Starting phenix.real_space_refine on Thu Mar 5 11:52:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wu6_21906/03_2026/6wu6_21906.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wu6_21906/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6wu6_21906/03_2026/6wu6_21906.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wu6_21906/03_2026/6wu6_21906.map" model { file = "/net/cci-nas-00/data/ceres_data/6wu6_21906/03_2026/6wu6_21906.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wu6_21906/03_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 5.41, per 1000 atoms: 0.25 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: 1.97 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: 0.60 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: 3.12 Time building geometry restraints manager: 2.66 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: 11618 17.61 - 35.21: 1288 35.21 - 52.81: 300 52.81 - 70.42: 42 70.42 - 88.02: 51 Dihedral angle restraints: 13299 sinusoidal: 5343 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 13296 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: 0.05 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: 0.250 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: 0.300 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.540 Find NCS groups from input model: 0.170 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 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 : 16.337 88.025 8187 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 covalent geometry : bond 0.03348 (22473) covalent geometry : angle 1.50448 (30561) hydrogen bonds : bond 0.14918 ( 1032) hydrogen bonds : angle 7.18997 ( 2988) metal coordination : bond 0.52386 ( 27) metal coordination : angle 32.58937 ( 72) Misc. bond : bond 0.43847 ( 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 : 0.596 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: 0.1505 time to fit residues: 125.6480 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 : 0.626 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.247476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.210101 restraints weight = 33232.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.207974 restraints weight = 29325.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.210129 restraints weight = 24535.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.210158 restraints weight = 17956.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.210635 restraints weight = 15993.564| |-----------------------------------------------------------------------------| r_work (final): 0.4215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.201 22503 Z= 0.286 Angle : 1.648 56.307 30633 Z= 0.530 Chirality : 0.087 2.525 3408 Planarity : 0.006 0.074 3879 Dihedral : 10.569 97.420 3220 Min Nonbonded Distance : 1.541 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.89 % Favored : 89.11 % Rotamer: Outliers : 3.42 % Allowed : 18.68 % Favored : 77.91 % 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 : -3.25 (0.15), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 20 TYR 0.034 0.002 TYR H 29 PHE 0.032 0.003 PHE H 51 TRP 0.043 0.002 TRP F 163 HIS 0.013 0.002 HIS E 354 Details of bonding type rmsd covalent geometry : bond 0.00631 (22473) covalent geometry : angle 1.25341 (30561) hydrogen bonds : bond 0.05599 ( 1032) hydrogen bonds : angle 5.56186 ( 2988) metal coordination : bond 0.02745 ( 27) metal coordination : angle 22.11717 ( 72) Misc. bond : bond 0.10807 ( 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 541 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 462 time to evaluate : 0.778 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: 0.6163 (mmt) cc_final: 0.5863 (mmt) REVERT: F 53 ARG cc_start: 0.6237 (pmt-80) cc_final: 0.5866 (ptt90) REVERT: H 29 TYR cc_start: 0.8193 (t80) cc_final: 0.7548 (t80) REVERT: H 83 TYR cc_start: 0.8015 (m-10) cc_final: 0.7657 (m-10) REVERT: J 9 ARG cc_start: 0.5568 (ttp80) cc_final: 0.5310 (mtp180) REVERT: J 23 TYR cc_start: 0.4744 (OUTLIER) cc_final: 0.4366 (m-10) REVERT: K 28 ILE cc_start: 0.7430 (mm) cc_final: 0.7186 (mt) REVERT: A 43 ARG cc_start: 0.8264 (mpt90) cc_final: 0.7154 (mmt180) REVERT: A 139 ASP cc_start: 0.6005 (t0) cc_final: 0.5773 (t0) REVERT: A 392 VAL cc_start: 0.7076 (p) cc_final: 0.6227 (t) REVERT: A 461 LYS cc_start: 0.7695 (mmpt) cc_final: 0.7317 (tttp) REVERT: E 86 GLU cc_start: 0.7436 (tp30) cc_final: 0.7097 (tp30) REVERT: E 155 LYS cc_start: 0.8103 (tmmt) cc_final: 0.7806 (tmmt) REVERT: E 235 ASP cc_start: 0.7140 (t0) cc_final: 0.6768 (t70) REVERT: E 356 MET cc_start: 0.6220 (ttp) cc_final: 0.5912 (ttp) REVERT: E 392 VAL cc_start: 0.6965 (p) cc_final: 0.6032 (t) REVERT: E 461 LYS cc_start: 0.7657 (mmpt) cc_final: 0.7372 (tttp) REVERT: E 465 GLU cc_start: 0.6539 (tp30) cc_final: 0.6301 (tp30) REVERT: E 475 ARG cc_start: 0.4069 (ptp-170) cc_final: 0.2673 (ptp-170) REVERT: E 499 LEU cc_start: 0.6721 (tp) cc_final: 0.6388 (tt) REVERT: I 43 ARG cc_start: 0.8448 (mpt90) cc_final: 0.7480 (mmt180) REVERT: I 63 ASP cc_start: 0.6594 (p0) cc_final: 0.6040 (p0) REVERT: I 356 MET cc_start: 0.6566 (ttp) cc_final: 0.5996 (ttp) REVERT: I 392 VAL cc_start: 0.6972 (p) cc_final: 0.6063 (t) REVERT: I 461 LYS cc_start: 0.7975 (mmpt) cc_final: 0.7594 (tttp) REVERT: I 465 GLU cc_start: 0.6691 (tp30) cc_final: 0.6192 (tp30) REVERT: I 475 ARG cc_start: 0.4055 (ptp-170) cc_final: 0.2780 (ptp-170) REVERT: I 540 HIS cc_start: 0.7482 (OUTLIER) cc_final: 0.7280 (t70) outliers start: 79 outliers final: 56 residues processed: 498 average time/residue: 0.1411 time to fit residues: 109.8797 Evaluate side-chains 493 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 435 time to evaluate : 0.768 ------------------------------------------------------------------------------- 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 F residue 226 ILE 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 A residue 566 MET Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 50 GLN 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 Chi-restraints excluded: chain I residue 540 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 53 optimal weight: 5.9990 chunk 160 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 200 optimal weight: 7.9990 chunk 150 optimal weight: 8.9990 chunk 156 optimal weight: 8.9990 chunk 229 optimal weight: 6.9990 chunk 144 optimal weight: 40.0000 chunk 121 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 98 optimal weight: 0.7980 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 94 GLN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4586 r_free = 0.4586 target = 0.249941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.212801 restraints weight = 33617.