Starting phenix.real_space_refine on Sun Sep 29 10:04:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu6_21906/09_2024/6wu6_21906.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu6_21906/09_2024/6wu6_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu6_21906/09_2024/6wu6_21906.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu6_21906/09_2024/6wu6_21906.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu6_21906/09_2024/6wu6_21906.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wu6_21906/09_2024/6wu6_21906.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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, H, L, E, I, G, K Time building chain proxies: 11.31, per 1000 atoms: 0.51 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: 5.83 Conformation dependent library (CDL) restraints added in 3.0 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: 1.82 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: 6.26 Time building geometry restraints manager: 6.50 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } 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' } 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: 0.130 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: 0.770 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 48.260 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.130 ------------------------------------------------------------------------------- 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 : 0.033 1.694 22473 Z= 2.116 Angle : 1.504 50.848 30561 Z= 0.700 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.014 0.002 TRP H 48 HIS 0.007 0.001 HIS H 71 PHE 0.026 0.002 PHE H 37 TYR 0.015 0.002 TYR L 29 ARG 0.005 0.001 ARG A 196 *********************** 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 fitting. rotamer outliers: 31 poor density : 529 time to evaluate : 2.273 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: 0.6987 (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: 0.3430 time to fit residues: 282.4316 Evaluate side-chains 459 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 443 time to evaluate : 2.361 ------------------------------------------------------------------------------- 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 230 optimal weight: 3.9990 chunk 206 optimal weight: 0.0270 chunk 114 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 139 optimal weight: 30.0000 chunk 110 optimal weight: 1.9990 chunk 213 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 247 optimal weight: 0.9990 overall best weight: 2.0046 ------------------------------------------------------------------------------- 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 556 HIS E 25 GLN E 518 ASN E 556 HIS I 25 GLN I 556 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.204 22473 Z= 0.338 Angle : 1.220 52.011 30561 Z= 0.500 Chirality : 0.085 2.474 3408 Planarity : 0.006 0.067 3879 Dihedral : 10.315 97.331 3220 Min Nonbonded Distance : 1.543 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 3.11 % Allowed : 17.08 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.86 (0.15), residues: 2745 helix: -0.65 (0.13), residues: 1323 sheet: -3.40 (0.43), residues: 105 loop : -3.20 (0.15), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP F 163 HIS 0.014 0.002 HIS E 354 PHE 0.026 0.002 PHE H 51 TYR 0.036 0.002 TYR H 29 ARG 0.004 0.001 ARG E 228 *********************** 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 550 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 478 time to evaluate : 2.048 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 10 TYR cc_start: 0.5450 (p90) cc_final: 0.4876 (p90) REVERT: B 20 MET cc_start: 0.5740 (mmt) cc_final: 0.5491 (mmt) REVERT: F 1 MET cc_start: 0.3603 (ttt) cc_final: 0.3355 (ttt) REVERT: F 53 ARG cc_start: 0.6374 (pmt-80) cc_final: 0.6092 (ptt90) REVERT: H 29 TYR cc_start: 0.8023 (t80) cc_final: 0.7481 (t80) REVERT: H 83 TYR cc_start: 0.7976 (m-10) cc_final: 0.7617 (m-10) REVERT: J 9 ARG cc_start: 0.5632 (ttp80) cc_final: 0.5335 (mtp180) REVERT: J 23 TYR cc_start: 0.4221 (OUTLIER) cc_final: 0.3877 (m-10) REVERT: K 28 ILE cc_start: 0.7210 (mm) cc_final: 0.6920 (mt) REVERT: A 43 ARG cc_start: 0.8023 (mpt90) cc_final: 0.7070 (mmt180) REVERT: A 108 ARG cc_start: 0.7019 (mmt180) cc_final: 0.6685 (tpt170) REVERT: A 139 ASP cc_start: 0.5854 (t70) cc_final: 0.5653 (t0) REVERT: A 392 VAL cc_start: 0.6956 (p) cc_final: 0.5952 (t) REVERT: A 461 LYS cc_start: 0.7189 (mmpt) cc_final: 0.6980 (tttp) REVERT: A 475 ARG cc_start: 0.4479 (ptp-170) cc_final: 0.2721 (ptp-170) REVERT: E 43 ARG cc_start: 0.8023 (mpt90) cc_final: 0.6688 (mmt180) REVERT: E 53 ILE cc_start: 0.8139 (tp) cc_final: 0.7931 (tp) REVERT: E 86 GLU cc_start: 0.6716 (tp30) cc_final: 0.6476 (tp30) REVERT: E 155 LYS cc_start: 0.7510 (tmmt) cc_final: 0.7303 (tmmt) REVERT: E 235 ASP cc_start: 0.6186 (t0) cc_final: 0.5905 (t70) REVERT: E 356 MET cc_start: 0.5890 (ttp) cc_final: 0.5660 (ttp) REVERT: E 392 VAL cc_start: 0.6974 (p) cc_final: 0.5945 (t) REVERT: E 465 GLU cc_start: 0.6167 (tp30) cc_final: 0.5905 (tp30) REVERT: E 475 ARG cc_start: 0.4175 (ptp-170) cc_final: 0.2994 (ptp-170) REVERT: I 43 ARG cc_start: 0.8185 (mpt90) cc_final: 0.7058 (mmt180) REVERT: I 63 ASP cc_start: 0.5595 (p0) cc_final: 0.5026 (p0) REVERT: I 392 VAL cc_start: 0.6796 (p) cc_final: 0.5685 (t) REVERT: I 465 GLU cc_start: 0.6388 (tp30) cc_final: 0.5928 (tp30) REVERT: I 475 ARG cc_start: 0.4095 (ptp-170) cc_final: 0.2915 (ptp-170) REVERT: I 494 LEU cc_start: 0.6105 (pp) cc_final: 0.5713 (tt) outliers start: 72 outliers final: 47 residues processed: 511 average time/residue: 0.3319 time to fit residues: 259.4302 Evaluate side-chains 489 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 441 time to evaluate : 2.418 ------------------------------------------------------------------------------- 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 C residue 22 ILE 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 226 ILE Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 89 ILE 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 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 28 LEU Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain A residue 55 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 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 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 480 MET Chi-restraints excluded: chain E residue 520 MET Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 389 ILE Chi-restraints excluded: chain I residue 520 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 20.0000 chunk 76 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 248 optimal weight: 8.9990 chunk 268 optimal weight: 0.3980 chunk 221 optimal weight: 6.9990 chunk 246 optimal weight: 0.1980 chunk 84 optimal weight: 6.9990 chunk 199 optimal weight: 0.0060 overall best weight: 2.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 94 GLN L 94 GLN A 25 GLN A 45 HIS ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 395 HIS ** A 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 45 HIS E 214 ASN ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 45 HIS ** I 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 22473 Z= 0.273 Angle : 1.190 84.837 30561 Z= 0.480 Chirality : 0.057 1.314 3408 Planarity : 0.005 0.066 3879 Dihedral : 9.527 89.089 3205 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 3.29 % Allowed : 20.28 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.15), residues: 2745 helix: -0.12 (0.14), residues: 1323 sheet: -3.25 (0.42), residues: 105 loop : -3.01 (0.15), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 163 HIS 0.010 0.001 HIS I 354 PHE 0.018 0.002 PHE I 506 TYR 0.025 0.002 TYR L 29 ARG 0.005 0.000 ARG A 21 *********************** 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 516 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 440 time to evaluate : 2.242 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: symmetry clash revert: symmetry clash REVERT: D 37 PHE cc_start: 0.4742 (OUTLIER) cc_final: 0.4217 (t80) REVERT: F 20 MET cc_start: 0.4342 (mmt) cc_final: 0.3835 (mmp) REVERT: F 53 ARG cc_start: 0.6367 (pmt-80) cc_final: 0.5971 (ptt90) REVERT: G 74 MET cc_start: 0.8103 (mmt) cc_final: 0.7828 (mmm) REVERT: H 29 TYR cc_start: 0.8077 (t80) cc_final: 0.7570 (t80) REVERT: H 83 TYR cc_start: 0.7922 (m-10) cc_final: 0.7543 (m-10) REVERT: J 5 PHE cc_start: 0.5933 (m-80) cc_final: 0.5574 (m-80) REVERT: J 9 ARG cc_start: 0.5555 (ttp80) cc_final: 0.5316 (mtp180) REVERT: J 23 TYR cc_start: 0.4014 (OUTLIER) cc_final: 0.3730 (m-10) REVERT: J 210 MET cc_start: 0.4708 (mtt) cc_final: 0.4438 (mmt) REVERT: L 29 TYR cc_start: 0.8164 (t80) cc_final: 0.7604 (t80) REVERT: A 43 ARG cc_start: 0.8058 (mpt90) cc_final: 0.6805 (mmt180) REVERT: A 356 MET cc_start: 0.6293 (ttp) cc_final: 0.5566 (ttp) REVERT: A 392 VAL cc_start: 0.6906 (p) cc_final: 0.5811 (t) REVERT: A 475 ARG cc_start: 0.4649 (ptp-170) cc_final: 0.3067 (ptp-170) REVERT: E 43 ARG cc_start: 0.8058 (mpt90) cc_final: 0.7132 (mmt180) REVERT: E 53 ILE cc_start: 0.8114 (tp) cc_final: 0.7879 (tp) REVERT: E 235 ASP cc_start: 0.6010 (t0) cc_final: 0.5751 (t70) REVERT: E 392 VAL cc_start: 0.6879 (p) cc_final: 0.5839 (t) REVERT: E 475 ARG cc_start: 0.4202 (ptp-170) cc_final: 0.2880 (ptp-170) REVERT: I 43 ARG cc_start: 0.8207 (mpt90) cc_final: 0.6949 (mmt180) REVERT: I 63 ASP cc_start: 0.5489 (p0) cc_final: 0.5012 (p0) REVERT: I 236 MET cc_start: 0.5899 (mmm) cc_final: 0.5409 (mpp) REVERT: I 356 MET cc_start: 0.6279 (ttp) cc_final: 0.6034 (ttp) REVERT: I 392 VAL cc_start: 0.6783 (p) cc_final: 0.5726 (t) REVERT: I 465 GLU cc_start: 0.6405 (tp30) cc_final: 0.5972 (tp30) REVERT: I 475 ARG cc_start: 0.4068 (ptp-170) cc_final: 0.3014 (ptp-170) outliers start: 76 outliers final: 54 residues processed: 484 average time/residue: 0.3263 time to fit residues: 243.7492 Evaluate side-chains 485 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 429 time to evaluate : 2.