.959A pdb=" N ARG J 193 " --> pdb=" O GLU J 189 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP J 199 " --> pdb=" O ASP J 195 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA J 200 " --> pdb=" O GLY J 196 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 216 removed outlier: 4.490A pdb=" N SER J 214 " --> pdb=" O MET J 210 " (cutoff:3.500A) Processing helix chain 'J' and resid 221 through 238 removed outlier: 3.915A pdb=" N ALA J 225 " --> pdb=" O ASN J 221 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS J 230 " --> pdb=" O ILE J 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 53 removed outlier: 3.747A pdb=" N ALA K 26 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N HIS K 30 " --> pdb=" O ALA K 26 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG K 31 " --> pdb=" O SER K 27 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER K 33 " --> pdb=" O LEU K 29 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL K 39 " --> pdb=" O VAL K 35 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLY K 42 " --> pdb=" O PHE K 38 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER K 53 " --> pdb=" O GLY K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 65 removed outlier: 3.899A pdb=" N GLU K 59 " --> pdb=" O PRO K 55 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLN K 60 " --> pdb=" O GLU K 56 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 96 Processing helix chain 'K' and resid 102 through 129 Processing helix chain 'L' and resid 12 through 39 Processing helix chain 'L' and resid 44 through 53 Processing helix chain 'L' and resid 54 through 83 removed outlier: 3.650A pdb=" N LYS L 58 " --> pdb=" O SER L 54 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE L 74 " --> pdb=" O ILE L 70 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 113 Processing helix chain 'A' and resid 17 through 30 removed outlier: 3.922A pdb=" N ARG A 21 " --> pdb=" O GLY A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 48 removed outlier: 5.707A pdb=" N HIS A 45 " --> pdb=" O THR A 42 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N THR A 46 " --> pdb=" O ARG A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 76 removed outlier: 3.597A pdb=" N SER A 76 " --> pdb=" O THR A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 101 Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 140 through 156 Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 223 through 230 Processing helix chain 'A' and resid 402 through 418 removed outlier: 3.880A pdb=" N GLY A 412 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 426 removed outlier: 4.283A pdb=" N GLU A 425 " --> pdb=" O GLU A 421 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 448 removed outlier: 4.188A pdb=" N SER A 440 " --> pdb=" O ASP A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 471 removed outlier: 3.672A pdb=" N ILE A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 494 Processing helix chain 'A' and resid 508 through 530 removed outlier: 3.917A pdb=" N ASP A 517 " --> pdb=" O CYS A 513 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR A 522 " --> pdb=" O ASN A 518 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 523 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 17 through 30 removed outlier: 3.922A pdb=" N ARG E 21 " --> pdb=" O GLY E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 48 removed outlier: 5.708A pdb=" N HIS E 45 " --> pdb=" O THR E 42 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N THR E 46 " --> pdb=" O ARG E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 76 removed outlier: 3.597A pdb=" N SER E 76 " --> pdb=" O THR E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 101 Proline residue: E 93 - end of helix Processing helix chain 'E' and resid 140 through 156 Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 223 through 230 Processing helix chain 'E' and resid 402 through 418 removed outlier: 3.880A pdb=" N GLY E 412 " --> pdb=" O LEU E 408 " (cutoff:3.500A) Processing helix chain 'E' and resid 419 through 426 removed outlier: 4.283A pdb=" N GLU E 425 " --> pdb=" O GLU E 421 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN E 426 " --> pdb=" O SER E 422 " (cutoff:3.500A) Processing helix chain 'E' and resid 436 through 448 removed outlier: 4.189A pdb=" N SER E 440 " --> pdb=" O ASP E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 471 removed outlier: 3.672A pdb=" N ILE E 459 " --> pdb=" O ASP E 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 494 Processing helix chain 'E' and resid 508 through 530 removed outlier: 3.917A pdb=" N ASP E 517 " --> pdb=" O CYS E 513 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU E 521 " --> pdb=" O ASP E 517 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR E 522 " --> pdb=" O ASN E 518 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA E 523 " --> pdb=" O LEU E 519 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR E 526 " --> pdb=" O THR E 522 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 30 removed outlier: 3.923A pdb=" N ARG I 21 " --> pdb=" O GLY I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 48 removed outlier: 5.707A pdb=" N HIS I 45 " --> pdb=" O THR I 42 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N THR I 46 " --> pdb=" O ARG I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 76 removed outlier: 3.597A pdb=" N SER I 76 " --> pdb=" O THR I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 101 Proline residue: I 93 - end of helix Processing helix chain 'I' and resid 140 through 156 Processing helix chain 'I' and resid 205 through 209 Processing helix chain 'I' and resid 223 through 230 Processing helix chain 'I' and resid 402 through 418 removed outlier: 3.880A pdb=" N GLY I 412 " --> pdb=" O LEU I 408 " (cutoff:3.500A) Processing helix chain 'I' and resid 419 through 426 removed outlier: 4.283A pdb=" N GLU I 425 " --> pdb=" O GLU I 421 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLN I 426 " --> pdb=" O SER I 422 " (cutoff:3.500A) Processing helix chain 'I' and resid 436 through 448 removed outlier: 4.188A pdb=" N SER I 440 " --> pdb=" O ASP I 436 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 471 removed outlier: 3.671A pdb=" N ILE I 459 " --> pdb=" O ASP I 455 " (cutoff:3.500A) Processing helix chain 'I' and resid 476 through 494 Processing helix chain 'I' and resid 508 through 530 removed outlier: 3.917A pdb=" N ASP I 517 " --> pdb=" O CYS I 513 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU I 521 " --> pdb=" O ASP I 517 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR I 522 " --> pdb=" O ASN I 518 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA I 523 " --> pdb=" O LEU I 519 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR I 526 " --> pdb=" O THR I 522 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AA3, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AA4, first strand: chain 'F' and resid 66 through 67 Processing sheet with id=AA5, first strand: chain 'J' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'J' and resid 66 through 67 Processing sheet with id=AA7, first strand: chain 'A' and resid 5 through 13 removed outlier: 7.716A pdb=" N VAL A 5 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE A 193 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLU A 7 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA A 195 " --> pdb=" O GLU A 7 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP A 9 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A 197 " --> pdb=" O ASP A 9 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 5 through 13 removed outlier: 7.716A pdb=" N VAL A 5 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE A 193 " --> pdb=" O VAL A 5 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLU A 7 " --> pdb=" O PHE A 193 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA A 195 " --> pdb=" O GLU A 7 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP A 9 " --> pdb=" O ALA A 195 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A 197 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 28.062A pdb=" N VAL A 378 " --> pdb=" O TYR A 192 " (cutoff:3.500A) removed outlier: 22.230A pdb=" N LYS A 194 " --> pdb=" O VAL A 378 " (cutoff:3.500A) removed outlier: 18.194A pdb=" N VAL A 380 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 10.852A pdb=" N ARG A 196 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY A 382 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR A 198 " --> pdb=" O GLY A 382 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ALA A 368 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 116 through 117 Processing sheet with id=AB1, first strand: chain 'A' and resid 239 through 242 removed outlier: 6.512A pdb=" N GLN A 240 " --> pdb=" O HIS A 354 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 556 through 560 Processing sheet with id=AB3, first strand: chain 'E' and resid 5 through 13 removed outlier: 7.716A pdb=" N VAL E 5 " --> pdb=" O VAL E 191 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N PHE E 193 " --> pdb=" O VAL E 5 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLU E 7 " --> pdb=" O PHE E 193 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA E 195 " --> pdb=" O GLU E 7 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP E 9 " --> pdb=" O ALA E 195 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA E 197 " --> pdb=" O ASP E 9 