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.211284 restraints weight = 29867.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.213092 restraints weight = 24249.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.213611 restraints weight = 16784.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.213775 restraints weight = 15292.075| |-----------------------------------------------------------------------------| r_work (final): 0.4246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.122 22503 Z= 0.185 Angle : 1.445 84.968 30633 Z= 0.489 Chirality : 0.058 1.342 3408 Planarity : 0.005 0.069 3879 Dihedral : 9.571 88.752 3205 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 3.46 % Allowed : 21.27 % Favored : 75.27 % 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: -2.44 (0.15), residues: 2745 helix: -0.27 (0.14), residues: 1323 sheet: -3.33 (0.42), residues: 105 loop : -3.01 (0.15), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 108 TYR 0.024 0.002 TYR H 29 PHE 0.022 0.002 PHE E 506 TRP 0.026 0.001 TRP F 163 HIS 0.010 0.002 HIS A 354 Details of bonding type rmsd covalent geometry : bond 0.00417 (22473) covalent geometry : angle 1.19338 (30561) hydrogen bonds : bond 0.04830 ( 1032) hydrogen bonds : angle 5.06622 ( 2988) metal coordination : bond 0.00987 ( 27) metal coordination : angle 16.85924 ( 72) Misc. bond : bond 0.08850 ( 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 514 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 434 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: 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: 0.5941 (ttp80) cc_final: 0.5471 (mtp180) REVERT: B 23 TYR cc_start: 0.4369 (OUTLIER) cc_final: 0.3900 (m-10) REVERT: D 37 PHE cc_start: 0.5180 (OUTLIER) cc_final: 0.3711 (t80) REVERT: F 20 MET cc_start: 0.4961 (mmt) cc_final: 0.4378 (mmp) REVERT: G 74 MET cc_start: 0.8005 (mmt) cc_final: 0.7768 (mmm) REVERT: H 29 TYR cc_start: 0.8167 (t80) cc_final: 0.7672 (t80) REVERT: H 83 TYR cc_start: 0.7921 (m-10) cc_final: 0.7531 (m-10) REVERT: J 5 PHE cc_start: 0.6246 (m-80) cc_final: 0.5756 (m-80) REVERT: J 9 ARG cc_start: 0.5398 (ttp80) cc_final: 0.5108 (mtp180) REVERT: J 23 TYR cc_start: 0.4446 (OUTLIER) cc_final: 0.3882 (m-10) REVERT: L 29 TYR cc_start: 0.8240 (t80) cc_final: 0.7652 (t80) REVERT: A 20 MET cc_start: 0.7458 (OUTLIER) cc_final: 0.7122 (mmt) REVERT: A 43 ARG cc_start: 0.8281 (mpt90) cc_final: 0.7157 (mmt180) REVERT: A 139 ASP cc_start: 0.5978 (t70) cc_final: 0.5736 (t0) REVERT: A 392 VAL cc_start: 0.6895 (p) cc_final: 0.5937 (t) REVERT: A 461 LYS cc_start: 0.7558 (mmpt) cc_final: 0.7271 (tttp) REVERT: E 69 MET cc_start: 0.6569 (mtt) cc_final: 0.6193 (mtt) REVERT: E 86 GLU cc_start: 0.7393 (tp30) cc_final: 0.7177 (tp30) REVERT: E 235 ASP cc_start: 0.7037 (t0) cc_final: 0.6667 (t70) REVERT: E 392 VAL cc_start: 0.6886 (p) cc_final: 0.5944 (t) REVERT: E 461 LYS cc_start: 0.7547 (mmpt) cc_final: 0.7297 (tttp) REVERT: E 465 GLU cc_start: 0.6518 (tp30) cc_final: 0.6158 (tp30) REVERT: E 475 ARG cc_start: 0.4053 (ptp-170) cc_final: 0.2653 (ptp-170) REVERT: E 499 LEU cc_start: 0.6584 (tp) cc_final: 0.6219 (tt) REVERT: I 43 ARG cc_start: 0.8409 (mpt90) cc_final: 0.7359 (mmt180) REVERT: I 63 ASP cc_start: 0.6485 (p0) cc_final: 0.6048 (p0) REVERT: I 69 MET cc_start: 0.6558 (mtt) cc_final: 0.6121 (mtt) REVERT: I 236 MET cc_start: 0.5784 (mmm) cc_final: 0.5417 (mpp) REVERT: I 356 MET cc_start: 0.6385 (ttp) cc_final: 0.6153 (ttp) REVERT: I 392 VAL cc_start: 0.6758 (p) cc_final: 0.5725 (t) REVERT: I 461 LYS cc_start: 0.7798 (mmpt) cc_final: 0.7455 (tttp) outliers start: 80 outliers final: 56 residues processed: 481 average time/residue: 0.1448 time to fit residues: 108.4377 Evaluate side-chains 474 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 414 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 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 68 ILE 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 42 LEU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 44 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 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 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 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 507 ASN Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 566 MET 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 520 MET 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 214 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 chunk 202 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 189 optimal weight: 8.9990 chunk 181 optimal weight: 7.9990 chunk 175 optimal weight: 40.0000 chunk 185 optimal weight: 50.0000 chunk 16 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 25 GLN ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 GLN ** 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 = 0.4558 r_free = 0.4558 target = 0.247211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.209031 restraints weight = 32899.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.207383 restraints weight = 34640.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.209128 restraints weight = 28252.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.209393 restraints weight = 19796.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.210325 restraints weight = 17538.576| |-----------------------------------------------------------------------------| r_work (final): 0.4210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.142 22503 Z= 0.236 Angle : 1.459 84.182 30633 Z= 0.501 Chirality : 0.061 1.467 3408 Planarity : 0.005 0.072 3879 Dihedral : 9.650 88.636 3204 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.42 % Favored : 89.58 % Rotamer: Outliers : 4.54 % Allowed : 22.27 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.39 (0.15), residues: 2745 helix: -0.25 (0.13), residues: 1326 sheet: -3.41 (0.42), residues: 105 loop : -2.95 (0.15), residues: 1314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 224 TYR 0.019 0.002 TYR D 107 PHE 0.023 0.002 PHE L 36 TRP 0.020 0.002 TRP F 163 HIS 0.007 0.002 HIS I 469 Details of bonding type rmsd covalent geometry : bond 0.00544 (22473) covalent geometry : angle 1.21708 (30561) hydrogen bonds : bond 0.05194 ( 1032) hydrogen bonds : angle 5.18092 ( 2988) metal coordination : bond 0.01693 ( 27) metal