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain B residue 91 ILE Chi-restraints excluded: chain B residue 117 ILE Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 226 ILE Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 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 212 CYS Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 89 ILE Chi-restraints excluded: chain H residue 28 LEU 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 212 CYS Chi-restraints excluded: chain K residue 22 ILE 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 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 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 377 ASP Chi-restraints excluded: chain E residue 520 MET Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 190 VAL 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 245 optimal weight: 10.0000 chunk 186 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 118 optimal weight: 8.9990 chunk 166 optimal weight: 3.9990 chunk 249 optimal weight: 3.9990 chunk 263 optimal weight: 8.9990 chunk 130 optimal weight: 2.9990 chunk 236 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 214 ASN ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 214 ASN ** I 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6265 moved from start: 0.2476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 22473 Z= 0.245 Angle : 1.156 83.627 30561 Z= 0.460 Chirality : 0.059 1.434 3408 Planarity : 0.005 0.061 3879 Dihedral : 9.271 88.019 3204 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 3.72 % Allowed : 21.23 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.15), residues: 2745 helix: 0.21 (0.14), residues: 1335 sheet: -3.26 (0.43), residues: 105 loop : -2.84 (0.15), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 163 HIS 0.008 0.001 HIS I 354 PHE 0.015 0.001 PHE H 36 TYR 0.025 0.001 TYR H 29 ARG 0.004 0.000 ARG F 9 *********************** 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 521 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 435 time to evaluate : 2.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 ARG cc_start: 0.5821 (ttp80) cc_final: 0.5425 (mtp180) REVERT: D 37 PHE cc_start: 0.4845 (OUTLIER) cc_final: 0.4405 (t80) REVERT: F 9 ARG cc_start: 0.5844 (ttp-170) cc_final: 0.5373 (mtp180) REVERT: F 20 MET cc_start: 0.4157 (mmt) cc_final: 0.3683 (mmp) REVERT: F 53 ARG cc_start: 0.6381 (pmt-80) cc_final: 0.5917 (ptt90) REVERT: H 29 TYR cc_start: 0.7971 (t80) cc_final: 0.7616 (t80) REVERT: H 83 TYR cc_start: 0.7884 (m-10) cc_final: 0.7495 (m-10) REVERT: J 5 PHE cc_start: 0.5982 (m-80) cc_final: 0.5625 (m-80) REVERT: L 29 TYR cc_start: 0.8040 (t80) cc_final: 0.7470 (t80) REVERT: A 43 ARG cc_start: 0.8039 (mpt90) cc_final: 0.6361 (mmt180) REVERT: A 155 LYS cc_start: 0.7530 (tmmt) cc_final: 0.7047 (tmmt) REVERT: A 235 ASP cc_start: 0.6209 (t0) cc_final: 0.5630 (t70) REVERT: A 356 MET cc_start: 0.6039 (ttp) cc_final: 0.5356 (ttp) REVERT: A 392 VAL cc_start: 0.6671 (p) cc_final: 0.5654 (t) REVERT: A 395 HIS cc_start: 0.4594 (m-70) cc_final: 0.4295 (m-70) REVERT: A 420 GLN cc_start: 0.7616 (pm20) cc_final: 0.7284 (mp10) REVERT: E 43 ARG cc_start: 0.8028 (mpt90) cc_final: 0.6320 (mmt180) REVERT: E 53 ILE cc_start: 0.7992 (tp) cc_final: 0.7766 (tp) REVERT: E 235 ASP cc_start: 0.5803 (t0) cc_final: 0.5527 (t70) REVERT: E 392 VAL cc_start: 0.6805 (p) cc_final: 0.5724 (t) REVERT: E 475 ARG cc_start: 0.4210 (ptp-170) cc_final: 0.2949 (ptp-170) REVERT: I 43 ARG cc_start: 0.8181 (mpt90) cc_final: 0.6593 (mmt180) REVERT: I 63 ASP cc_start: 0.5430 (p0) cc_final: 0.5007 (p0) REVERT: I 236 MET cc_start: 0.6138 (mmm) cc_final: 0.5693 (tpp) REVERT: I 392 VAL cc_start: 0.6544 (p) cc_final: 0.5430 (t) outliers start: 86 outliers final: 58 residues processed: 491 average time/residue: 0.3285 time to fit residues: 248.8779 Evaluate side-chains 480 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 421 time to evaluate : 2.216 ------------------------------------------------------------------------------- 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 89 ILE Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 37 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 50 SER 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 89 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 60 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 109 PHE Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 91 ILE 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 113 SER Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 28 LEU 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 A residue 566 MET Chi-restraints excluded: chain E residue 20 MET 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 377 ASP Chi-restraints excluded: chain E residue 520 MET Chi-restraints excluded: chain E residue 540 HIS Chi-restraints excluded: chain I residue 35 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 5.9990 chunk 149 optimal weight: 8.9990 chunk 3 optimal weight: 8.9990 chunk 196 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 225 optimal weight: 50.0000 chunk 182 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 134 optimal weight: 7.9990 chunk 236 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- 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** ** A 552 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 GLN ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 395 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 214 ASN ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6387 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 22473 Z= 0.353 Angle : 1.207 83.434 30561 Z= 0.489 Chirality : 0.060 1.442 3408 Planarity : 0.005 0.063 3879 Dihedral : 9.490 89.310 3204 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.73 % Favored : 90.27 % Rotamer: Outliers : 4.32 % Allowed : 22.65 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.15), residues: 2745 helix: 0.02 (0.14), residues: 1335 sheet: -3.30 (0.44), residues: 105 loop : -2.88 (0.15), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 553 HIS 0.009 0.002 HIS A 395 PHE 0.020 0.002 PHE L 36 TYR 0.020 0.002 TYR