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 5 through 13 removed outlier: 7.716A pdb=" N VAL E 5 " --> pdb=" O VAL E 191 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N PHE E 193 " --> pdb=" O VAL E 5 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLU E 7 " --> pdb=" O PHE E 193 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA E 195 " --> pdb=" O GLU E 7 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP E 9 " --> pdb=" O ALA E 195 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA E 197 " --> pdb=" O ASP E 9 " (cutoff:3.500A) removed outlier: 28.062A pdb=" N VAL E 378 " --> pdb=" O TYR E 192 " (cutoff:3.500A) removed outlier: 22.230A pdb=" N LYS E 194 " --> pdb=" O VAL E 378 " (cutoff:3.500A) removed outlier: 18.194A pdb=" N VAL E 380 " --> pdb=" O LYS E 194 " (cutoff:3.500A) removed outlier: 10.852A pdb=" N ARG E 196 " --> pdb=" O VAL E 380 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLY E 382 " --> pdb=" O ARG E 196 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR E 198 " --> pdb=" O GLY E 382 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ALA E 368 " --> pdb=" O VAL E 380 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 116 through 117 Processing sheet with id=AB6, first strand: chain 'E' and resid 239 through 242 removed outlier: 6.512A pdb=" N GLN E 240 " --> pdb=" O HIS E 354 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 556 through 560 Processing sheet with id=AB8, first strand: chain 'I' and resid 5 through 13 removed outlier: 7.716A pdb=" N VAL I 5 " --> pdb=" O VAL I 191 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE I 193 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLU I 7 " --> pdb=" O PHE I 193 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA I 195 " --> pdb=" O GLU I 7 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP I 9 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA I 197 " --> pdb=" O ASP I 9 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 5 through 13 removed outlier: 7.716A pdb=" N VAL I 5 " --> pdb=" O VAL I 191 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE I 193 " --> pdb=" O VAL I 5 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N GLU I 7 " --> pdb=" O PHE I 193 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA I 195 " --> pdb=" O GLU I 7 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASP I 9 " --> pdb=" O ALA I 195 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA I 197 " --> pdb=" O ASP I 9 " (cutoff:3.500A) removed outlier: 28.063A pdb=" N VAL I 378 " --> pdb=" O TYR I 192 " (cutoff:3.500A) removed outlier: 22.230A pdb=" N LYS I 194 " --> pdb=" O VAL I 378 " (cutoff:3.500A) removed outlier: 18.194A pdb=" N VAL I 380 " --> pdb=" O LYS I 194 " (cutoff:3.500A) removed outlier: 10.852A pdb=" N ARG I 196 " --> pdb=" O VAL I 380 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N GLY I 382 " --> pdb=" O ARG I 196 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N THR I 198 " --> pdb=" O GLY I 382 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ALA I 368 " --> pdb=" O VAL I 380 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 116 through 117 Processing sheet with id=AC2, first strand: chain 'I' and resid 239 through 242 removed outlier: 6.513A pdb=" N GLN I 240 " --> pdb=" O HIS I 354 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 556 through 560 1041 hydrogen bonds defined for protein. 2988 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: 3.40 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.76: 22140 1.76 - 2.30: 318 2.30 - 2.84: 6 2.84 - 3.38: 0 3.38 - 3.93: 9 Bond restraints: 22473 Sorted by residual: bond pdb=" S4 F3S B 303 " pdb="FE1 F3S B 303 " ideal model delta sigma weight residual 2.233 3.927 -1.694 2.00e-02 2.50e+03 7.17e+03 bond pdb=" S4 F3S F 303 " pdb="FE1 F3S F 303 " ideal model delta sigma weight residual 2.233 3.927 -1.694 2.00e-02 2.50e+03 7.17e+03 bond pdb=" S4 F3S J 303 " pdb="FE1 F3S J 303 " ideal model delta sigma weight residual 2.233 3.926 -1.693 2.00e-02 2.50e+03 7.17e+03 bond pdb=" S2 F3S J 303 " pdb="FE3 F3S J 303 " ideal model delta sigma weight residual 2.300 3.925 -1.625 2.00e-02 2.50e+03 6.60e+03 bond pdb=" S2 F3S B 303 " pdb="FE3 F3S B 303 " ideal model delta sigma weight residual 2.300 3.925 -1.625 2.00e-02 2.50e+03 6.60e+03 ... (remaining 22468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.17: 30516 10.17 - 20.34: 15 20.34 - 30.51: 9 30.51 - 40.68: 15 40.68 - 50.85: 6 Bond angle restraints: 30561 Sorted by residual: angle pdb=" S1 F3S F 303 " pdb="FE4 F3S F 303 " pdb=" S3 F3S F 303 " ideal model delta sigma weight residual 114.75 63.90 50.85 3.00e+00 1.11e-01 2.87e+02 angle pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " pdb=" S3 F3S B 303 " ideal model delta sigma weight residual 114.75 63.91 50.84 3.00e+00 1.11e-01 2.87e+02 angle pdb=" S1 F3S J 303 " pdb="FE4 F3S J 303 " pdb=" S3 F3S J 303 " ideal model delta sigma weight residual 114.75 63.92 50.83 3.00e+00 1.11e-01 2.87e+02 angle pdb=" S3 F3S F 303 " pdb="FE1 F3S F 303 " pdb=" S4 F3S F 303 " ideal model delta sigma weight residual 112.59 64.06 48.53 3.00e+00 1.11e-01 2.62e+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 64.07 48.52 3.00e+00 1.11e-01 2.62e+02 ... (remaining 30556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 11537 17.61 - 35.21: 1270 35.21 - 52.81: 273 52.81 - 70.42: 39 70.42 - 88.02: 51 Dihedral angle restraints: 13170 sinusoidal: 5214 harmonic: 7956 Sorted by residual: dihedral pdb=" CA SER F 54 " pdb=" C SER F 54 " pdb=" N CYS F 55 " pdb=" CA CYS F 55 " ideal model delta harmonic sigma weight residual -180.00 -150.12 -29.88 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA SER J 54 " pdb=" C SER J 54 " pdb=" N CYS J 55 " pdb=" CA CYS J 55 " ideal model delta harmonic sigma weight residual 180.00 -150.13 -29.87 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA SER B 54 " pdb=" C SER B 54 " pdb=" N CYS B 55 " pdb=" CA CYS B 55 " ideal model delta harmonic sigma weight residual -180.00 -150.15 -29.85 0 5.00e+00 4.00e-02 3.56e+01 ... (remaining 13167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.650: 3405 0.650 - 1.300: 0 1.300 - 1.949: 0 1.949 - 2.599: 0 2.599 - 3.249: 3 Chirality restraints: 3408 Sorted by residual: 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 7.52 3.25 2.00e-01 2.50e+01 2.64e+02 chirality pdb=" S2 F3S J 303 " pdb="FE1 F3S J 303 " pdb="FE3 F3S J 303 " pdb="FE4 F3S J 303 " both_signs ideal model delta sigma weight residual False 10.77 7.52 3.25 2.00e-01 2.50e+01 2.64e+02 chirality pdb=" S2 F3S F 303 " pdb="FE1 F3S F 303 " pdb="FE3 F3S F 303 " pdb="FE4 F3S F 303 " both_signs ideal model delta sigma weight residual False 10.77 7.52 3.25 2.00e-01 2.50e+01 2.64e+02 ... (remaining 3405 not shown) Planarity restraints: 3879 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 92 " 0.048 5.00e-02 4.00e+02 7.34e-02 8.63e+00 pdb=" N PRO B 93 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 93 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 93 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG F 92 " 0.048 5.00e-02 4.00e+02 7.34e-02 8.63e+00 pdb=" N PRO F 93 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO F 93 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 93 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG J 92 " 0.048 5.00e-02 4.00e+02 7.34e-02 8.63e+00 pdb=" N PRO J 93 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO J 93 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO J 93 " 0.040 5.00e-02 4.00e+02 ... (remaining 3876 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 4197 2.76 - 3.30: 24231 3.30 - 3.83: 37134 3.83 - 4.37: 42216 4.37 - 4.90: 68711 Nonbonded interactions: 176489 Sorted by model distance: nonbonded pdb=" S1 F3S J 303 " pdb="FE1 F3S J 303 " model vdw 2.228 2.688 nonbonded pdb=" S1 F3S B 303 " pdb="FE1 F3S B 303 " model vdw 2.228 2.688 nonbonded pdb=" S1 F3S F 303 " pdb="FE1 F3S F 303 " model vdw 2.229 2.688 nonbonded pdb=" N LYS I 171 " pdb=" OD2 ASP I 436 " model vdw 2.233 3.120 nonbonded pdb=" N LYS E 171 " pdb=" OD2 ASP E 436 " model vdw 2.234 3.120 ... (remaining 176484 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: 0.06 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' } ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.230 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 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 : 0.038 1.694 22503 Z= 1.806 Angle : 2.180 54.185 30633 Z= 0.712 Chirality : 0.110 3.249 3408 Planarity : 0.006 0.073 3879 Dihedral : 16.141 88.025 8058 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 26.