coordination : angle 16.65350 ( 72) Misc. bond : bond 0.10743 ( 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 540 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 435 time to evaluate : 0.521 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: 0.5748 (ttp80) cc_final: 0.5377 (mtp180) REVERT: B 10 TYR cc_start: 0.5324 (p90) cc_final: 0.5015 (p90) REVERT: B 224 ARG cc_start: 0.7345 (tpt170) cc_final: 0.6663 (tpt90) REVERT: C 29 LEU cc_start: 0.6438 (OUTLIER) cc_final: 0.6074 (mm) REVERT: D 37 PHE cc_start: 0.5464 (OUTLIER) cc_final: 0.4012 (t80) REVERT: F 20 MET cc_start: 0.4813 (mmt) cc_final: 0.4277 (mmp) REVERT: G 74 MET cc_start: 0.8036 (mmt) cc_final: 0.7747 (mmm) REVERT: G 78 LEU cc_start: 0.6002 (OUTLIER) cc_final: 0.5476 (mp) REVERT: H 29 TYR cc_start: 0.8199 (t80) cc_final: 0.7708 (t80) REVERT: J 9 ARG cc_start: 0.5744 (ttp80) cc_final: 0.5495 (mtp180) REVERT: J 23 TYR cc_start: 0.4380 (OUTLIER) cc_final: 0.3897 (m-10) REVERT: K 29 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6250 (mm) REVERT: L 29 TYR cc_start: 0.8264 (t80) cc_final: 0.7584 (t80) REVERT: A 20 MET cc_start: 0.7463 (mmt) cc_final: 0.7224 (mmt) REVERT: A 43 ARG cc_start: 0.8297 (mpt90) cc_final: 0.7120 (mmt180) REVERT: A 139 ASP cc_start: 0.6084 (t70) cc_final: 0.5844 (t0) REVERT: A 155 LYS cc_start: 0.8139 (tmmt) cc_final: 0.7635 (tmmt) REVERT: A 356 MET cc_start: 0.6373 (ttp) cc_final: 0.5759 (mtp) REVERT: A 420 GLN cc_start: 0.8420 (pm20) cc_final: 0.7979 (mp10) REVERT: A 461 LYS cc_start: 0.7608 (mmpt) cc_final: 0.7326 (tttp) REVERT: A 463 LEU cc_start: 0.5641 (OUTLIER) cc_final: 0.5321 (tt) REVERT: E 69 MET cc_start: 0.6641 (mtt) cc_final: 0.6142 (mtt) REVERT: E 235 ASP cc_start: 0.7081 (t0) cc_final: 0.6552 (t70) REVERT: E 392 VAL cc_start: 0.7017 (p) cc_final: 0.6082 (t) REVERT: E 461 LYS cc_start: 0.7739 (mmpt) cc_final: 0.7516 (tttp) REVERT: E 475 ARG cc_start: 0.4141 (OUTLIER) cc_final: 0.2906 (ptp-170) REVERT: I 43 ARG cc_start: 0.8471 (mpt90) cc_final: 0.7981 (mmt90) REVERT: I 63 ASP cc_start: 0.6567 (p0) cc_final: 0.6243 (p0) REVERT: I 69 MET cc_start: 0.6455 (mtt) cc_final: 0.6054 (mtt) REVERT: I 145 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.7023 (tp) REVERT: I 236 MET cc_start: 0.6195 (mmm) cc_final: 0.5839 (mpp) REVERT: I 392 VAL cc_start: 0.6738 (p) cc_final: 0.5796 (t) REVERT: I 461 LYS cc_start: 0.7820 (mmpt) cc_final: 0.7519 (tttp) REVERT: I 465 GLU cc_start: 0.6707 (tp30) cc_final: 0.6247 (tp30) outliers start: 105 outliers final: 75 residues processed: 503 average time/residue: 0.1404 time to fit residues: 110.4310 Evaluate side-chains 511 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 428 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 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 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 50 GLN 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 34 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 238 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 259 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 224 optimal weight: 50.0000 chunk 84 optimal weight: 0.9980 chunk 239 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 94 GLN A 45 HIS ** 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 45 HIS 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 45 HIS I 214 ASN ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4587 r_free = 0.4587 target = 0.250351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.212958 restraints weight = 33009.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.210885 restraints weight = 31372.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.212740 restraints weight = 24337.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.213000 restraints weight = 18349.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.213396 restraints weight = 16113.427| |-----------------------------------------------------------------------------| r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.2687 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 : 1.402 84.033 30633 Z= 0.470 Chirality : 0.059 1.462 3408 Planarity : 0.005 0.067 3879 Dihedral : 9.260 88.277 3204 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 4.32 % Allowed : 24.17 % Favored : 71.51 % 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: 0.14 (0.14), residues: 1335 sheet: -3.34 (0.43), residues: 105 loop : -2.81 (0.15), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 108 TYR 0.026 0.001 TYR H 29 PHE 0.047 0.001 PHE A 506 TRP 0.038 0.002 TRP A 553 HIS 0.007 0.001 HIS L 71 Details of bonding type rmsd covalent geometry : bond 0.00390 (22473) covalent geometry : angle 1.16323 (30561) hydrogen bonds : bond 0.04451 ( 1032) hydrogen bonds : angle 4.81021 ( 2988) metal coordination : bond 0.01333 ( 27) metal coordination : angle 16.20231 ( 72) Misc. bond : bond 0.06591 ( 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 531 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 431 time to evaluate : 0.759 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: B 9 ARG cc_start: 0.5825 (ttp80) cc_final: 0.5525 (mtp180) REVERT: B 10 TYR cc_start: 0.5431 (p90) cc_final: 0.5049 (p90) REVERT: B 210 MET cc_start: 0.4373 (mtt) cc_final: 0.4161 (mtt) REVERT: B 224 ARG cc_start: 0.7299 (tpt170) cc_final: 0.6927 (tpt90) REVERT: B 228 HIS cc_start: 0.6439 (t-170) cc_final: 0.6153 (t70) REVERT: D 37 PHE cc_start: 0.5378 (OUTLIER) cc_final: 0.4081 (t80) REVERT: F 20 MET cc_start: 0.4859 (mmt) cc_final: 0.4428 (mmp) REVERT: F 36 LEU cc_start: 0.1038 (OUTLIER) cc_final: 0.0521 (mt) REVERT: G 90 ARG cc_start: 0.7372 (ttt180) cc_final: 0.6978 (ttt90) REVERT: H 29 TYR cc_start: 0.7997 (t80) cc_final: 0.7665 (t80) REVERT: H 37 PHE cc_start: 0.5161 (OUTLIER) cc_final: 0.4550 (t80) REVERT: J 23 TYR cc_start: 0.4499 (OUTLIER) cc_final: 0.3920 (m-10) REVERT: J 210 MET cc_start: 0.5137 (mmt) cc_final: 0.4858 (mmt) REVERT: K 78 LEU cc_start: 0.5938 (OUTLIER) cc_final: 0.5490 (mp) REVERT: L 29 TYR cc_start: 0.8093 (t80) cc_final: 0.7393 (t80) REVERT: A 43 ARG cc_start: 0.8271 (mpt90) cc_final: 0.6810 (mmt180) REVERT: A 235 ASP cc_start: 0.6891 (t0) cc_final: 0.6447 (t70) REVERT: A 405 LEU cc_start: 0.5300 (mt) cc_final: 0.4338 (mp) REVERT: A 420 GLN cc_start: 0.8458 (pm20) cc_final: 0.8015 (mp10) REVERT: A 461 LYS cc_start: 0.7486 (mmpt) cc_final: 0.7272 (tttp) REVERT: E 69 MET cc_start: 0.6738 (mtt) cc_final: 0.6369 (mtt) REVERT: E 86 GLU cc_start: 0.7380 (OUTLIER) cc_final: 0.7180 (tp30) REVERT: E 235 ASP cc_start: 0.6831 (t0) cc_final: 0.6472 (t70) REVERT: E 392 VAL cc_start: 0.6799 (p) cc_final: 0.5824 (t) REVERT: E 461 LYS cc_start: 0.7631 (mmpt) cc_final: 0.7402 (tttp) REVERT: E 475 ARG cc_start: 0.4030 (ptp-170) cc_final: 0.2645 (ptp-170) REVERT: I 43 ARG cc_start: 0.8413 (mpt90) cc_final: 0.6903 (mmt180) REVERT: I 63 ASP cc_start: 0.6714 (p0) cc_final: 0.6442 (p0) REVERT: I 69 MET cc_start: 0.6510 (mtt) cc_final: 0.6242 (mtt) REVERT: I 98 GLU cc_start: 0.7058 (tm-30) cc_final: 0.6524 (tm-30) REVERT: I 236 MET cc_start: 0.5971 (mmm) cc_final: 0.5627 (mpp) REVERT: I 392 VAL cc_start: 0.6419 (p) cc_final: 0.5388 (t) REVERT: I 461 LYS cc_start: 0.7777 (mmpt) cc_final: 0.7530 (tttp) outliers start: 100 outliers final: 72 residues processed: 497 average time/residue: 0.1422 time to fit residues: 110.6062 Evaluate side-chains 494 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 416 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 A residue 540 HIS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 86 GLU 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 377 ASP 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 20 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 531 ASN 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: 0.5980 chunk 126 optimal weight: 7.9990 chunk 205 optimal weight: 20.0000 chunk 189 optimal weight: 8.9990 chunk 196 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 220 optimal weight: 30.0000 chunk 6 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 254 optimal weight: 9.9990 overall best weight: 6.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 94 GLN ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 GLN ** 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 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 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 = 0.4550 r_free = 0.4550 target = 0.246274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.207587 restraints weight = 33079.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.206097 restraints weight = 28902.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.207488 restraints weight = 27265.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.208351 restraints weight = 17834.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.208570 restraints weight = 16999.093| |-----------------------------------------------------------------------------| r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6628 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.109 22503 Z= 0.260 Angle : 1.469 83.230 30633 Z= 0.505 Chirality : 0.061 1.474 3408 Planarity : 0.006 0.069 3879 Dihedral : 9.538 88.526 3204 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.75 % Favored : 89.25 % Rotamer: Outliers : 5.45 % Allowed : 24.38 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -2.22 (0.15), residues: 2745 helix: -0.10 (0.14), residues: 1329 sheet: -3.25 (0.43), residues: 99 loop : -2.88 (0.15), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 9 TYR 0.019 0.002 TYR D 107 PHE 0.038 0.002 PHE A 506 TRP 0.017 0.002 TRP F 163 HIS 0.006 0.002 HIS L 71 Details of bonding type rmsd covalent geometry : bond 0.00603 (22473) covalent geometry : angle 1.22477 (30561) hydrogen bonds : bond 0.05162 ( 1032) hydrogen bonds : angle 5.14284 ( 2988) metal coordination : bond 0.01977 ( 27) metal coordination : angle 16.76739 ( 72) Misc. bond : bond 0.08085 ( 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 543 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 417 time to evaluate : 0.614 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: 0.5761 (ttp80) cc_final: 0.5503 (mtp180) REVERT: B 10 TYR cc_start: 0.5499 (p90) cc_final: 0.5106 (p90) REVERT: C 29 LEU cc_start: 0.6423 (OUTLIER) cc_final: 0.6069 (mm) REVERT: C 78 LEU cc_start: 0.6132 (OUTLIER) cc_final: 0.5740 (mp) REVERT: D 37 PHE cc_start: 0.5453 (OUTLIER) cc_final: 0.4220 (t80) REVERT: F 9 ARG cc_start: 0.6005 (ttp-170) cc_final: 0.5477 (mtp180) REVERT: F 20 MET cc_start: 0.4817 (mmt) cc_final: 0.4347 (mmp) REVERT: F 36 LEU cc_start: 0.1162 (OUTLIER) cc_final: 0.0928 (mt) REVERT: G 78 LEU cc_start: 0.5847 (OUTLIER) cc_final: 0.5310 (mp) REVERT: G 90 ARG cc_start: 0.7450 (ttt180) cc_final: 0.7017 (ttt90) REVERT: H 29 TYR cc_start: 0.8129 (t80) cc_final: 0.7779 (t80) REVERT: H 37 PHE cc_start: 0.5415 (OUTLIER) cc_final: 0.4475 (t80) REVERT: J 23 TYR cc_start: 0.4646 (OUTLIER) cc_final: 0.3981 (m-10) REVERT: J 36 LEU cc_start: 0.0760 (OUTLIER) cc_final: 0.0490 (mt) REVERT: J 228 HIS cc_start: 0.6268 (t70) cc_final: 0.5997 (t70) REVERT: K 78 LEU cc_start: 0.5874 (OUTLIER) cc_final: 0.5448 (mp) REVERT: L 29 TYR cc_start: 0.8202 (t80) cc_final: 0.7653 (t80) REVERT: A 43 ARG cc_start: 0.8318 (mpt90) cc_final: 0.7302 (mmt180) REVERT: A 139 ASP cc_start: 0.5827 (t70) cc_final: 0.5593 (t0) REVERT: A 420 GLN cc_start: 0.8432 (pm20) cc_final: 0.8030 (mp10) REVERT: A 461 LYS cc_start: 0.7664 (mmpt) cc_final: 0.7375 (tttp) REVERT: A 463 LEU cc_start: 0.5635 (OUTLIER) cc_final: 0.5378 (tt) REVERT: E 20 MET cc_start: 0.7325 (mmt) cc_final: 0.7116 (mmt) REVERT: E 69 MET cc_start: 0.6630 (mtt) cc_final: 0.6171 (mtt) REVERT: E 235 ASP cc_start: 0.7054 (t0) cc_final: 0.6617 (t70) REVERT: E 392 VAL cc_start: 0.7008 (p) cc_final: 0.6080 (t) REVERT: E 463 LEU cc_start: 0.5928 (OUTLIER) cc_final: 0.5615 (tt) REVERT: E 475 ARG cc_start: 0.4156 (OUTLIER) cc_final: 0.2682 (ptp-170) REVERT: I 43 ARG cc_start: 0.8431 (mpt90) cc_final: 0.7400 (mmt180) REVERT: I 63 ASP cc_start: 0.6742 (p0) cc_final: 0.6481 (p0) REVERT: I 69 MET cc_start: 0.6552 (mtt) cc_final: 0.6078 (mtt) REVERT: I 145 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7042 (tp) REVERT: I 155 LYS cc_start: 0.7840 (tmmt) cc_final: 0.7377 (tmmt) REVERT: I 236 MET cc_start: 0.6048 (mmm) cc_final: 0.5806 (mpp) REVERT: I 392 VAL cc_start: 0.6770 (p) cc_final: 0.5848 (t) REVERT: I 461 LYS cc_start: 0.7883 (mmpt) cc_final: 0.7617 (tttp) REVERT: I 465 GLU cc_start: 0.6674 (tp30) cc_final: 0.6199 (tp30) REVERT: I 506 PHE cc_start: 0.3532 (m-80) cc_final: 0.3006 (t80) outliers start: 126 outliers final: 96 residues processed: 504 average time/residue: 0.1421 time to fit residues: 111.9215 Evaluate side-chains 519 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 410 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 148 GLU 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 73 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 176 LEU 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 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 