D 107 ARG 0.007 0.001 ARG J 9 *********************** 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 528 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 428 time to evaluate : 2.426 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: 0.5960 (ttp80) cc_final: 0.5698 (mtp180) REVERT: B 228 HIS cc_start: 0.6228 (t70) cc_final: 0.6012 (t70) REVERT: D 37 PHE cc_start: 0.5106 (OUTLIER) cc_final: 0.4517 (t80) REVERT: F 9 ARG cc_start: 0.5919 (ttp-170) cc_final: 0.5572 (ttp-170) REVERT: F 20 MET cc_start: 0.4218 (mmt) cc_final: 0.3692 (mmp) REVERT: F 53 ARG cc_start: 0.6381 (pmt-80) cc_final: 0.6136 (pmt-80) REVERT: H 29 TYR cc_start: 0.7996 (t80) cc_final: 0.7643 (t80) REVERT: K 29 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6259 (mm) REVERT: L 29 TYR cc_start: 0.8137 (t80) cc_final: 0.7509 (t80) REVERT: A 43 ARG cc_start: 0.8043 (mpt90) cc_final: 0.6647 (mmt180) REVERT: A 356 MET cc_start: 0.6332 (ttp) cc_final: 0.5785 (ttp) REVERT: A 392 VAL cc_start: 0.6765 (p) cc_final: 0.5752 (t) REVERT: A 420 GLN cc_start: 0.7607 (pm20) cc_final: 0.7291 (mp10) REVERT: A 463 LEU cc_start: 0.5846 (OUTLIER) cc_final: 0.5479 (tt) REVERT: E 86 GLU cc_start: 0.6698 (tp30) cc_final: 0.6469 (tp30) REVERT: E 235 ASP cc_start: 0.6119 (t0) cc_final: 0.5742 (t70) REVERT: E 392 VAL cc_start: 0.6965 (p) cc_final: 0.6000 (t) REVERT: E 407 ASP cc_start: 0.4490 (t0) cc_final: 0.3882 (t70) REVERT: E 475 ARG cc_start: 0.4289 (OUTLIER) cc_final: 0.3117 (ptp-170) REVERT: I 43 ARG cc_start: 0.8230 (mpt90) cc_final: 0.7389 (mmt180) REVERT: I 98 GLU cc_start: 0.7004 (tm-30) cc_final: 0.6653 (tm-30) REVERT: I 236 MET cc_start: 0.6244 (mmm) cc_final: 0.5832 (mpp) REVERT: I 356 MET cc_start: 0.5873 (ttp) cc_final: 0.5664 (ttp) REVERT: I 392 VAL cc_start: 0.6673 (p) cc_final: 0.5686 (t) REVERT: I 465 GLU cc_start: 0.6506 (tp30) cc_final: 0.6095 (tp30) outliers start: 100 outliers final: 75 residues processed: 493 average time/residue: 0.3251 time to fit residues: 249.2708 Evaluate side-chains 489 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 410 time to evaluate : 2.265 ------------------------------------------------------------------------------- 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 226 ILE Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 89 ILE Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 37 PHE Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 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 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 73 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 42 LEU 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 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 24 ILE 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 47 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 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 47 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 20.0000 chunk 237 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 154 optimal weight: 0.9990 chunk 65 optimal weight: 0.0670 chunk 264 optimal weight: 4.9990 chunk 219 optimal weight: 0.3980 chunk 122 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 138 optimal weight: 7.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 94 GLN A 214 ASN A 540 HIS A 552 ASN E 214 ASN E 395 HIS E 540 HIS I 214 ASN ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 395 HIS I 540 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 22473 Z= 0.227 Angle : 1.149 83.841 30561 Z= 0.454 Chirality : 0.059 1.456 3408 Planarity : 0.005 0.063 3879 Dihedral : 9.002 87.821 3202 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.29 % Allowed : 24.17 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.15), residues: 2745 helix: 0.52 (0.14), residues: 1335 sheet: -3.16 (0.43), residues: 102 loop : -2.73 (0.15), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 553 HIS 0.007 0.001 HIS E 354 PHE 0.021 0.001 PHE I 506 TYR 0.018 0.001 TYR H 29 ARG 0.007 0.000 ARG J 9 *********************** 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 521 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 445 time to evaluate : 2.422 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: 0.5799 (ttp80) cc_final: 0.5585 (mtp180) REVERT: B 210 MET cc_start: 0.4748 (mtt) cc_final: 0.4379 (mtm) REVERT: D 37 PHE cc_start: 0.4888 (OUTLIER) cc_final: 0.4507 (t80) REVERT: H 29 TYR cc_start: 0.7936 (t80) cc_final: 0.7627 (t80) REVERT: H 83 TYR cc_start: 0.7896 (m-10) cc_final: 0.7378 (m-10) REVERT: J 23 TYR cc_start: 0.5515 (m-80) cc_final: 0.5231 (m-80) REVERT: K 78 LEU cc_start: 0.5928 (OUTLIER) cc_final: 0.5553 (mp) REVERT: L 29 TYR cc_start: 0.7929 (t80) cc_final: 0.7366 (t80) REVERT: A 20 MET cc_start: 0.7036 (mmt) cc_final: 0.6697 (mmt) REVERT: A 43 ARG cc_start: 0.7908 (mpt90) cc_final: 0.5301 (mpt90) REVERT: A 235 ASP cc_start: 0.5826 (t0) cc_final: 0.5224 (t0) REVERT: A 356 MET cc_start: 0.5757 (ttp) cc_final: 0.5480 (ttp) REVERT: A 392 VAL cc_start: 0.6474 (p) cc_final: 0.5472 (t) REVERT: A 395 HIS cc_start: 0.4597 (m-70) cc_final: 0.4133 (m90) REVERT: A 420 GLN cc_start: 0.7625 (pm20) cc_final: 0.7333 (mp10) REVERT: E 43 ARG cc_start: 0.7989 (mpt90) cc_final: 0.5370 (mpt90) REVERT: E 235 ASP cc_start: 0.5459 (t0) cc_final: 0.5200 (t0) REVERT: E 392 VAL cc_start: 0.6564 (p) cc_final: 0.5456 (t) REVERT: E 475 ARG cc_start: 0.4182 (OUTLIER) cc_final: 0.2990 (ptp-170) REVERT: E 559 TYR cc_start: 0.4513 (t80) cc_final: 0.3909 (t80) REVERT: I 43 ARG cc_start: 0.8132 (mpt90) cc_final: 0.6806 (mpt90) REVERT: I 98 GLU cc_start: 0.6738 (tm-30) cc_final: 0.6457 (tm-30) REVERT: I 236 MET cc_start: 0.6105 (mmm) cc_final: 0.5743 (mpp) REVERT: I 392 VAL cc_start: 0.6395 (p) cc_final: 0.5315 (t) REVERT: I 506 PHE cc_start: 0.2826 (m-80) cc_final: 0.2529 (t80) outliers start: 76 outliers final: 57 residues processed: 490 average time/residue: 0.3311 time to fit residues: 249.0621 Evaluate side-chains 482 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 422 time to evaluate : 2.097 ------------------------------------------------------------------------------- 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 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 109 PHE 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 148 GLU Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 65 MET 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 109 PHE 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 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 109 PHE Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 377 ASP 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 532 PHE Chi-restraints excluded: chain A residue 540 HIS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 55 VAL Chi-restraints excluded: chain E residue 65 TRP Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 212 THR Chi-restraints excluded: chain E residue 377 ASP Chi-restraints excluded: chain E residue 475 ARG 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 212 THR Chi-restraints excluded: chain I residue 520 MET 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 254 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 150 optimal weight: 6.9990 chunk 192 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 chunk 222 optimal weight: 20.0000 chunk 147 optimal weight: 6.9990 chunk 263 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 25 GLN ** A 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 HIS E 25 GLN E 214 ASN ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 367 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 540 HIS ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 214 ASN ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 540 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.104 22473 Z= 0.338 Angle : 1.191 83.169 30561 Z= 0.480 Chirality : 0.061 1.473 3408 Planarity : 0.005 0.064 3879 Dihedral : 9.240 87.742 3202 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 3.98 % Allowed : 24.60 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.15), residues: 2745 helix: 0.33 (0.14), residues: 1335 sheet: -3.21 (0.44), residues: 105 loop : -2.77 (0.15), residues: 1305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 65 HIS 0.016 0.002 HIS E 540 PHE 0.044 0.002 PHE A 506 TYR 0.020 0.002 TYR D 107 ARG 0.011 0.001 ARG A 443 *********************** 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 506 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 414 time to evaluate : 2.621 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 210 MET cc_start: 0.4727 (mtt) cc_final: 0.4455 (mtm) REVERT: B 228 HIS cc_start: 0.6134 (t70) cc_final: 0.5849 (t70) REVERT: C 29 LEU cc_start: 0.6548 (OUTLIER) cc_final: 0.6183 (mm) REVERT: C 78 LEU cc_start: 0.6097 (OUTLIER) cc_final: 0.5751 (mp) REVERT: D 37 PHE cc_start: 0.5082 (OUTLIER) cc_final: 0.4568 (t80) REVERT: F 9 ARG cc_start: 0.6050 (ttp-170) cc_final: 0.5664 (mtp180) REVERT: G 78 LEU cc_start: 0.6087 (OUTLIER) cc_final: 0.5656 (mp) REVERT: H 29 TYR cc_start: 0.8089 (t80) cc_final: 0.7758 (t80) REVERT: J 23 TYR cc_start: 0.5526 (m-80) cc_final: 0.5225 (m-80) REVERT: K 78 LEU cc_start: 0.5883 (OUTLIER) cc_final: 0.5476 (mp) REVERT: L 29 TYR cc_start: 0.8078 (t80) cc_final: 0.7608 (t80) REVERT: A 43 ARG cc_start: 0.8026 (mpt90) cc_final: 0.6255 (mmt180) REVERT: A 98 GLU cc_start: 0.6657 (tm-30) cc_final: 0.6315 (tm-30) REVERT: A 356 MET cc_start: 0.6294 (ttp) cc_final: 0.5900 (ttp) REVERT: A 392 VAL cc_start: 0.6629 (p) cc_final: 0.5632 (t) REVERT: A 420 GLN cc_start: 0.7588 (pm20) cc_final: 0.7310 (mp10) REVERT: A 463 LEU cc_start: 0.5839 (OUTLIER) cc_final: 0.5499 (tt) REVERT: E 392 VAL cc_start: 0.6839 (p) cc_final: 0.5780 (t) REVERT: E 475 ARG cc_start: 0.4172 (OUTLIER) cc_final: 0.2851 (ptp-170) REVERT: E 559 TYR cc_start: 0.4689 (t80) cc_final: 0.4134 (t80) REVERT: I 43 ARG cc_start: 0.8230 (mpt90) cc_final: 0.6807 (mmt180) REVERT: I 98 GLU cc_start: 0.6955 (tm-30) cc_final: 0.6635 (tm-30) REVERT: I 156 ASN cc_start: 0.6881 (OUTLIER) cc_final: 0.6657 (m110) REVERT: I 236 MET cc_start: 0.6165 (mmm) cc_final: 0.5867 (mpp) REVERT: I 392 VAL cc_start: 0.6598 (p) cc_final: 0.5582 (t) outliers start: 92 outliers final: 77 residues processed: 473 average time/residue: 0.3297 time to fit residues: 240.3073 Evaluate side-chains 487 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 402 time to evaluate : 2.309 ------------------------------------------------------------------------------- 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 226 ILE Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 29 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 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 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 78 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 