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.11 % Favored : 86.89 % Rotamer: Outliers : 1.34 % Allowed : 10.77 % Favored : 87.89 % 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: -4.47 (0.13), residues: 2745 helix: -2.23 (0.12), residues: 1296 sheet: -3.30 (0.44), residues: 99 loop : -3.78 (0.14), residues: 1350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 196 TYR 0.015 0.002 TYR L 29 PHE 0.026 0.002 PHE H 37 TRP 0.014 0.002 TRP H 48 HIS 0.007 0.001 HIS H 71 Details of bonding type rmsd/Z covalent geometry : bond 0.03348 / 1.67 (22473) covalent geometry : angle 1.50448 / 0.70 (30561) hydrogen bonds : bond 0.14918 / 9.77 ( 1032) hydrogen bonds : angle 7.18997 / 5.12 ( 2988) metal coordination : bond 0.52386 / 33.44 ( 27) metal coordination : angle 32.58937 / 19.95 ( 72) Misc. bond : bond 0.43847 / 21.98 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 529 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 MET cc_start: 0.5720 (mmt) cc_final: 0.5419 (mmt) REVERT: F 1 MET cc_start: 0.3589 (ttt) cc_final: 0.3370 (ttt) REVERT: F 53 ARG cc_start: 0.6447 (pmt-80) cc_final: 0.6115 (ptt90) REVERT: J 223 THR cc_start: 0.7734 (m) cc_final: 0.7521 (m) REVERT: A 43 ARG cc_start: 0.8162 (mpt90) cc_final: 0.6979 (mmt180) REVERT: A 139 ASP cc_start: 0.5862 (t0) cc_final: 0.5605 (t0) REVERT: A 156 ASN cc_start: 0.6949 (t0) cc_final: 0.6204 (m-40) REVERT: A 356 MET cc_start: 0.6641 (ttp) cc_final: 0.6358 (ttp) REVERT: A 392 VAL cc_start: 0.6831 (p) cc_final: 0.5779 (t) REVERT: A 480 MET cc_start: 0.6056 (ttp) cc_final: 0.5736 (ttp) REVERT: E 43 ARG cc_start: 0.8111 (mpt90) cc_final: 0.6975 (mmt180) REVERT: E 53 ILE cc_start: 0.8174 (tp) cc_final: 0.7953 (tp) REVERT: E 156 ASN cc_start: 0.6986 (t0) cc_final: 0.6486 (m-40) REVERT: E 185 ILE cc_start: 0.6998 (tt) cc_final: 0.6760 (tt) REVERT: E 356 MET cc_start: 0.6223 (ttp) cc_final: 0.6017 (ttp) REVERT: E 392 VAL cc_start: 0.6742 (p) cc_final: 0.5650 (t) REVERT: E 454 GLU cc_start: 0.4283 (OUTLIER) cc_final: 0.3895 (tp30) REVERT: E 461 LYS cc_start: 0.7562 (mmpt) cc_final: 0.7361 (tttp) REVERT: I 43 ARG cc_start: 0.8330 (mpt90) cc_final: 0.7059 (mmt180) REVERT: I 63 ASP cc_start: 0.5905 (p0) cc_final: 0.5298 (p0) REVERT: I 156 ASN cc_start: 0.6887 (t0) cc_final: 0.6363 (m-40) REVERT: I 356 MET cc_start: 0.6463 (ttp) cc_final: 0.6047 (ttp) REVERT: I 392 VAL cc_start: 0.6771 (p) cc_final: 0.5671 (t) REVERT: I 461 LYS cc_start: 0.7609 (mmpt) cc_final: 0.7356 (tttp) REVERT: I 475 ARG cc_start: 0.4393 (ptp-170) cc_final: 0.3213 (ptp-170) outliers start: 31 outliers final: 15 residues processed: 546 average time/residue: 0.1578 time to fit residues: 132.5421 Evaluate side-chains 459 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 443 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain F residue 201 PHE Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 115 GLU Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 454 GLU Chi-restraints excluded: chain I residue 212 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 7.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 113 GLN C 30 HIS F 113 GLN G 30 HIS J 113 GLN K 30 HIS A 25 GLN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 556 HIS E 25 GLN ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 518 ASN ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 556 HIS I 25 GLN ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 556 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.247550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.210599 restraints weight = 33239.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.207944 restraints weight = 33320.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.210368 restraints weight = 26955.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.210507 restraints weight = 18649.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.211064 restraints weight = 17145.249| |-----------------------------------------------------------------------------| r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.192 22503 Z= 0.286 Angle : 1.641 56.397 30633 Z= 0.528 Chirality : 0.090 2.622 3408 Planarity : 0.006 0.074 3879 Dihedral : 9.634 97.388 3091 Min Nonbonded Distance : 1.554 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.97 % Favored : 89.03 % Rotamer: Outliers : 3.33 % Allowed : 18.85 % Favored : 77.82 % 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: -3.15 (0.14), residues: 2745 helix: -0.96 (0.13), residues: 1326 sheet: -3.54 (0.41), residues: 105 loop : -3.26 (0.15), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 228 TYR 0.034 0.002 TYR H 29 PHE 0.032 0.003 PHE H 51 TRP 0.044 0.002 TRP F 163 HIS 0.013 0.002 HIS E 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00630 / 0.29 (22473) covalent geometry : angle 1.24427 / 0.52 (30561) hydrogen bonds : bond 0.05609 / 3.69 ( 1032) hydrogen bonds : angle 5.56245 / 3.93 ( 2988) metal coordination : bond 0.02532 / 1.66 ( 27) metal coordination : angle 22.11192 / 13.50 ( 72) Misc. bond : bond 0.10919 / 5.39 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 462 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 20 MET cc_start: 0.6160 (mmt) cc_final: 0.5859 (mmt) REVERT: F 53 ARG cc_start: 0.6233 (pmt-80) cc_final: 0.5865 (ptt90) REVERT: H 29 TYR cc_start: 0.8203 (t80) cc_final: 0.7509 (t80) REVERT: H 83 TYR cc_start: 0.8022 (m-10) cc_final: 0.7660 (m-10) REVERT: J 9 ARG cc_start: 0.5570 (ttp80) cc_final: 0.5310 (mtp180) REVERT: J 23 TYR cc_start: 0.4724 (OUTLIER) cc_final: 0.4364 (m-10) REVERT: K 28 ILE cc_start: 0.7433 (mm) cc_final: 0.7188 (mt) REVERT: A 43 ARG cc_start: 0.8266 (mpt90) cc_final: 0.7160 (mmt180) REVERT: A 139 ASP cc_start: 0.6012 (t0) cc_final: 0.5778 (t0) REVERT: A 392 VAL cc_start: 0.7078 (p) cc_final: 0.6223 (t) REVERT: A 461 LYS cc_start: 0.7692 (mmpt) cc_final: 0.7315 (tttp) REVERT: E 86 GLU cc_start: 0.7418 (tp30) cc_final: 0.7092 (tp30) REVERT: E 155 LYS cc_start: 0.8099 (tmmt) cc_final: 0.7802 (tmmt) REVERT: E 235 ASP cc_start: 0.7139 (t0) cc_final: 0.6769 (t70) REVERT: E 356 MET cc_start: 0.6217 (ttp) cc_final: 0.5913 (ttp) REVERT: E 392 VAL cc_start: 0.6959 (p) cc_final: 0.6026 (t) REVERT: E 461 LYS cc_start: 0.7656 (mmpt) cc_final: 0.7369 (tttp) REVERT: E 465 GLU cc_start: 0.6538 (tp30) cc_final: 0.6282 (tp30) REVERT: E 475 ARG cc_start: 0.4076 (ptp-170) cc_final: 0.2679 (ptp-170) REVERT: E 499 LEU cc_start: 0.6721 (tp) cc_final: 0.6392 (tt) REVERT: I 43 ARG cc_start: 0.8447 (mpt90) cc_final: 0.7482 (mmt180) REVERT: I 63 ASP cc_start: 0.6574 (p0) cc_final: 0.6024 (p0) REVERT: I 356 MET cc_start: 0.6563 (ttp) cc_final: 0.6001 (ttp) REVERT: I 392 VAL cc_start: 0.6973 (p) cc_final: 0.6062 (t) REVERT: I 461 LYS cc_start: 0.7972 (mmpt) cc_final: 0.7595 (tttp) REVERT: I 465 GLU cc_start: 0.6683 (tp30) cc_final: 0.6185 (tp30) REVERT: I 475 ARG cc_start: 0.4063 (ptp-170) cc_final: 0.2792 (ptp-170) outliers start: 77 outliers final: 53 residues processed: 498 average time/residue: 0.1433 time to fit residues: 112.2408 Evaluate side-chains 490 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 436 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 212 CYS Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain J residue 23 TYR Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 212 CYS Chi-restraints excluded: chain J residue 226 ILE Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 509 GLN Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 389 ILE Chi-restraints excluded: chain E residue 520 MET Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 389 ILE Chi-restraints excluded: chain I residue 520 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 53 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 chunk 200 optimal weight: 6.9990 chunk 150 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 229 optimal weight: 5.9990 chunk 144 optimal weight: 30.0000 chunk 121 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 94 GLN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.248377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.208380 restraints weight = 33213.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.209292 restraints weight = 25500.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.211157 restraints weight = 16940.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.210094 restraints weight = 15194.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.210535 restraints weight = 13735.302| |-----------------------------------------------------------------------------| r_work (final): 0.4213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.144 22503 Z= 0.208 Angle : 1.472 84.548 30633 Z= 0.499 Chirality : 0.059 1.365 3408 Planarity : 0.006 0.071 3879 Dihedral : 8.707 89.123 3076 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 3.76 % Allowed : 21.44 % Favored : 74.79 % 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: -2.59 (0.15), residues: 2745 helix: -0.42 (0.13), residues: 1323 sheet: -3.41 (0.42), residues: 105 loop : -3.05 (0.15), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 21 TYR 0.023 0.002 TYR H 29 PHE 0.020 0.002 PHE L 36 TRP 0.027 0.002 TRP F 163 HIS 0.010 0.002 HIS A 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 (22473) covalent geometry : angle 1.20913 / 0.49 (30561) hydrogen bonds : bond 0.05118 / 3.37 ( 1032) hydrogen bonds : angle 5.21150 / 3.68 ( 2988) metal coordination : bond 0.01038 / 0.64 ( 27) metal coordination : angle 17.35704 / 10.76 ( 72) Misc. bond : bond 0.10647 / 5.26 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 439 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 23 TYR cc_start: 0.4282 (OUTLIER) cc_final: 0.3945 (m-10) REVERT: D 37 PHE cc_start: 0.5287 (OUTLIER) cc_final: 0.3841 (t80) REVERT: F 20 MET cc_start: 0.4876 (mmt) cc_final: 0.4338 (mmp) REVERT: F 53 ARG cc_start: 0.6164 (pmt-80) cc_final: 0.5732 (ptt90) REVERT: G 74 MET cc_start: 0.8087 (mmt) cc_final: 0.7809 (mmm) REVERT: H 29 TYR cc_start: 0.8162 (t80) cc_final: 0.7675 (t80) REVERT: J 9 ARG cc_start: 0.5658 (ttp80) cc_final: 0.5136 (mtp180) REVERT: J 23 TYR cc_start: 0.4650 (OUTLIER) cc_final: 0.4107 (m-10) REVERT: L 29 TYR cc_start: 0.8182 (t80) cc_final: 0.7631 (t80) REVERT: A 20 MET cc_start: 0.7459 (mmt) cc_final: 0.7124 (mmt) REVERT: A 43 ARG cc_start: 0.8318 (mpt90) cc_final: 0.7153 (mmt180) REVERT: A 86 GLU cc_start: 0.7226 (tp30) cc_final: 0.7015 (tp30) REVERT: A 139 ASP cc_start: 0.5983 (t70) cc_final: 0.5737 (t0) REVERT: A 392 VAL cc_start: 0.6903 (p) cc_final: 0.5994 (t) REVERT: A 461 LYS cc_start: 0.7678 (mmpt) cc_final: 0.7354 (tttp) REVERT: E 69 MET cc_start: 0.6708 (mtt) cc_final: 0.6303 (mtt) REVERT: E 235 ASP cc_start: 0.7129 (t0) cc_final: 0.6737 (t70) REVERT: E 236 MET cc_start: 0.6161 (OUTLIER) cc_final: 0.5319 (mtm) REVERT: E 392 VAL cc_start: 0.6906 (p) cc_final: 0.6010 (t) REVERT: E 461 LYS cc_start: 0.7711 (mmpt) cc_final: 0.7426 (tttp) REVERT: E 465 GLU cc_start: 0.6634 (tp30) cc_final: 0.6210 (tp30) REVERT: E 475 ARG cc_start: 0.4116 (ptp-170) cc_final: 0.2681 (ptp-170) REVERT: E 499 LEU cc_start: 0.6576 (tp) cc_final: 0.6203 (tt) REVERT: I 43 ARG cc_start: 0.8476 (mpt90) cc_final: 0.7609 (mmt180) REVERT: I 63 ASP cc_start: 0.6534 (p0) cc_final: 0.6080 (p0) REVERT: I 69 MET cc_start: 0.6582 (mtt) cc_final: 0.6110 (mtt) REVERT: I 145 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6942 (tp) REVERT: I 236 MET cc_start: 0.5752 (mmm) cc_final: 0.5438 (mpp) REVERT: I 356 MET cc_start: 0.6390 (ttp) cc_final: 0.6078 (ttp) REVERT: I 392 VAL cc_start: 0.6830 (p) cc_final: 0.5928 (t) REVERT: I 461 LYS cc_start: 0.7961 (mmpt) cc_final: 0.7592 (tttp) outliers start: 87 outliers final: 65 residues processed: 494 average time/residue: 0.1477 time to fit residues: 114.5557 Evaluate side-chains 490 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 420 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 212 CYS Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 60 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 23 TYR Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 212 CYS Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 52 PHE Chi-restraints excluded: chain L residue 60 PHE Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 85 ILE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 520 MET Chi-restraints excluded: chain E residue 531 ASN Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 389 ILE Chi-restraints excluded: chain I residue 520 MET Chi-restraints excluded: chain I residue 531 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 214 optimal weight: 8.9990 chunk 226 optimal weight: 6.9990 chunk 202 optimal weight: 0.7980 chunk 97 optimal weight: 0.0010 chunk 121 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 175 optimal weight: 40.0000 chunk 185 optimal weight: 30.0000 chunk 16 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 overall best weight: 3.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 94 GLN A 25 GLN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 HIS ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 HIS ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.249497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.209698 restraints weight = 33037.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.209733 restraints weight = 26704.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.212062 restraints weight = 18395.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.211379 restraints weight = 15078.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.211822 restraints weight = 14073.272| |-----------------------------------------------------------------------------| r_work (final): 0.4220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 22503 Z= 0.192 Angle : 1.428 83.311 30633 Z= 0.479 Chirality : 0.060 1.450 3408 Planarity : 0.005 0.068 3879 Dihedral : 8.482 88.533 3073 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 4.45 % Allowed : 22.61 % Favored : 72.94 % 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: -2.24 (0.15), residues: 2745 helix: -0.09 (0.14), residues: 1326 sheet: -3.38 (0.42), residues: 105 loop : -2.90 (0.15), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 224 TYR 0.021 0.002 TYR H 29 PHE 0.020 0.002 PHE A 506 TRP 0.019 0.001 TRP F 163 HIS 0.008 0.001 HIS E 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (22473) covalent geometry : angle 1.17635 / 0.47 (30561) hydrogen bonds : bond 0.04742 / 3.13 ( 1032) hydrogen bonds : angle 4.99695 / 3.54 ( 2988) metal coordination : bond 0.01353 / 0.86 ( 27) metal coordination : angle 16.73221 / 10.56 ( 72) Misc. bond : bond 0.08529 / 4.21 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 429 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 ARG cc_start: 0.5699 (ttp80) cc_final: 0.5300 (mtp180) REVERT: B 10 TYR cc_start: 0.5283 (p90) cc_final: 0.4947 (p90) REVERT: B 224 ARG cc_start: 0.7240 (tpt170) cc_final: 0.6606 (tpt90) REVERT: D 37 PHE cc_start: 0.5221 (OUTLIER) cc_final: 0.3788 (t80) REVERT: F 9 ARG cc_start: 0.5915 (ttp-170) cc_final: 0.5319 (mtp180) REVERT: F 20 MET cc_start: 0.4815 (mmt) cc_final: 0.4303 (mmp) REVERT: G 78 LEU cc_start: 0.6059 (OUTLIER) cc_final: 0.5594 (mp) REVERT: H 29 TYR cc_start: 0.8106 (t80) cc_final: 0.7626 (t80) REVERT: J 9 ARG cc_start: 0.5626 (ttp80) cc_final: 0.5395 (mtp180) REVERT: J 23 TYR cc_start: 0.4314 (OUTLIER) cc_final: 0.3870 (m-10) REVERT: K 29 LEU cc_start: 0.6480 (OUTLIER) cc_final: 0.6155 (mm) REVERT: L 29 TYR cc_start: 0.8113 (t80) cc_final: 0.7560 (t80) REVERT: A 43 ARG cc_start: 0.8319 (mpt90) cc_final: 0.6920 (mmt180) REVERT: A 86 GLU cc_start: 0.7036 (tp30) cc_final: 0.6824 (tp30) REVERT: A 139 ASP cc_start: 0.6110 (t70) cc_final: 0.5856 (t0) REVERT: A 155 LYS cc_start: 0.8186 (tmmt) cc_final: 0.7647 (tmmt) REVERT: A 235 ASP cc_start: 0.7164 (t0) cc_final: 0.6727 (t70) REVERT: A 392 VAL cc_start: 0.6812 (p) cc_final: 0.5889 (t) REVERT: A 420 GLN cc_start: 0.8533 (pm20) cc_final: 0.8078 (mp10) REVERT: A 461 LYS cc_start: 0.7594 (mmpt) cc_final: 0.7304 (tttp) REVERT: A 463 LEU cc_start: 0.5540 (OUTLIER) cc_final: 0.5218 (tt) REVERT: E 69 MET cc_start: 0.6633 (mtt) cc_final: 0.6162 (mtt) REVERT: E 235 ASP cc_start: 0.7136 (t0) cc_final: 0.6657 (t70) REVERT: E 236 MET cc_start: 0.6044 (OUTLIER) cc_final: 0.5178 (mtm) REVERT: E 392 VAL cc_start: 0.6847 (p) cc_final: 0.5925 (t) REVERT: E 461 LYS cc_start: 0.7753 (mmpt) cc_final: 0.7486 (tttp) REVERT: E 475 ARG cc_start: 0.4041 (OUTLIER) cc_final: 0.2815 (ptp-170) REVERT: E 499 LEU cc_start: 0.6477 (tp) cc_final: 0.6036 (tt) REVERT: I 43 ARG cc_start: 0.8426 (mpt90) cc_final: 0.7505 (mmt180) REVERT: I 63 ASP cc_start: 0.6588 (p0) cc_final: 0.6280 (p0) REVERT: I 69 MET cc_start: 0.6616 (mtt) cc_final: 0.6175 (mtt) REVERT: I 236 MET cc_start: 0.6078 (mmm) cc_final: 0.5795 (mpp) REVERT: I 356 MET cc_start: 0.6430 (ttp) cc_final: 0.6216 (ttp) REVERT: I 392 VAL cc_start: 0.6611 (p) cc_final: 0.5664 (t) REVERT: I 461 LYS cc_start: 0.7875 (mmpt) cc_final: 0.7531 (tttp) REVERT: I 465 GLU cc_start: 0.6701 (tp30) cc_final: 0.6248 (tp30) outliers start: 103 outliers final: 72 residues processed: 496 average time/residue: 0.1468 time to fit residues: 114.8303 Evaluate side-chains 495 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 416 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 TYR Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 60 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain J residue 23 TYR Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 212 CYS Chi-restraints excluded: chain J residue 226 ILE Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 52 PHE Chi-restraints excluded: chain L residue 60 PHE Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 109 PHE Chi-restraints excluded: chain L residue 111 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 236 MET Chi-restraints excluded: chain E residue 377 ASP Chi-restraints excluded: chain E residue 475 ARG Chi-restraints excluded: chain E residue 520 MET Chi-restraints excluded: chain E residue 531 ASN Chi-restraints excluded: chain E residue 540 HIS Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 520 MET Chi-restraints excluded: chain I residue 531 ASN Chi-restraints excluded: chain I residue 540 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 34 optimal weight: 6.9990 chunk 79 optimal weight: 7.9990 chunk 238 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 259 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 224 optimal weight: 50.0000 chunk 84 optimal weight: 1.9990 chunk 239 optimal weight: 9.9990 chunk 122 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 94 GLN A 45 HIS ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 HIS ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 ASN ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 214 ASN ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.250356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.210969 restraints weight = 33018.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.211239 restraints weight = 25503.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.213325 restraints weight = 17692.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.212960 restraints weight = 14953.