H residue 111 VAL Chi-restraints excluded: chain J residue 23 TYR Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 42 LEU 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 K residue 22 ILE Chi-restraints excluded: chain K residue 44 LEU 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 47 VAL Chi-restraints excluded: chain A residue 72 THR 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 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 E residue 46 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 134 THR 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 394 VAL Chi-restraints excluded: chain E residue 437 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 E residue 566 MET Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 39 VAL 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 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 475 ARG Chi-restraints excluded: chain I residue 531 ASN Chi-restraints excluded: chain I residue 540 HIS Chi-restraints excluded: chain I residue 566 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 257 optimal weight: 50.0000 chunk 92 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 205 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 237 optimal weight: 2.9990 chunk 137 optimal weight: 20.0000 chunk 28 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 GLN ** 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 25 GLN ** 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 = 0.4577 r_free = 0.4577 target = 0.249362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.211582 restraints weight = 33099.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.209425 restraints weight = 35282.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.212065 restraints weight = 25450.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.211994 restraints weight = 18108.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.212396 restraints weight = 17131.767| |-----------------------------------------------------------------------------| r_work (final): 0.4228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6550 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 22503 Z= 0.188 Angle : 1.390 83.397 30633 Z= 0.476 Chirality : 0.060 1.483 3408 Planarity : 0.005 0.069 3879 Dihedral : 9.287 88.195 3204 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 5.27 % Allowed : 25.16 % Favored : 69.56 % 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: 0.14 (0.14), residues: 1335 sheet: -3.18 (0.44), residues: 99 loop : -2.82 (0.15), residues: 1311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 9 TYR 0.019 0.001 TYR L 29 PHE 0.031 0.002 PHE A 506 TRP 0.025 0.001 TRP A 65 HIS 0.008 0.001 HIS L 71 Details of bonding type rmsd covalent geometry : bond 0.00429 (22473) covalent geometry : angle 1.17661 (30561) hydrogen bonds : bond 0.04608 ( 1032) hydrogen bonds : angle 4.88914 ( 2988) metal coordination : bond 0.01510 ( 27) metal coordination : angle 15.32263 ( 72) Misc. bond : bond 0.06328 ( 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 537 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 415 time to evaluate : 0.754 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: 0.5816 (ttp80) cc_final: 0.5571 (mtp180) REVERT: B 10 TYR cc_start: 0.5451 (p90) cc_final: 0.5064 (p90) REVERT: C 29 LEU cc_start: 0.6417 (OUTLIER) cc_final: 0.6042 (mm) REVERT: C 78 LEU cc_start: 0.6006 (OUTLIER) cc_final: 0.5646 (mp) REVERT: D 37 PHE cc_start: 0.5496 (OUTLIER) cc_final: 0.4198 (t80) REVERT: F 9 ARG cc_start: 0.6026 (ttp-170) cc_final: 0.5314 (ttp-170) REVERT: F 36 LEU cc_start: 0.1120 (OUTLIER) cc_final: 0.0785 (mp) REVERT: G 78 LEU cc_start: 0.5806 (OUTLIER) cc_final: 0.5327 (mp) REVERT: G 90 ARG cc_start: 0.7415 (ttt180) cc_final: 0.6987 (ttt90) REVERT: H 29 TYR cc_start: 0.8087 (t80) cc_final: 0.7727 (t80) REVERT: H 37 PHE cc_start: 0.5261 (OUTLIER) cc_final: 0.4476 (t80) REVERT: J 23 TYR cc_start: 0.4859 (OUTLIER) cc_final: 0.4319 (m-10) REVERT: J 228 HIS cc_start: 0.6248 (t70) cc_final: 0.6002 (t70) REVERT: K 78 LEU cc_start: 0.5870 (OUTLIER) cc_final: 0.5382 (mp) REVERT: A 20 MET cc_start: 0.7141 (mmt) cc_final: 0.6864 (mmt) REVERT: A 43 ARG cc_start: 0.8286 (mpt90) cc_final: 0.6767 (mmt180) REVERT: A 235 ASP cc_start: 0.6818 (t0) cc_final: 0.6346 (t70) REVERT: A 236 MET cc_start: 0.5715 (mmm) cc_final: 0.5008 (mmm) REVERT: A 356 MET cc_start: 0.6408 (ttp) cc_final: 0.6049 (mtp) REVERT: A 420 GLN cc_start: 0.8499 (pm20) cc_final: 0.8093 (mp10) REVERT: A 461 LYS cc_start: 0.7561 (mmpt) cc_final: 0.7310 (tttp) REVERT: A 463 LEU cc_start: 0.5547 (OUTLIER) cc_final: 0.5248 (tt) REVERT: E 69 MET cc_start: 0.6717 (mtt) cc_final: 0.6382 (mtt) REVERT: E 86 GLU cc_start: 0.7420 (OUTLIER) cc_final: 0.7197 (tp30) REVERT: E 235 ASP cc_start: 0.6848 (t0) cc_final: 0.6534 (t70) REVERT: E 392 VAL cc_start: 0.6834 (p) cc_final: 0.5874 (t) REVERT: E 463 LEU cc_start: 0.5771 (OUTLIER) cc_final: 0.5440 (tt) REVERT: E 475 ARG cc_start: 0.4081 (OUTLIER) cc_final: 0.2589 (ptp-170) REVERT: I 43 ARG cc_start: 0.8422 (mpt90) cc_final: 0.7379 (mmt180) REVERT: I 63 ASP cc_start: 0.6751 (p0) cc_final: 0.6506 (p0) REVERT: I 69 MET cc_start: 0.6471 (mtt) cc_final: 0.6075 (mtt) REVERT: I 152 GLN cc_start: 0.7341 (mm-40) cc_final: 0.6969 (mm-40) REVERT: I 155 LYS cc_start: 0.7852 (tmmt) cc_final: 0.6749 (tmmt) REVERT: I 392 VAL cc_start: 0.6526 (p) cc_final: 0.5528 (t) REVERT: I 461 LYS cc_start: 0.7807 (mmpt) cc_final: 0.7550 (tttp) REVERT: I 569 ARG cc_start: 0.7509 (tmm-80) cc_final: 0.7050 (tmm-80) outliers start: 122 outliers final: 90 residues processed: 502 average time/residue: 0.1408 time to fit residues: 109.6802 Evaluate side-chains 506 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 404 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 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 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 42 LEU 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 44 LEU Chi-restraints excluded: chain K residue 54 SER 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 102 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 217 ILE 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 46 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 134 THR 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 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 6 ARG 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 199 VAL Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 394 VAL 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: 0.0980 chunk 272 optimal weight: 20.0000 chunk 213 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 212 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 117 optimal weight: 0.0870 chunk 173 optimal weight: 9.9990 chunk 200 optimal weight: 5.9990 chunk 234 optimal weight: 6.9990 chunk 267 optimal weight: 5.9990 overall best weight: 2.2364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 HIS ** E 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 ASN ** 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 540 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.250962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.211137 restraints weight = 33059.