52 PHE Chi-restraints excluded: chain H residue 60 PHE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 109 PHE 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 148 GLU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 226 ILE Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 78 LEU Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 113 SER Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 24 ILE 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 46 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 65 TRP Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 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 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 394 VAL 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 E residue 566 MET 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 156 ASN Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 212 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 20.0000 chunk 105 optimal weight: 0.9990 chunk 157 optimal weight: 20.0000 chunk 79 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 50 optimal weight: 8.9990 chunk 167 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 130 optimal weight: 0.9990 chunk 24 optimal weight: 7.9990 chunk 206 optimal weight: 0.0030 overall best weight: 2.1998 ------------------------------------------------------------------------------- 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 367 GLN ** 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 367 GLN ** 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 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 22473 Z= 0.256 Angle : 1.169 83.244 30561 Z= 0.465 Chirality : 0.060 1.484 3408 Planarity : 0.005 0.063 3879 Dihedral : 9.080 88.231 3202 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer: Outliers : 3.76 % Allowed : 25.21 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.15), residues: 2745 helix: 0.50 (0.14), residues: 1335 sheet: -2.72 (0.41), residues: 123 loop : -2.81 (0.15), residues: 1287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 65 HIS 0.013 0.001 HIS I 540 PHE 0.055 0.001 PHE E 506 TYR 0.019 0.001 TYR F 10 ARG 0.008 0.000 ARG I 108 *********************** 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 498 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 411 time to evaluate : 2.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ILE cc_start: 0.4417 (OUTLIER) cc_final: 0.3986 (mm) REVERT: B 210 MET cc_start: 0.4651 (mtt) cc_final: 0.4410 (mtm) REVERT: C 29 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.6066 (mm) REVERT: C 78 LEU cc_start: 0.5993 (OUTLIER) cc_final: 0.5632 (mp) REVERT: D 37 PHE cc_start: 0.5223 (OUTLIER) cc_final: 0.4703 (t80) REVERT: F 9 ARG cc_start: 0.6044 (ttp-170) cc_final: 0.5572 (mtp180) REVERT: G 78 LEU cc_start: 0.6039 (OUTLIER) cc_final: 0.5640 (mp) REVERT: H 29 TYR cc_start: 0.7961 (t80) cc_final: 0.7692 (t80) REVERT: H 37 PHE cc_start: 0.5149 (OUTLIER) cc_final: 0.4516 (t80) REVERT: J 23 TYR cc_start: 0.5541 (m-80) cc_final: 0.5305 (m-80) REVERT: K 78 LEU cc_start: 0.5896 (OUTLIER) cc_final: 0.5493 (mp) REVERT: L 29 TYR cc_start: 0.7942 (t80) cc_final: 0.7513 (t80) REVERT: A 20 MET cc_start: 0.7090 (mmt) cc_final: 0.6735 (mmt) REVERT: A 43 ARG cc_start: 0.8015 (mpt90) cc_final: 0.5404 (mpt90) REVERT: A 235 ASP cc_start: 0.5986 (t0) cc_final: 0.5379 (t0) REVERT: A 356 MET cc_start: 0.5979 (ttp) cc_final: 0.5717 (ttp) REVERT: A 392 VAL cc_start: 0.6524 (p) cc_final: 0.5504 (t) REVERT: A 420 GLN cc_start: 0.7560 (pm20) cc_final: 0.7288 (mp10) REVERT: E 43 ARG cc_start: 0.8048 (mpt90) cc_final: 0.5359 (mpt90) REVERT: E 392 VAL cc_start: 0.6706 (p) cc_final: 0.5620 (t) REVERT: E 475 ARG cc_start: 0.4166 (OUTLIER) cc_final: 0.2837 (ptp-170) REVERT: I 43 ARG cc_start: 0.8183 (mpt90) cc_final: 0.7061 (mpt180) REVERT: I 69 MET cc_start: 0.5018 (mtt) cc_final: 0.4814 (mtt) REVERT: I 98 GLU cc_start: 0.6865 (tm-30) cc_final: 0.6609 (tm-30) REVERT: I 156 ASN cc_start: 0.6846 (OUTLIER) cc_final: 0.6605 (m110) REVERT: I 236 MET cc_start: 0.6119 (mmm) cc_final: 0.5661 (mpp) REVERT: I 392 VAL cc_start: 0.6442 (p) cc_final: 0.5393 (t) REVERT: I 569 ARG cc_start: 0.6902 (tmm-80) cc_final: 0.6627 (tmm-80) outliers start: 87 outliers final: 68 residues processed: 468 average time/residue: 0.3453 time to fit residues: 249.6122 Evaluate side-chains 477 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 400 time to evaluate : 2.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE 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 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 109 PHE 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 148 GLU Chi-restraints excluded: chain F residue 226 ILE Chi-restraints excluded: chain G residue 22 ILE Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 78 LEU 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 109 PHE Chi-restraints excluded: chain J residue 42 LEU Chi-restraints excluded: chain J residue 91 ILE Chi-restraints excluded: chain J residue 148 GLU Chi-restraints excluded: chain J residue 197 LEU 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 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 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 190 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 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 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 377 ASP 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 156 ASN 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 540 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 0.8980 chunk 252 optimal weight: 3.9990 chunk 229 optimal weight: 0.9990 chunk 245 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 221 optimal weight: 30.0000 chunk 231 optimal weight: 20.0000 chunk 244 optimal weight: 40.