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.213237 restraints weight = 12999.652| |-----------------------------------------------------------------------------| r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6574 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 22503 Z= 0.174 Angle : 1.421 84.188 30633 Z= 0.470 Chirality : 0.059 1.458 3408 Planarity : 0.005 0.065 3879 Dihedral : 8.298 88.204 3073 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 4.50 % Allowed : 23.87 % Favored : 71.64 % 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: -1.98 (0.15), residues: 2745 helix: 0.16 (0.14), residues: 1335 sheet: -3.36 (0.43), residues: 105 loop : -2.82 (0.15), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 569 TYR 0.023 0.001 TYR H 29 PHE 0.021 0.001 PHE I 506 TRP 0.037 0.002 TRP A 553 HIS 0.008 0.001 HIS E 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (22473) covalent geometry : angle 1.16063 / 0.46 (30561) hydrogen bonds : bond 0.04430 / 2.93 ( 1032) hydrogen bonds : angle 4.79666 / 3.41 ( 2988) metal coordination : bond 0.01287 / 0.82 ( 27) metal coordination : angle 16.96410 / 11.00 ( 72) Misc. bond : bond 0.06956 / 3.44 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 433 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 ARG cc_start: 0.5703 (ttp80) cc_final: 0.5379 (mtp180) REVERT: B 10 TYR cc_start: 0.5466 (p90) cc_final: 0.5077 (p90) REVERT: B 224 ARG cc_start: 0.7241 (tpt170) cc_final: 0.6893 (tpt90) REVERT: B 228 HIS cc_start: 0.6419 (t-170) cc_final: 0.6159 (t70) REVERT: C 29 LEU cc_start: 0.6421 (OUTLIER) cc_final: 0.6074 (mm) REVERT: D 37 PHE cc_start: 0.5334 (OUTLIER) cc_final: 0.4030 (t80) REVERT: F 9 ARG cc_start: 0.5886 (ttp-170) cc_final: 0.5508 (ttp-170) REVERT: F 20 MET cc_start: 0.4848 (mmt) cc_final: 0.4363 (mmp) REVERT: F 36 LEU cc_start: 0.1082 (OUTLIER) cc_final: 0.0585 (mt) REVERT: G 78 LEU cc_start: 0.5932 (OUTLIER) cc_final: 0.5480 (mp) REVERT: H 29 TYR cc_start: 0.8060 (t80) cc_final: 0.7749 (t80) REVERT: J 23 TYR cc_start: 0.4477 (OUTLIER) cc_final: 0.3942 (m-10) REVERT: K 78 LEU cc_start: 0.5960 (OUTLIER) cc_final: 0.5525 (mp) REVERT: L 29 TYR cc_start: 0.8024 (t80) cc_final: 0.7411 (t80) REVERT: A 20 MET cc_start: 0.7493 (OUTLIER) cc_final: 0.7264 (mmt) REVERT: A 43 ARG cc_start: 0.8267 (mpt90) cc_final: 0.6465 (mmt180) REVERT: A 235 ASP cc_start: 0.6996 (t0) cc_final: 0.6609 (t70) REVERT: A 392 VAL cc_start: 0.6667 (p) cc_final: 0.5785 (t) REVERT: A 405 LEU cc_start: 0.5057 (mt) cc_final: 0.4079 (mp) REVERT: A 420 GLN cc_start: 0.8509 (pm20) cc_final: 0.8074 (mp10) REVERT: A 461 LYS cc_start: 0.7624 (mmpt) cc_final: 0.7363 (tttp) REVERT: A 463 LEU cc_start: 0.5532 (OUTLIER) cc_final: 0.5206 (tt) REVERT: E 69 MET cc_start: 0.6488 (mtt) cc_final: 0.6037 (mtt) REVERT: E 235 ASP cc_start: 0.6981 (t0) cc_final: 0.6596 (t70) REVERT: E 392 VAL cc_start: 0.6758 (p) cc_final: 0.5814 (t) REVERT: E 461 LYS cc_start: 0.7656 (mmpt) cc_final: 0.7403 (tttp) REVERT: E 475 ARG cc_start: 0.4008 (OUTLIER) cc_final: 0.2732 (ptp-170) REVERT: E 499 LEU cc_start: 0.6501 (tp) cc_final: 0.6065 (tt) REVERT: I 43 ARG cc_start: 0.8420 (mpt90) cc_final: 0.6990 (mmt180) REVERT: I 63 ASP cc_start: 0.6729 (p0) cc_final: 0.6474 (p0) REVERT: I 69 MET cc_start: 0.6571 (mtt) cc_final: 0.6303 (mtt) REVERT: I 98 GLU cc_start: 0.6998 (tm-30) cc_final: 0.6503 (tm-30) REVERT: I 236 MET cc_start: 0.5951 (mmm) cc_final: 0.5732 (mpp) REVERT: I 392 VAL cc_start: 0.6526 (p) cc_final: 0.5577 (t) REVERT: I 405 LEU cc_start: 0.5211 (mt) cc_final: 0.4301 (mp) REVERT: I 461 LYS cc_start: 0.7796 (mmpt) cc_final: 0.7531 (tttp) outliers start: 104 outliers final: 76 residues processed: 498 average time/residue: 0.1475 time to fit residues: 115.3050 Evaluate side-chains 506 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 421 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 148 GLU Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 60 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain J residue 23 TYR Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 212 CYS Chi-restraints excluded: chain J residue 226 ILE Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 52 PHE Chi-restraints excluded: chain L residue 60 PHE Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 109 PHE Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain E residue 20 MET Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 377 ASP Chi-restraints excluded: chain E residue 475 ARG Chi-restraints excluded: chain E residue 520 MET Chi-restraints excluded: chain E residue 540 HIS Chi-restraints excluded: chain E residue 566 MET Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 475 ARG Chi-restraints excluded: chain I residue 520 MET Chi-restraints excluded: chain I residue 540 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 139 optimal weight: 8.9990 chunk 73 optimal weight: 0.4980 chunk 126 optimal weight: 7.9990 chunk 205 optimal weight: 2.9990 chunk 189 optimal weight: 8.9990 chunk 196 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 220 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 254 optimal weight: 10.0000 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 94 GLN L 94 GLN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 552 ASN E 214 ASN ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4589 r_free = 0.4589 target = 0.250642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.213462 restraints weight = 33270.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.211510 restraints weight = 34364.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.213770 restraints weight = 26310.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.213805 restraints weight = 19073.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.214273 restraints weight = 16814.763| |-----------------------------------------------------------------------------| r_work (final): 0.4251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 22503 Z= 0.176 Angle : 1.384 83.734 30633 Z= 0.467 Chirality : 0.060 1.472 3408 Planarity : 0.005 0.064 3879 Dihedral : 8.196 88.012 3073 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 5.23 % Allowed : 23.91 % Favored : 70.86 % 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: -1.84 (0.15), residues: 2745 helix: 0.28 (0.14), residues: 1335 sheet: -3.30 (0.43), residues: 105 loop : -2.77 (0.15), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 9 TYR 0.020 0.001 TYR H 29 PHE 0.017 0.001 PHE I 506 TRP 0.019 0.001 TRP A 553 HIS 0.007 0.001 HIS E 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.18 (22473) covalent geometry : angle 1.16110 / 0.46 (30561) hydrogen bonds : bond 0.04341 / 2.86 ( 1032) hydrogen bonds : angle 4.74176 / 3.37 ( 2988) metal coordination : bond 0.01438 / 0.94 ( 27) metal coordination : angle 15.58812 / 10.14 ( 72) Misc. bond : bond 0.05996 / 2.97 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 433 time to evaluate : 0.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 ARG cc_start: 0.5776 (ttp80) cc_final: 0.5510 (mtp180) REVERT: B 10 TYR cc_start: 0.5496 (p90) cc_final: 0.5153 (p90) REVERT: B 224 ARG cc_start: 0.7281 (tpt170) cc_final: 0.6922 (tpt90) REVERT: B 228 HIS cc_start: 0.6401 (t-170) cc_final: 0.6145 (t70) REVERT: C 29 LEU cc_start: 0.6256 (OUTLIER) cc_final: 0.5892 (mm) REVERT: C 78 LEU cc_start: 0.6085 (OUTLIER) cc_final: 0.5759 (mp) REVERT: D 37 PHE cc_start: 0.5462 (OUTLIER) cc_final: 0.4165 (t80) REVERT: F 9 ARG cc_start: 0.5974 (ttp-170) cc_final: 0.5320 (mtp180) REVERT: F 36 LEU cc_start: 0.1108 (OUTLIER) cc_final: 0.0074 (mt) REVERT: G 78 LEU cc_start: 0.6134 (OUTLIER) cc_final: 0.5700 (mp) REVERT: H 29 TYR cc_start: 0.8050 (t80) cc_final: 0.7758 (t80) REVERT: H 37 PHE cc_start: 0.5181 (OUTLIER) cc_final: 0.4649 (t80) REVERT: J 23 TYR cc_start: 0.4563 (OUTLIER) cc_final: 0.4049 (m-10) REVERT: J 228 HIS cc_start: 0.6276 (t70) cc_final: 0.6041 (t70) REVERT: K 29 LEU cc_start: 0.6473 (OUTLIER) cc_final: 0.6133 (mm) REVERT: K 78 LEU cc_start: 0.5977 (OUTLIER) cc_final: 0.5541 (mp) REVERT: L 29 TYR cc_start: 0.7979 (t80) cc_final: 0.7343 (t80) REVERT: A 43 ARG cc_start: 0.8312 (mpt90) cc_final: 0.6477 (mmt180) REVERT: A 65 TRP cc_start: 0.5466 (t60) cc_final: 0.5183 (t60) REVERT: A 86 GLU cc_start: 0.7154 (tp30) cc_final: 0.6590 (tp30) REVERT: A 98 GLU cc_start: 0.6745 (tm-30) cc_final: 0.6324 (tm-30) REVERT: A 235 ASP cc_start: 0.6849 (t0) cc_final: 0.6559 (t70) REVERT: A 236 MET cc_start: 0.5718 (mmm) cc_final: 0.5069 (mmm) REVERT: A 392 VAL cc_start: 0.6631 (p) cc_final: 0.5709 (t) REVERT: A 405 LEU cc_start: 0.5112 (mt) cc_final: 0.4085 (mp) REVERT: A 420 GLN cc_start: 0.8510 (pm20) cc_final: 0.8100 (mp10) REVERT: A 461 LYS cc_start: 0.7578 (mmpt) cc_final: 0.7348 (tttp) REVERT: A 463 LEU cc_start: 0.5571 (OUTLIER) cc_final: 0.5238 (tt) REVERT: E 69 MET cc_start: 0.6479 (mtt) cc_final: 0.6019 (mtt) REVERT: E 235 ASP cc_start: 0.6880 (t0) cc_final: 0.6591 (t70) REVERT: E 392 VAL cc_start: 0.6748 (p) cc_final: 0.5761 (t) REVERT: E 465 GLU cc_start: 0.6482 (tp30) cc_final: 0.6174 (tp30) REVERT: E 475 ARG cc_start: 0.3993 (OUTLIER) cc_final: 0.2590 (ptp-170) REVERT: I 43 ARG cc_start: 0.8393 (mpt90) cc_final: 0.6529 (mmt180) REVERT: I 63 ASP cc_start: 0.6701 (p0) cc_final: 0.6427 (p0) REVERT: I 69 MET cc_start: 0.6604 (mtt) cc_final: 0.6104 (mtt) REVERT: I 236 MET cc_start: 0.5984 (mmm) cc_final: 0.5746 (mpp) REVERT: I 392 VAL cc_start: 0.6383 (p) cc_final: 0.5371 (t) REVERT: I 405 LEU cc_start: 0.4978 (mt) cc_final: 0.4049 (mp) REVERT: I 461 LYS cc_start: 0.7698 (mmpt) cc_final: 0.7487 (tttp) REVERT: I 463 LEU cc_start: 0.5846 (OUTLIER) cc_final: 0.5464 (tt) outliers start: 121 outliers final: 92 residues processed: 520 average time/residue: 0.1507 time to fit residues: 122.9324 Evaluate side-chains 520 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 416 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 148 GLU Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 37 PHE Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 60 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain J residue 23 TYR Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 212 CYS Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 37 PHE Chi-restraints excluded: chain L residue 52 PHE Chi-restraints excluded: chain L residue 60 PHE Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 109 PHE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain A residue 566 MET Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 377 ASP Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 437 VAL Chi-restraints excluded: chain E residue 475 ARG Chi-restraints excluded: chain E residue 531 ASN Chi-restraints excluded: chain E residue 540 HIS Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 156 ASN Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 394 VAL Chi-restraints excluded: chain I residue 463 LEU Chi-restraints excluded: chain I residue 475 ARG Chi-restraints excluded: chain I residue 531 ASN Chi-restraints excluded: chain I residue 540 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 257 optimal weight: 0.7980 chunk 92 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 205 optimal weight: 8.9990 chunk 180 optimal weight: 6.9990 chunk 237 optimal weight: 1.9990 chunk 137 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 249 optimal weight: 5.9990 chunk 107 optimal weight: 20.