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.212793 restraints weight = 24693.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.214095 restraints weight = 16347.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.213161 restraints weight = 13670.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.213743 restraints weight = 12594.852| |-----------------------------------------------------------------------------| r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.3149 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= 0.172 Angle : 1.359 83.317 30633 Z= 0.468 Chirality : 0.060 1.492 3408 Planarity : 0.005 0.066 3879 Dihedral : 9.114 87.381 3204 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 5.19 % Allowed : 25.42 % Favored : 69.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.77 (0.15), residues: 2745 helix: 0.37 (0.14), residues: 1335 sheet: -2.78 (0.41), residues: 123 loop : -2.80 (0.15), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 108 TYR 0.019 0.001 TYR L 29 PHE 0.028 0.001 PHE A 506 TRP 0.020 0.001 TRP A 65 HIS 0.007 0.001 HIS L 71 Details of bonding type rmsd covalent geometry : bond 0.00387 (22473) covalent geometry : angle 1.16515 (30561) hydrogen bonds : bond 0.04282 ( 1032) hydrogen bonds : angle 4.70050 ( 2988) metal coordination : bond 0.01392 ( 27) metal coordination : angle 14.48438 ( 72) Misc. bond : bond 0.04892 ( 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 542 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 422 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: symmetry clash revert: symmetry clash REVERT: B 4 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.6337 (tm-30) REVERT: B 9 ARG cc_start: 0.5772 (ttp80) cc_final: 0.5558 (mtp180) REVERT: B 10 TYR cc_start: 0.5393 (p90) cc_final: 0.5007 (p90) REVERT: B 228 HIS cc_start: 0.6316 (t70) cc_final: 0.6072 (t70) REVERT: C 78 LEU cc_start: 0.6023 (OUTLIER) cc_final: 0.5687 (mp) REVERT: D 37 PHE cc_start: 0.5331 (OUTLIER) cc_final: 0.4133 (t80) REVERT: F 9 ARG cc_start: 0.6137 (ttp-170) cc_final: 0.5538 (mtp180) REVERT: F 36 LEU cc_start: 0.1082 (OUTLIER) cc_final: 0.0570 (mt) REVERT: G 78 LEU cc_start: 0.6012 (OUTLIER) cc_final: 0.5584 (mp) REVERT: H 29 TYR cc_start: 0.8038 (t80) cc_final: 0.7744 (t80) REVERT: H 37 PHE cc_start: 0.5129 (OUTLIER) cc_final: 0.4514 (t80) REVERT: J 23 TYR cc_start: 0.4856 (OUTLIER) cc_final: 0.4411 (m-10) REVERT: J 228 HIS cc_start: 0.6324 (t70) cc_final: 0.5962 (t70) REVERT: K 78 LEU cc_start: 0.5872 (OUTLIER) cc_final: 0.5410 (mp) REVERT: A 20 MET cc_start: 0.7242 (mmt) cc_final: 0.6947 (mmt) REVERT: A 43 ARG cc_start: 0.8339 (mpt90) cc_final: 0.6431 (mmt180) REVERT: A 235 ASP cc_start: 0.6997 (t0) cc_final: 0.6744 (t70) REVERT: A 236 MET cc_start: 0.5559 (mmm) cc_final: 0.4958 (mmm) REVERT: A 420 GLN cc_start: 0.8541 (pm20) cc_final: 0.8127 (mp10) REVERT: A 463 LEU cc_start: 0.5486 (OUTLIER) cc_final: 0.5183 (tt) REVERT: E 69 MET cc_start: 0.6784 (mtt) cc_final: 0.6465 (mtt) REVERT: E 86 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7286 (tp30) REVERT: E 235 ASP cc_start: 0.6836 (t0) cc_final: 0.6440 (t70) REVERT: E 238 MET cc_start: 0.3561 (tpt) cc_final: 0.3223 (tpt) REVERT: E 392 VAL cc_start: 0.6688 (p) cc_final: 0.5771 (t) REVERT: E 463 LEU cc_start: 0.5610 (OUTLIER) cc_final: 0.5278 (tt) REVERT: E 475 ARG cc_start: 0.3908 (OUTLIER) cc_final: 0.2433 (ptp-170) REVERT: I 43 ARG cc_start: 0.8438 (mpt90) cc_final: 0.7047 (mpt90) REVERT: I 69 MET cc_start: 0.6705 (mtt) cc_final: 0.6178 (mtt) REVERT: I 155 LYS cc_start: 0.7978 (tmmt) cc_final: 0.7714 (tmmt) REVERT: I 392 VAL cc_start: 0.6376 (p) cc_final: 0.5417 (t) REVERT: I 461 LYS cc_start: 0.7744 (mmpt) cc_final: 0.7486 (tttp) REVERT: I 552 ASN cc_start: 0.6636 (OUTLIER) cc_final: 0.6202 (p0) REVERT: I 569 ARG cc_start: 0.7351 (tmm-80) cc_final: 0.7012 (tmm-80) outliers start: 120 outliers final: 89 residues processed: 509 average time/residue: 0.1418 time to fit residues: 111.9293 Evaluate side-chains 507 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 405 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 GLU 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 226 ILE Chi-restraints excluded: chain C residue 22 ILE 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 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 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 44 LEU Chi-restraints excluded: chain K residue 54 SER 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 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 102 MET 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 463 LEU Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 134 THR 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 225 MET 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 46 THR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 55 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 475 ARG Chi-restraints excluded: chain I residue 520 MET Chi-restraints excluded: chain I residue 531 ASN Chi-restraints excluded: chain I residue 540 HIS Chi-restraints excluded: chain I residue 552 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 223 optimal weight: 7.9990 chunk 184 optimal weight: 30.0000 chunk 175 optimal weight: 40.0000 chunk 199 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 191 optimal weight: 20.0000 chunk 264 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 247 optimal weight: 0.5980 chunk 136 optimal weight: 5.9990 overall best weight: 1.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 94 GLN ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 ASN ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 HIS E 214 ASN ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 HIS ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 218 ASN I 395 HIS I 540 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4597 r_free = 0.4597 target = 0.251833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.211951 restraints weight = 33318.