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- 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** E 214 ASN ** E 218 ASN ** 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 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6319 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 22473 Z= 0.288 Angle : 1.180 82.915 30561 Z= 0.472 Chirality : 0.060 1.490 3408 Planarity : 0.005 0.062 3879 Dihedral : 9.143 87.938 3202 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 4.19 % Allowed : 25.12 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.15), residues: 2745 helix: 0.38 (0.14), residues: 1350 sheet: -2.72 (0.41), residues: 123 loop : -2.78 (0.15), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 65 HIS 0.007 0.001 HIS H 71 PHE 0.048 0.002 PHE E 506 TYR 0.017 0.002 TYR F 10 ARG 0.009 0.000 ARG I 108 *********************** 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 504 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 407 time to evaluate : 2.469 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 7 ILE cc_start: 0.4470 (OUTLIER) cc_final: 0.3992 (mm) REVERT: C 29 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6140 (mm) REVERT: C 78 LEU cc_start: 0.6058 (OUTLIER) cc_final: 0.5698 (mp) REVERT: D 37 PHE cc_start: 0.5131 (OUTLIER) cc_final: 0.4593 (t80) REVERT: F 9 ARG cc_start: 0.6027 (ttp-170) cc_final: 0.5508 (mtp180) REVERT: G 78 LEU cc_start: 0.6053 (OUTLIER) cc_final: 0.5619 (mp) REVERT: H 29 TYR cc_start: 0.7998 (t80) cc_final: 0.7718 (t80) REVERT: H 37 PHE cc_start: 0.5075 (OUTLIER) cc_final: 0.4387 (t80) REVERT: J 23 TYR cc_start: 0.5437 (m-80) cc_final: 0.5195 (m-80) REVERT: K 78 LEU cc_start: 0.5916 (OUTLIER) cc_final: 0.5505 (mp) REVERT: L 29 TYR cc_start: 0.7977 (t80) cc_final: 0.7555 (t80) REVERT: A 20 MET cc_start: 0.7205 (mmt) cc_final: 0.6937 (mmt) REVERT: A 43 ARG cc_start: 0.7975 (mpt90) cc_final: 0.5350 (mpt90) REVERT: A 235 ASP cc_start: 0.6148 (t0) cc_final: 0.5504 (t0) REVERT: A 356 MET cc_start: 0.6140 (ttp) cc_final: 0.5935 (ttp) REVERT: A 392 VAL cc_start: 0.6562 (p) cc_final: 0.5570 (t) REVERT: A 420 GLN cc_start: 0.7473 (pm20) cc_final: 0.7208 (mp10) REVERT: A 463 LEU cc_start: 0.5876 (OUTLIER) cc_final: 0.5492 (tt) REVERT: A 531 ASN cc_start: 0.6705 (OUTLIER) cc_final: 0.6402 (m-40) REVERT: E 238 MET cc_start: 0.3563 (tpt) cc_final: 0.3362 (tpt) REVERT: E 392 VAL cc_start: 0.6770 (p) cc_final: 0.5718 (t) REVERT: E 475 ARG cc_start: 0.4135 (OUTLIER) cc_final: 0.2753 (ptp-170) REVERT: I 43 ARG cc_start: 0.8181 (mpt90) cc_final: 0.6890 (mpt90) REVERT: I 98 GLU cc_start: 0.6951 (tm-30) cc_final: 0.6593 (tm-30) REVERT: I 392 VAL cc_start: 0.6455 (p) cc_final: 0.5440 (t) REVERT: I 463 LEU cc_start: 0.6151 (OUTLIER) cc_final: 0.5757 (tt) outliers start: 97 outliers final: 80 residues processed: 472 average time/residue: 0.3417 time to fit residues: 247.4968 Evaluate side-chains 488 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 397 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE 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 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 42 LEU Chi-restraints excluded: chain F residue 50 SER 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 78 LEU 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 42 LEU 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 226 ILE 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 46 THR Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 509 GLN 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 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 394 VAL Chi-restraints excluded: chain E residue 475 ARG Chi-restraints excluded: chain E residue 531 ASN Chi-restraints excluded: chain E residue 540 HIS Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 47 VAL Chi-restraints excluded: chain I residue 102 MET Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 394 VAL Chi-restraints excluded: chain I residue 463 LEU Chi-restraints excluded: chain I residue 475 ARG Chi-restraints excluded: chain I residue 531 ASN Chi-restraints excluded: chain I residue 540 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 5.9990 chunk 259 optimal weight: 10.0000 chunk 158 optimal weight: 0.2980 chunk 123 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 271 optimal weight: 4.9990 chunk 250 optimal weight: 10.0000 chunk 216 optimal weight: 20.0000 chunk 22 optimal weight: 0.9980 chunk 167 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 HIS ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 214 ASN ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 518 ASN E 540 HIS ** I 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 540 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 22473 Z= 0.276 Angle : 1.181 82.773 30561 Z= 0.472 Chirality : 0.061 1.502 3408 Planarity : 0.005 0.059 3879 Dihedral : 9.094 87.718 3202 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 4.19 % Allowed : 25.34 