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 94 GLN ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 ASN ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 518 ASN ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.250341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.212586 restraints weight = 33191.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.211196 restraints weight = 29177.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.212717 restraints weight = 26770.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.213841 restraints weight = 17231.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.214084 restraints weight = 16371.578| |-----------------------------------------------------------------------------| r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6559 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 22503 Z= 0.183 Angle : 1.382 83.447 30633 Z= 0.469 Chirality : 0.060 1.477 3408 Planarity : 0.005 0.070 3879 Dihedral : 8.172 87.890 3073 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 4.89 % Allowed : 24.99 % Favored : 70.13 % 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: -1.80 (0.15), residues: 2745 helix: 0.32 (0.14), residues: 1335 sheet: -3.31 (0.43), residues: 105 loop : -2.74 (0.15), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 443 TYR 0.018 0.001 TYR L 29 PHE 0.016 0.001 PHE D 36 TRP 0.014 0.001 TRP F 163 HIS 0.007 0.001 HIS E 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (22473) covalent geometry : angle 1.16468 / 0.46 (30561) hydrogen bonds : bond 0.04357 / 2.87 ( 1032) hydrogen bonds : angle 4.73537 / 3.37 ( 2988) metal coordination : bond 0.01688 / 1.15 ( 27) metal coordination : angle 15.40144 / 9.94 ( 72) Misc. bond : bond 0.05398 / 2.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 413 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 ARG cc_start: 0.5794 (ttp80) cc_final: 0.5486 (mtp180) REVERT: B 10 TYR cc_start: 0.5527 (p90) cc_final: 0.5174 (p90) REVERT: B 36 LEU cc_start: 0.1299 (OUTLIER) cc_final: 0.1043 (mt) REVERT: C 29 LEU cc_start: 0.6300 (OUTLIER) cc_final: 0.5922 (mm) REVERT: C 78 LEU cc_start: 0.6088 (OUTLIER) cc_final: 0.5750 (mp) REVERT: D 37 PHE cc_start: 0.5463 (OUTLIER) cc_final: 0.4197 (t80) REVERT: F 9 ARG cc_start: 0.6012 (ttp-170) cc_final: 0.5352 (mtp180) REVERT: F 36 LEU cc_start: 0.1159 (OUTLIER) cc_final: 0.0573 (mt) REVERT: G 74 MET cc_start: 0.8111 (mmm) cc_final: 0.7848 (mmt) REVERT: G 78 LEU cc_start: 0.5875 (OUTLIER) cc_final: 0.5440 (mp) REVERT: H 29 TYR cc_start: 0.8083 (t80) cc_final: 0.7801 (t80) REVERT: H 37 PHE cc_start: 0.5258 (OUTLIER) cc_final: 0.4696 (t80) REVERT: J 23 TYR cc_start: 0.4800 (OUTLIER) cc_final: 0.4328 (m-10) REVERT: J 228 HIS cc_start: 0.6272 (t70) cc_final: 0.6038 (t70) REVERT: K 29 LEU cc_start: 0.6383 (OUTLIER) cc_final: 0.6017 (mm) REVERT: K 78 LEU cc_start: 0.5930 (OUTLIER) cc_final: 0.5485 (mp) REVERT: L 29 TYR cc_start: 0.7993 (t80) cc_final: 0.7523 (t80) REVERT: A 20 MET cc_start: 0.7559 (mmt) cc_final: 0.7292 (mmt) REVERT: A 43 ARG cc_start: 0.8267 (mpt90) cc_final: 0.6420 (mmt180) REVERT: A 98 GLU cc_start: 0.6705 (tm-30) cc_final: 0.6277 (tm-30) REVERT: A 235 ASP cc_start: 0.6878 (t0) cc_final: 0.6566 (t70) REVERT: A 236 MET cc_start: 0.5700 (mmm) cc_final: 0.5047 (mmm) REVERT: A 392 VAL cc_start: 0.6663 (p) cc_final: 0.5759 (t) REVERT: A 405 LEU cc_start: 0.5086 (mt) cc_final: 0.4077 (mp) REVERT: A 420 GLN cc_start: 0.8474 (pm20) cc_final: 0.8054 (mp10) REVERT: A 461 LYS cc_start: 0.7573 (mmpt) cc_final: 0.7338 (tttp) REVERT: A 463 LEU cc_start: 0.5491 (OUTLIER) cc_final: 0.5159 (tt) REVERT: E 69 MET cc_start: 0.6393 (mtt) cc_final: 0.5931 (mtt) REVERT: E 235 ASP cc_start: 0.6843 (t0) cc_final: 0.6598 (t0) REVERT: E 392 VAL cc_start: 0.6747 (p) cc_final: 0.5784 (t) REVERT: E 463 LEU cc_start: 0.5447 (OUTLIER) cc_final: 0.5096 (tt) REVERT: E 465 GLU cc_start: 0.6492 (tp30) cc_final: 0.6164 (tp30) REVERT: E 475 ARG cc_start: 0.4008 (OUTLIER) cc_final: 0.2557 (ptp-170) REVERT: I 43 ARG cc_start: 0.8398 (mpt90) cc_final: 0.6501 (mmt180) REVERT: I 63 ASP cc_start: 0.6713 (p0) cc_final: 0.6480 (p0) REVERT: I 69 MET cc_start: 0.6422 (mtt) cc_final: 0.5917 (mtt) REVERT: I 392 VAL cc_start: 0.6494 (p) cc_final: 0.5560 (t) REVERT: I 405 LEU cc_start: 0.5126 (mt) cc_final: 0.4249 (mp) REVERT: I 463 LEU cc_start: 0.5805 (OUTLIER) cc_final: 0.5433 (tt) outliers start: 113 outliers final: 88 residues processed: 495 average time/residue: 0.1489 time to fit residues: 116.0610 Evaluate side-chains 502 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 400 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 148 GLU Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 37 PHE Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 60 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain J residue 23 TYR Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 212 CYS Chi-restraints excluded: chain J residue 226 ILE Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 37 PHE Chi-restraints excluded: chain L residue 52 PHE Chi-restraints excluded: chain L residue 60 PHE Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 109 PHE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 507 ASN Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 377 ASP Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 463 LEU Chi-restraints excluded: chain E residue 475 ARG Chi-restraints excluded: chain E residue 531 ASN Chi-restraints excluded: chain E residue 540 HIS Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 394 VAL Chi-restraints excluded: chain I residue 463 LEU Chi-restraints excluded: chain I residue 475 ARG Chi-restraints excluded: chain I residue 531 ASN Chi-restraints excluded: chain I residue 540 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 67 optimal weight: 10.0000 chunk 272 optimal weight: 0.9980 chunk 213 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 chunk 212 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 200 optimal weight: 1.9990 chunk 234 optimal weight: 3.9990 chunk 267 optimal weight: 20.0000 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 94 GLN ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 HIS E 214 ASN ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.250726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.210848 restraints weight = 33113.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.210917 restraints weight = 27841.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.212887 restraints weight = 19763.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.212613 restraints weight = 15427.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.213068 restraints weight = 14402.353| |-----------------------------------------------------------------------------| r_work (final): 0.4236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6582 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 22503 Z= 0.181 Angle : 1.368 83.195 30633 Z= 0.470 Chirality : 0.060 1.486 3408 Planarity : 0.005 0.063 3879 Dihedral : 8.130 87.776 3073 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 4.97 % Allowed : 25.03 % Favored : 70.00 % 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: -1.75 (0.15), residues: 2745 helix: 0.35 (0.14), residues: 1347 sheet: -2.81 (0.41), residues: 123 loop : -2.76 (0.16), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 108 TYR 0.017 0.001 TYR L 29 PHE 0.015 0.001 PHE D 36 TRP 0.014 0.001 TRP A 65 HIS 0.006 0.001 HIS H 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (22473) covalent geometry : angle 1.16817 / 0.47 (30561) hydrogen bonds : bond 0.04333 / 2.84 ( 1032) hydrogen bonds : angle 4.71355 / 3.35 ( 2988) metal coordination : bond 0.01604 / 1.06 ( 27) metal coordination : angle 14.73772 / 9.65 ( 72) Misc. bond : bond 0.04853 / 2.40 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 408 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 ARG cc_start: 0.5736 (ttp80) cc_final: 0.5481 (mtp180) REVERT: B 10 TYR cc_start: 0.5481 (p90) cc_final: 0.5114 (p90) REVERT: B 36 LEU cc_start: 0.1064 (OUTLIER) cc_final: 0.0800 (mt) REVERT: B 228 HIS cc_start: 0.6525 (t-170) cc_final: 0.6258 (t70) REVERT: C 29 LEU cc_start: 0.6440 (OUTLIER) cc_final: 0.6082 (mm) REVERT: C 78 LEU cc_start: 0.6087 (OUTLIER) cc_final: 0.5750 (mp) REVERT: D 37 PHE cc_start: 0.5221 (OUTLIER) cc_final: 0.4234 (t80) REVERT: F 9 ARG cc_start: 0.6130 (ttp-170) cc_final: 0.5525 (mtp180) REVERT: F 36 LEU cc_start: 0.1103 (OUTLIER) cc_final: 0.0651 (mt) REVERT: G 74 MET cc_start: 0.8181 (mmm) cc_final: 0.7887 (mmt) REVERT: G 78 LEU cc_start: 0.5884 (OUTLIER) cc_final: 0.5434 (mp) REVERT: H 29 TYR cc_start: 0.8040 (t80) cc_final: 0.7762 (t80) REVERT: H 37 PHE cc_start: 0.5146 (OUTLIER) cc_final: 0.4594 (t80) REVERT: J 23 TYR cc_start: 0.4887 (OUTLIER) cc_final: 0.4464 (m-10) REVERT: J 228 HIS cc_start: 0.6284 (t70) cc_final: 0.6080 (t70) REVERT: K 29 LEU cc_start: 0.6289 (OUTLIER) cc_final: 0.5971 (mm) REVERT: K 78 LEU cc_start: 0.5935 (OUTLIER) cc_final: 0.5467 (mp) REVERT: A 43 ARG cc_start: 0.8283 (mpt90) cc_final: 0.6407 (mmt180) REVERT: A 86 GLU cc_start: 0.7213 (tp30) cc_final: 0.6768 (tp30) REVERT: A 235 ASP cc_start: 0.6987 (t0) cc_final: 0.6722 (t70) REVERT: A 236 MET cc_start: 0.5615 (mmm) cc_final: 0.4931 (mmm) REVERT: A 392 VAL cc_start: 0.6621 (p) cc_final: 0.5735 (t) REVERT: A 405 LEU cc_start: 0.4936 (mt) cc_final: 0.3896 (mp) REVERT: A 420 GLN cc_start: 0.8546 (pm20) cc_final: 0.8133 (mp10) REVERT: A 461 LYS cc_start: 0.7626 (mmpt) cc_final: 0.7385 (tttp) REVERT: A 463 LEU cc_start: 0.5536 (OUTLIER) cc_final: 0.5203 (tt) REVERT: E 69 MET cc_start: 0.6514 (mtt) cc_final: 0.6051 (mtt) REVERT: E 235 ASP cc_start: 0.6830 (t0) cc_final: 0.6577 (t70) REVERT: E 392 VAL cc_start: 0.6703 (p) cc_final: 0.5776 (t) REVERT: E 463 LEU cc_start: 0.5422 (OUTLIER) cc_final: 0.5086 (tt) REVERT: E 475 ARG cc_start: 0.3900 (OUTLIER) cc_final: 0.2441 (ptp-170) REVERT: I 43 ARG cc_start: 0.8439 (mpt90) cc_final: 0.7833 (mmt-90) REVERT: I 63 ASP cc_start: 0.6863 (p0) cc_final: 0.6651 (p0) REVERT: I 69 MET cc_start: 0.6583 (mtt) cc_final: 0.6123 (mtt) REVERT: I 392 VAL cc_start: 0.6504 (p) cc_final: 0.5594 (t) REVERT: I 405 LEU cc_start: 0.5093 (mt) cc_final: 0.4255 (mp) REVERT: I 463 LEU cc_start: 0.5770 (OUTLIER) cc_final: 0.5422 (tt) outliers start: 115 outliers final: 90 residues processed: 494 average time/residue: 0.1460 time to fit residues: 113.8603 Evaluate side-chains 501 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 397 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 148 GLU Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 37 PHE Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 60 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain J residue 23 TYR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 212 CYS Chi-restraints excluded: chain J residue 226 ILE Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 37 PHE Chi-restraints excluded: chain L residue 52 PHE Chi-restraints excluded: chain L residue 60 PHE Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 109 PHE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 377 ASP Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 463 LEU Chi-restraints excluded: chain E residue 475 ARG Chi-restraints excluded: chain E residue 531 ASN Chi-restraints excluded: chain E residue 540 HIS Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 394 VAL Chi-restraints excluded: chain I residue 463 LEU Chi-restraints excluded: chain I residue 475 ARG Chi-restraints excluded: chain I residue 531 ASN Chi-restraints excluded: chain I residue 540 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 223 optimal weight: 6.9990 chunk 184 optimal weight: 30.0000 chunk 175 optimal weight: 30.0000 chunk 199 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 191 optimal weight: 20.0000 chunk 264 optimal weight: 30.0000 chunk 35 optimal weight: 6.9990 chunk 247 optimal weight: 4.9990 chunk 136 optimal weight: 0.9980 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 94 GLN A 25 GLN ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 HIS ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.249177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.211577 restraints weight = 33417.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.209427 restraints weight = 34475.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.211778 restraints weight = 25161.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.211703 restraints weight = 17802.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.212307 restraints weight = 16149.039| |-----------------------------------------------------------------------------| r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 22503 Z= 0.215 Angle : 1.406 82.876 30633 Z= 0.486 Chirality : 0.061 1.486 3408 Planarity : 0.005 0.062 3879 Dihedral : 8.268 87.778 3073 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.25 % Favored : 90.75 % Rotamer: Outliers : 5.10 % Allowed : 25.21 % Favored : 69.69 % 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: -1.90 (0.15), residues: 2745 helix: 0.21 (0.14), residues: 1347 sheet: -2.82 (0.42), residues: 123 loop : -2.83 (0.15), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 108 TYR 0.017 0.002 TYR F 10 PHE 0.023 0.002 PHE E 506 TRP 0.014 0.001 TRP F 163 HIS 0.020 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.21 (22473) covalent geometry : angle 1.19749 / 0.48 (30561) hydrogen bonds : bond 0.04655 / 3.05 ( 1032) hydrogen bonds : angle 4.86147 / 3.46 ( 2988) metal coordination : bond 0.01753 / 1.13 ( 27) metal coordination : angle 15.24357 / 10.30 ( 72) Misc. bond : bond 0.04715 / 2.32 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 411 time to evaluate : 0.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 ARG cc_start: 0.5810 (ttp80) cc_final: 0.5543 (mtp180) REVERT: B 10 TYR cc_start: 0.5506 (p90) cc_final: 0.5133 (p90) REVERT: B 228 HIS cc_start: 0.6267 (t-170) cc_final: 0.6046 (t70) REVERT: C 29 LEU cc_start: 0.6351 (OUTLIER) cc_final: 0.5973 (mm) REVERT: C 78 LEU cc_start: 0.6052 (OUTLIER) cc_final: 0.5705 (mp) REVERT: D 37 PHE cc_start: 0.5261 (OUTLIER) cc_final: 0.4192 (t80) REVERT: F 9 ARG cc_start: 0.6034 (ttp-170) cc_final: 0.5382 (mtp180) REVERT: F 36 LEU cc_start: 0.1426 (OUTLIER) cc_final: 0.1095 (mp) REVERT: G 74 MET cc_start: 0.8169 (mmm) cc_final: 0.7958 (mmm) REVERT: G 78 LEU cc_start: 0.6068 (OUTLIER) cc_final: 0.5599 (mp) REVERT: H 29 TYR cc_start: 0.8095 (t80) cc_final: 0.7790 (t80) REVERT: H 37 PHE cc_start: 0.5403 (OUTLIER) cc_final: 0.4597 (t80) REVERT: J 23 TYR cc_start: 0.4963 (OUTLIER) cc_final: 0.4451 (m-10) REVERT: K 29 LEU cc_start: 0.6497 (OUTLIER) cc_final: 0.6162 (mm) REVERT: K 78 LEU cc_start: 0.5883 (OUTLIER) cc_final: 0.5398 (mp) REVERT: A 20 MET cc_start: 0.7181 (mmt) cc_final: 0.6951 (mmt) REVERT: A 43 ARG cc_start: 0.8338 (mpt90) cc_final: 0.6777 (mmt180) REVERT: A 63 ASP cc_start: 0.6139 (p0) cc_final: 0.5717 (p0) REVERT: A 65 TRP cc_start: 0.5673 (t60) cc_final: 0.5128 (t60) REVERT: A 86 GLU cc_start: 0.7164 (tp30) cc_final: 0.6723 (tp30) REVERT: A 235 ASP cc_start: 0.6934 (t0) cc_final: 0.6477 (t70) REVERT: A 236 MET cc_start: 0.5687 (mmm) cc_final: 0.5046 (mmm) REVERT: A 392 VAL cc_start: 0.6680 (p) cc_final: 0.5788 (t) REVERT: A 420 GLN cc_start: 0.8404 (pm20) cc_final: 0.8018 (mp10) REVERT: A 461 LYS cc_start: 0.7604 (mmpt) cc_final: 0.7335 (tttp) REVERT: A 463 LEU cc_start: 0.5588 (OUTLIER) cc_final: 0.5302 (tt) REVERT: E 20 MET cc_start: 0.7308 (mmt) cc_final: 0.7108 (mmt) REVERT: E 64 ASN cc_start: 0.6348 (p0) cc_final: 0.6076 (p0) REVERT: E 69 MET cc_start: 0.6383 (mtt) cc_final: 0.5948 (mtt) REVERT: E 235 ASP cc_start: 0.6827 (t0) cc_final: 0.6551 (t70) REVERT: E 392 VAL cc_start: 0.6826 (p) cc_final: 0.5900 (t) REVERT: E 463 LEU cc_start: 0.5521 (OUTLIER) cc_final: 0.5191 (tt) REVERT: E 475 ARG cc_start: 0.4036 (OUTLIER) cc_final: 0.2535 (ptp-170) REVERT: E 506 PHE cc_start: 0.3403 (m-80) cc_final: 0.2618 (t80) REVERT: I 43 ARG cc_start: 0.8415 (mpt90) cc_final: 0.7365 (mmt180) REVERT: I 69 MET cc_start: 0.6428 (mtt) cc_final: 0.6011 (mtt) REVERT: I 392 VAL cc_start: 0.6635 (p) cc_final: 0.5718 (t) REVERT: I 405 LEU cc_start: 0.4978 (mt) cc_final: 0.4051 (mp) REVERT: I 463 LEU cc_start: 0.5749 (OUTLIER) cc_final: 0.5414 (tt) outliers start: 118 outliers final: 94 residues processed: 498 average time/residue: 0.1449 time to fit residues: 113.5890 Evaluate side-chains 510 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 403 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 50 SER Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 148 GLU Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 116 ILE Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 37 PHE Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 60 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain J residue 23 TYR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 212 CYS Chi-restraints excluded: chain J residue 226 ILE Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 37 PHE Chi-restraints excluded: chain L residue 52 PHE Chi-restraints excluded: chain L residue 60 PHE Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 109 PHE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 377 ASP Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 463 LEU Chi-restraints excluded: chain E residue 475 ARG Chi-restraints excluded: chain E residue 531 ASN Chi-restraints excluded: chain E residue 540 HIS Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 156 ASN Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 353 CYS Chi-restraints excluded: chain I residue 394 VAL Chi-restraints excluded: chain I residue 463 LEU Chi-restraints excluded: chain I residue 475 ARG Chi-restraints excluded: chain I residue 531 ASN Chi-restraints excluded: chain I residue 540 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 215 optimal weight: 10.0000 chunk 236 optimal weight: 7.9990 chunk 244 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 230 optimal weight: 3.9990 chunk 167 optimal weight: 9.9990 chunk 241 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 200 optimal weight: 0.9990 chunk 270 optimal weight: 0.9980 chunk 90 optimal weight: 20.