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.213974 restraints weight = 23146.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.214706 restraints weight = 15730.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.214809 restraints weight = 14093.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.214907 restraints weight = 12924.255| |-----------------------------------------------------------------------------| r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 moved from start: 0.3291 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= 0.168 Angle : 1.348 83.221 30633 Z= 0.468 Chirality : 0.060 1.493 3408 Planarity : 0.005 0.065 3879 Dihedral : 9.029 86.763 3204 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 4.54 % Allowed : 26.42 % Favored : 69.04 % 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: -1.68 (0.15), residues: 2745 helix: 0.45 (0.14), residues: 1347 sheet: -2.73 (0.41), residues: 123 loop : -2.80 (0.15), residues: 1275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 108 TYR 0.020 0.001 TYR L 29 PHE 0.026 0.001 PHE A 506 TRP 0.017 0.001 TRP L 48 HIS 0.018 0.001 HIS I 540 Details of bonding type rmsd covalent geometry : bond 0.00376 (22473) covalent geometry : angle 1.16353 (30561) hydrogen bonds : bond 0.04144 ( 1032) hydrogen bonds : angle 4.62616 ( 2988) metal coordination : bond 0.01225 ( 27) metal coordination : angle 14.07481 ( 72) Misc. bond : bond 0.04460 ( 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 521 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 416 time to evaluate : 0.796 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: 0.5787 (ttp80) cc_final: 0.5558 (mtp180) REVERT: B 10 TYR cc_start: 0.5365 (p90) cc_final: 0.4984 (p90) REVERT: B 228 HIS cc_start: 0.6222 (t70) cc_final: 0.5978 (t70) REVERT: C 78 LEU cc_start: 0.6005 (OUTLIER) cc_final: 0.5687 (mp) REVERT: D 37 PHE cc_start: 0.5170 (OUTLIER) cc_final: 0.4261 (t80) REVERT: F 9 ARG cc_start: 0.6071 (ttp-170) cc_final: 0.5483 (mtp180) REVERT: F 210 MET cc_start: 0.4842 (mtt) cc_final: 0.4556 (mmt) REVERT: G 78 LEU cc_start: 0.5837 (OUTLIER) cc_final: 0.5388 (mp) REVERT: H 29 TYR cc_start: 0.8013 (t80) cc_final: 0.7734 (t80) REVERT: H 37 PHE cc_start: 0.5021 (OUTLIER) cc_final: 0.4552 (t80) REVERT: J 23 TYR cc_start: 0.4957 (OUTLIER) cc_final: 0.4569 (m-10) REVERT: J 228 HIS cc_start: 0.6240 (t70) cc_final: 0.5989 (t70) REVERT: K 78 LEU cc_start: 0.5828 (OUTLIER) cc_final: 0.5385 (mp) REVERT: A 43 ARG cc_start: 0.8329 (mpt90) cc_final: 0.5521 (mpt90) REVERT: A 235 ASP cc_start: 0.6911 (t0) cc_final: 0.6555 (t0) REVERT: A 236 MET cc_start: 0.5515 (mmm) cc_final: 0.4928 (mmm) REVERT: A 420 GLN cc_start: 0.8487 (pm20) cc_final: 0.8086 (mp10) REVERT: A 463 LEU cc_start: 0.5538 (OUTLIER) cc_final: 0.5240 (tt) REVERT: E 69 MET cc_start: 0.6712 (mtt) cc_final: 0.6421 (mtt) REVERT: E 86 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7279 (tp30) REVERT: E 235 ASP cc_start: 0.6878 (t0) cc_final: 0.6625 (t70) REVERT: E 238 MET cc_start: 0.3408 (tpt) cc_final: 0.3098 (tpt) REVERT: E 392 VAL cc_start: 0.6635 (p) cc_final: 0.5662 (t) REVERT: E 463 LEU cc_start: 0.5450 (OUTLIER) cc_final: 0.5100 (tt) REVERT: E 475 ARG cc_start: 0.3903 (OUTLIER) cc_final: 0.2437 (ptp-170) REVERT: I 43 ARG cc_start: 0.8383 (mpt90) cc_final: 0.6986 (mpt90) REVERT: I 69 MET cc_start: 0.6614 (mtt) cc_final: 0.6117 (mtt) REVERT: I 392 VAL cc_start: 0.6278 (p) cc_final: 0.5286 (t) REVERT: I 461 LYS cc_start: 0.7732 (mmpt) cc_final: 0.7473 (tttp) REVERT: I 569 ARG cc_start: 0.7258 (tmm-80) cc_final: 0.6977 (tmm-80) outliers start: 105 outliers final: 84 residues processed: 491 average time/residue: 0.1375 time to fit residues: 105.6213 Evaluate side-chains 497 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 403 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 226 ILE Chi-restraints excluded: chain C residue 22 ILE 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 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 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 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 44 LEU Chi-restraints excluded: chain K residue 54 SER 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 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 102 MET 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 463 LEU Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 520 MET Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 134 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 212 THR 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 46 THR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 55 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 475 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 215 optimal weight: 8.9990 chunk 236 optimal weight: 9.9990 chunk 244 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 230 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 241 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 chunk 270 optimal weight: 0.9990 chunk 90 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 94 GLN ** A 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 ASN ** E 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 HIS ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 540 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.249460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.208763 restraints weight = 33333.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.208692 restraints weight = 26666.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.211452 restraints weight = 17555.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.210805 restraints weight = 15006.