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.15), residues: 2745 helix: 0.40 (0.14), residues: 1350 sheet: -2.49 (0.37), residues: 153 loop : -2.76 (0.16), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 65 HIS 0.007 0.001 HIS L 71 PHE 0.040 0.001 PHE E 506 TYR 0.016 0.001 TYR H 29 ARG 0.010 0.000 ARG I 108 ********************** 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 504 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 407 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ILE cc_start: 0.4499 (OUTLIER) cc_final: 0.4057 (mm) REVERT: C 29 LEU cc_start: 0.6401 (OUTLIER) cc_final: 0.6041 (mm) REVERT: C 78 LEU cc_start: 0.6007 (OUTLIER) cc_final: 0.5640 (mp) REVERT: D 37 PHE cc_start: 0.5107 (OUTLIER) cc_final: 0.4574 (t80) REVERT: F 9 ARG cc_start: 0.6046 (ttp-170) cc_final: 0.5588 (mtp180) REVERT: G 78 LEU cc_start: 0.6020 (OUTLIER) cc_final: 0.5576 (mp) REVERT: H 29 TYR cc_start: 0.7979 (t80) cc_final: 0.7704 (t80) REVERT: H 37 PHE cc_start: 0.5052 (OUTLIER) cc_final: 0.4390 (t80) REVERT: J 23 TYR cc_start: 0.5346 (m-80) cc_final: 0.5032 (m-80) REVERT: K 78 LEU cc_start: 0.5876 (OUTLIER) cc_final: 0.5469 (mp) REVERT: L 29 TYR cc_start: 0.7973 (t80) cc_final: 0.7489 (t80) REVERT: A 20 MET cc_start: 0.7111 (mmt) cc_final: 0.6886 (mmt) REVERT: A 43 ARG cc_start: 0.8023 (mpt90) cc_final: 0.5363 (mpt90) REVERT: A 235 ASP cc_start: 0.6024 (t0) cc_final: 0.5403 (t0) REVERT: A 392 VAL cc_start: 0.6542 (p) cc_final: 0.5559 (t) REVERT: A 420 GLN cc_start: 0.7451 (pm20) cc_final: 0.7183 (mp10) REVERT: A 463 LEU cc_start: 0.5851 (OUTLIER) cc_final: 0.5456 (tt) REVERT: A 531 ASN cc_start: 0.6847 (OUTLIER) cc_final: 0.6603 (m-40) REVERT: E 238 MET cc_start: 0.3760 (tpt) cc_final: 0.3516 (tpt) REVERT: E 392 VAL cc_start: 0.6724 (p) cc_final: 0.5650 (t) REVERT: E 463 LEU cc_start: 0.5657 (OUTLIER) cc_final: 0.5223 (tt) REVERT: E 475 ARG cc_start: 0.4180 (OUTLIER) cc_final: 0.2816 (ptp-170) REVERT: I 43 ARG cc_start: 0.8148 (mpt90) cc_final: 0.6870 (mpt90) REVERT: I 98 GLU cc_start: 0.6913 (tm-30) cc_final: 0.6542 (tm-30) REVERT: I 392 VAL cc_start: 0.6423 (p) cc_final: 0.5402 (t) REVERT: I 463 LEU cc_start: 0.6147 (OUTLIER) cc_final: 0.5734 (tt) outliers start: 97 outliers final: 82 residues processed: 473 average time/residue: 0.3334 time to fit residues: 244.0072 Evaluate side-chains 494 residues out of total 2316 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 400 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 7 ILE 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 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 78 LEU 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 42 LEU 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 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 141 THR Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 212 THR Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain A residue 463 LEU Chi-restraints excluded: chain A residue 475 ARG Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 532 PHE 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 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 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 102 MET Chi-restraints excluded: chain I residue 199 VAL Chi-restraints excluded: chain I residue 212 THR Chi-restraints excluded: chain I residue 394 VAL Chi-restraints excluded: chain I residue 463 LEU Chi-restraints excluded: chain I residue 475 ARG Chi-restraints excluded: chain I residue 531 ASN Chi-restraints excluded: chain I residue 540 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 10.0000 chunk 230 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 199 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 216 optimal weight: 20.0000 chunk 90 optimal weight: 8.9990 chunk 222 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 overall best weight: 5.1986 ------------------------------------------------------------------------------- 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 509 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 HIS E 214 ASN ** E 218 ASN ** 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 214 ASN ** I 218 ASN ** 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 = 0.4576 r_free = 0.4576 target = 0.249001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.208094 restraints weight = 33335.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.208438 restraints weight = 26445.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.210262 restraints weight = 18069.921| |-----------------------------------------------------------------------------| r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 22473 Z= 0.356 Angle : 1.212 82.733 30561 Z= 0.491 Chirality : 0.062 1.495 3408 Planarity : 0.005 0.062 3879 Dihedral : 9.242 87.475 3202 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 4.19 % Allowed : 25.59 % Favored : 70.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.15), residues: 2745 helix: 0.20 (0.14), residues: 1350 sheet: -2.72 (0.41), residues: 123 loop : -2.84 (0.15), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 65 HIS 0.010 0.002 HIS E 540 PHE 0.042 0.002 PHE E 506 TYR 0.018 0.002 TYR D 107 ARG 0.017 0.001 ARG I 108 =============================================================================== Job complete usr+sys time: 4843.91 seconds wall clock time: 87 minutes 12.73 seconds (5232.73 seconds total)