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 94 GLN ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 HIS ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 507 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.250891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.213481 restraints weight = 33325.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.211858 restraints weight = 30309.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.213939 restraints weight = 22027.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.214159 restraints weight = 15248.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.214630 restraints weight = 14635.469| |-----------------------------------------------------------------------------| r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6554 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 22503 Z= 0.183 Angle : 1.383 82.906 30633 Z= 0.481 Chirality : 0.061 1.495 3408 Planarity : 0.005 0.063 3879 Dihedral : 8.155 87.689 3073 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 4.63 % Allowed : 26.11 % Favored : 69.26 % 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: -1.80 (0.15), residues: 2745 helix: 0.32 (0.14), residues: 1347 sheet: -2.84 (0.41), residues: 123 loop : -2.80 (0.15), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 108 TYR 0.018 0.001 TYR F 10 PHE 0.024 0.001 PHE E 506 TRP 0.015 0.001 TRP L 48 HIS 0.011 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (22473) covalent geometry : angle 1.18766 / 0.48 (30561) hydrogen bonds : bond 0.04469 / 2.94 ( 1032) hydrogen bonds : angle 4.77276 / 3.40 ( 2988) metal coordination : bond 0.01476 / 0.94 ( 27) metal coordination : angle 14.66726 / 9.91 ( 72) Misc. bond : bond 0.04083 / 2.02 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5490 Ramachandran restraints generated. 2745 Oldfield, 0 Emsley, 2745 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 401 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 ARG cc_start: 0.5764 (ttp80) cc_final: 0.5513 (mtp180) REVERT: B 10 TYR cc_start: 0.5494 (p90) cc_final: 0.5097 (p90) REVERT: C 29 LEU cc_start: 0.6226 (OUTLIER) cc_final: 0.5884 (mm) REVERT: C 78 LEU cc_start: 0.6038 (OUTLIER) cc_final: 0.5692 (mp) REVERT: D 37 PHE cc_start: 0.5277 (OUTLIER) cc_final: 0.4272 (t80) REVERT: F 1 MET cc_start: 0.4247 (ttt) cc_final: 0.3959 (ttt) REVERT: F 9 ARG cc_start: 0.5965 (ttp-170) cc_final: 0.5327 (mtp180) REVERT: F 36 LEU cc_start: 0.1182 (OUTLIER) cc_final: 0.0882 (mp) REVERT: G 74 MET cc_start: 0.8143 (mmm) cc_final: 0.7858 (mmt) REVERT: G 78 LEU cc_start: 0.5876 (OUTLIER) cc_final: 0.5397 (mp) REVERT: H 29 TYR cc_start: 0.8057 (t80) cc_final: 0.7755 (t80) REVERT: H 37 PHE cc_start: 0.5222 (OUTLIER) cc_final: 0.4564 (t80) REVERT: J 23 TYR cc_start: 0.4965 (OUTLIER) cc_final: 0.4523 (m-10) REVERT: K 29 LEU cc_start: 0.6436 (OUTLIER) cc_final: 0.6100 (mm) REVERT: K 78 LEU cc_start: 0.5988 (OUTLIER) cc_final: 0.5531 (mp) REVERT: A 43 ARG cc_start: 0.8273 (mpt90) cc_final: 0.6377 (mmt180) REVERT: A 63 ASP cc_start: 0.6057 (p0) cc_final: 0.5627 (p0) REVERT: A 65 TRP cc_start: 0.5311 (t60) cc_final: 0.4810 (t60) REVERT: A 86 GLU cc_start: 0.7191 (tp30) cc_final: 0.6759 (tp30) REVERT: A 235 ASP cc_start: 0.6893 (t0) cc_final: 0.6598 (t0) REVERT: A 236 MET cc_start: 0.5618 (mmm) cc_final: 0.4987 (mmm) REVERT: A 392 VAL cc_start: 0.6535 (p) cc_final: 0.5632 (t) REVERT: A 420 GLN cc_start: 0.8386 (pm20) cc_final: 0.7998 (mp10) REVERT: A 461 LYS cc_start: 0.7601 (mmpt) cc_final: 0.7361 (tttp) REVERT: A 463 LEU cc_start: 0.5576 (OUTLIER) cc_final: 0.5231 (tt) REVERT: A 573 MET cc_start: 0.7016 (tpp) cc_final: 0.6200 (tpp) REVERT: E 20 MET cc_start: 0.7308 (mmt) cc_final: 0.7083 (mmt) REVERT: E 69 MET cc_start: 0.6323 (mtt) cc_final: 0.5897 (mtt) REVERT: E 235 ASP cc_start: 0.6776 (t0) cc_final: 0.6543 (t70) REVERT: E 392 VAL cc_start: 0.6697 (p) cc_final: 0.5754 (t) REVERT: E 463 LEU cc_start: 0.5475 (OUTLIER) cc_final: 0.5138 (tt) REVERT: E 475 ARG cc_start: 0.3976 (OUTLIER) cc_final: 0.2448 (ptp-170) REVERT: I 43 ARG cc_start: 0.8409 (mpt90) cc_final: 0.8038 (mmt90) REVERT: I 69 MET cc_start: 0.6349 (mtt) cc_final: 0.5957 (mtt) REVERT: I 392 VAL cc_start: 0.6520 (p) cc_final: 0.5597 (t) REVERT: I 405 LEU cc_start: 0.5116 (mt) cc_final: 0.4279 (mp) REVERT: I 463 LEU cc_start: 0.5794 (OUTLIER) cc_final: 0.5421 (tt) outliers start: 107 outliers final: 89 residues processed: 480 average time/residue: 0.1425 time to fit residues: 108.1052 Evaluate side-chains 492 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 390 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 99 VAL Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 29 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 60 PHE Chi-restraints excluded: chain D residue 99 VAL Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 42 LEU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 148 GLU Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 78 LEU Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 128 VAL Chi-restraints excluded: chain H residue 27 THR Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 37 PHE Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 60 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain J residue 23 TYR Chi-restraints excluded: chain J residue 59 VAL Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 99 VAL Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 212 CYS Chi-restraints excluded: chain J residue 226 ILE Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 24 ILE Chi-restraints excluded: chain L residue 28 LEU Chi-restraints excluded: chain L residue 37 PHE Chi-restraints excluded: chain L residue 52 PHE Chi-restraints excluded: chain L residue 60 PHE Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 109 PHE Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 96 ILE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 217 ILE Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 217 ILE Chi-restraints excluded: chain E residue 377 ASP Chi-restraints excluded: chain E residue 463 LEU Chi-restraints excluded: chain E residue 475 ARG Chi-restraints excluded: chain E residue 531 ASN Chi-restraints excluded: chain E residue 540 HIS Chi-restraints excluded: chain I residue 31 GLN Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 394 VAL Chi-restraints excluded: chain I residue 463 LEU Chi-restraints excluded: chain I residue 475 ARG Chi-restraints excluded: chain I residue 531 ASN Chi-restraints excluded: chain I residue 540 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 50 optimal weight: 7.9990 chunk 262 optimal weight: 30.0000 chunk 79 optimal weight: 6.9990 chunk 137 optimal weight: 30.0000 chunk 132 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 220 optimal weight: 0.5980 chunk 227 optimal weight: 0.1980 chunk 155 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 94 GLN L 94 GLN ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 HIS ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.250882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.213041 restraints weight = 33239.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.211240 restraints weight = 30320.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.213170 restraints weight = 23765.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.213329 restraints weight = 15816.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.213721 restraints weight = 14593.303| |-----------------------------------------------------------------------------| r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6572 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 22503 Z= 0.188 Angle : 1.372 82.811 30633 Z= 0.480 Chirality : 0.061 1.495 3408 Planarity : 0.005 0.063 3879 Dihedral : 8.145 87.192 3073 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 4.80 % Allowed : 26.11 % Favored : 69.09 % 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: -1.81 (0.15), residues: 2745 helix: 0.28 (0.14), residues: 1356 sheet: -2.86 (0.40), residues: 123 loop : -2.79 (0.16), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG I 108 TYR 0.018 0.002 TYR F 10 PHE 0.023 0.002 PHE E 506 TRP 0.015 0.001 TRP L 48 HIS 0.014 0.001 HIS A 540 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (22473) covalent geometry : angle 1.18538 / 0.48 (30561) hydrogen bonds : bond 0.04460 / 2.93 ( 1032) hydrogen bonds : angle 4.75802 / 3.38 ( 2988) metal coordination : bond 0.01620 / 1.04 ( 27) metal coordination : angle 14.28394 / 9.34 ( 72) Misc. bond : bond 0.03706 / 1.83 ( 3) =============================================================================== Job complete usr+sys time: 3881.33 seconds wall clock time: 68 minutes 3.75 seconds (4083.75 seconds total)