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.211179 restraints weight = 13356.881| |-----------------------------------------------------------------------------| r_work (final): 0.4209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.3288 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= 0.212 Angle : 1.388 82.839 30633 Z= 0.489 Chirality : 0.061 1.492 3408 Planarity : 0.005 0.064 3879 Dihedral : 9.175 86.224 3204 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 4.50 % Allowed : 26.59 % Favored : 68.91 % 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: -1.85 (0.15), residues: 2745 helix: 0.26 (0.14), residues: 1350 sheet: -2.51 (0.43), residues: 117 loop : -2.86 (0.15), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 108 TYR 0.021 0.002 TYR F 10 PHE 0.028 0.002 PHE A 506 TRP 0.040 0.002 TRP I 553 HIS 0.018 0.002 HIS I 540 Details of bonding type rmsd covalent geometry : bond 0.00488 (22473) covalent geometry : angle 1.20092 (30561) hydrogen bonds : bond 0.04568 ( 1032) hydrogen bonds : angle 4.81088 ( 2988) metal coordination : bond 0.01674 ( 27) metal coordination : angle 14.40770 ( 72) Misc. bond : bond 0.04003 ( 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 510 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 406 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: B 4 GLU cc_start: 0.6596 (OUTLIER) cc_final: 0.6309 (tm-30) REVERT: B 9 ARG cc_start: 0.5814 (ttp80) cc_final: 0.5601 (mtp180) REVERT: B 10 TYR cc_start: 0.5365 (p90) cc_final: 0.4981 (p90) REVERT: B 210 MET cc_start: 0.4692 (mtt) cc_final: 0.4468 (mtm) REVERT: B 228 HIS cc_start: 0.6289 (t70) cc_final: 0.6051 (t70) REVERT: C 29 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.6111 (mm) REVERT: C 78 LEU cc_start: 0.6074 (OUTLIER) cc_final: 0.5725 (mp) REVERT: D 37 PHE cc_start: 0.5330 (OUTLIER) cc_final: 0.4316 (t80) REVERT: F 1 MET cc_start: 0.4238 (ttt) cc_final: 0.3954 (ttt) REVERT: F 9 ARG cc_start: 0.6121 (ttp-170) cc_final: 0.5386 (mtp180) REVERT: F 36 LEU cc_start: 0.1166 (OUTLIER) cc_final: 0.0813 (mp) REVERT: F 210 MET cc_start: 0.5211 (mtt) cc_final: 0.4684 (mmt) REVERT: G 78 LEU cc_start: 0.6075 (OUTLIER) cc_final: 0.5614 (mp) REVERT: H 29 TYR cc_start: 0.8085 (t80) cc_final: 0.7799 (t80) REVERT: H 37 PHE cc_start: 0.5311 (OUTLIER) cc_final: 0.4589 (t80) REVERT: J 23 TYR cc_start: 0.5067 (OUTLIER) cc_final: 0.4556 (m-10) REVERT: J 228 HIS cc_start: 0.6292 (t70) cc_final: 0.6041 (t70) REVERT: K 78 LEU cc_start: 0.5881 (OUTLIER) cc_final: 0.5424 (mp) REVERT: A 20 MET cc_start: 0.7626 (mmt) cc_final: 0.7390 (mmt) REVERT: A 43 ARG cc_start: 0.8316 (mpt90) cc_final: 0.6424 (mmt180) REVERT: A 235 ASP cc_start: 0.7050 (t0) cc_final: 0.6667 (t70) REVERT: A 236 MET cc_start: 0.5512 (mmm) cc_final: 0.4933 (mmm) REVERT: A 420 GLN cc_start: 0.8495 (pm20) cc_final: 0.8090 (mp10) REVERT: A 463 LEU cc_start: 0.5507 (OUTLIER) cc_final: 0.5208 (tt) REVERT: A 573 MET cc_start: 0.7280 (tpp) cc_final: 0.6400 (tpp) REVERT: E 20 MET cc_start: 0.7410 (mmt) cc_final: 0.7176 (mmt) REVERT: E 69 MET cc_start: 0.6822 (mtt) cc_final: 0.6496 (mtt) REVERT: E 86 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7355 (tp30) REVERT: E 235 ASP cc_start: 0.7048 (t0) cc_final: 0.6668 (t70) REVERT: E 392 VAL cc_start: 0.6775 (p) cc_final: 0.5854 (t) REVERT: E 463 LEU cc_start: 0.5462 (OUTLIER) cc_final: 0.5151 (tt) REVERT: E 475 ARG cc_start: 0.3977 (OUTLIER) cc_final: 0.2452 (ptp-170) REVERT: I 20 MET cc_start: 0.7192 (mmt) cc_final: 0.6978 (mmt) REVERT: I 43 ARG cc_start: 0.8447 (mpt90) cc_final: 0.6856 (mmt180) REVERT: I 69 MET cc_start: 0.6689 (mtt) cc_final: 0.6239 (mtt) REVERT: I 98 GLU cc_start: 0.7009 (tm-30) cc_final: 0.6419 (tm-30) REVERT: I 392 VAL cc_start: 0.6466 (p) cc_final: 0.5549 (t) REVERT: I 461 LYS cc_start: 0.7794 (mmpt) cc_final: 0.7545 (tttp) REVERT: I 569 ARG cc_start: 0.7259 (tmm-80) cc_final: 0.6990 (tmm-80) outliers start: 104 outliers final: 88 residues processed: 479 average time/residue: 0.1430 time to fit residues: 106.4921 Evaluate side-chains 502 residues out of total 2316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 401 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 GLU 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 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 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 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 44 LEU Chi-restraints excluded: chain K residue 54 SER 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 102 MET 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 463 LEU Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 86 GLU Chi-restraints excluded: chain E residue 134 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 389 ILE 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 46 THR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 55 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 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: 9.9990 chunk 262 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 137 optimal weight: 30.0000 chunk 132 optimal weight: 8.9990 chunk 48 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 chunk 220 optimal weight: 4.9990 chunk 227 optimal weight: 9.9990 chunk 155 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 94 GLN ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 HIS ** I 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 540 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.248099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.210258 restraints weight = 33067.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.208469 restraints weight = 33623.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.209942 restraints weight = 27967.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.210782 restraints weight = 18127.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.211090 restraints weight = 16080.311| |-----------------------------------------------------------------------------| r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 22503 Z= 0.240 Angle : 1.418 82.760 30633 Z= 0.502 Chirality : 0.062 1.492 3408 Planarity : 0.005 0.065 3879 Dihedral : 9.307 86.337 3204 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 16.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 4.84 % Allowed : 26.63 % Favored : 68.53 % 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: -2.03 (0.15), residues: 2745 helix: 0.07 (0.14), residues: 1350 sheet: -2.53 (0.43), residues: 117 loop : -2.92 (0.15), residues: 1278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 108 TYR 0.021 0.002 TYR F 10 PHE 0.029 0.002 PHE A 506 TRP 0.042 0.002 TRP I 553 HIS 0.016 0.002 HIS I 540 Details of bonding type rmsd covalent geometry : bond 0.00556 (22473) covalent geometry : angle 1.22184 (30561) hydrogen bonds : bond 0.04885 ( 1032) hydrogen bonds : angle 4.98017 ( 2988) metal coordination : bond 0.01946 ( 27) metal coordination : angle 14.88647 ( 72) Misc. bond : bond 0.03873 ( 3) =============================================================================== Job complete usr+sys time: 3588.05 seconds wall clock time: 62 minutes 53.20 seconds (3773.20 seconds total)