Starting phenix.real_space_refine on Thu Sep 18 19:33:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7awt_11930/09_2025/7awt_11930.cif Found real_map, /net/cci-nas-00/data/ceres_data/7awt_11930/09_2025/7awt_11930.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7awt_11930/09_2025/7awt_11930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7awt_11930/09_2025/7awt_11930.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7awt_11930/09_2025/7awt_11930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7awt_11930/09_2025/7awt_11930.map" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.244 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 673 atoms to isotropic. 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 32 7.16 5 P 1 5.49 5 Mg 8 5.21 5 S 146 5.16 5 C 11815 2.51 5 N 3292 2.21 5 O 3597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 123 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18891 Number of models: 1 Model: "" Number of chains: 17 Chain: "B" Number of atoms: 1100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1100 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 130} Chain breaks: 2 Chain: "D" Number of atoms: 4760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4760 Classifications: {'peptide': 589} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 551} Chain: "E" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1219 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "F" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3406 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 413} Chain: "G" Number of atoms: 7045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 907, 7045 Classifications: {'peptide': 907} Link IDs: {'PTRANS': 41, 'TRANS': 865} Chain: "I" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1133 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 11, 'TRANS': 131} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 40 Unusual residues: {' MG': 1, 'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 34 Unusual residues: {' MG': 6, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "F" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "G" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 567 SG CYS B 129 53.974 72.139 43.114 1.00101.08 S ATOM 104 SG CYS B 64 58.313 75.962 39.701 1.00116.62 S ATOM 98 SG CYS B 63 53.592 78.862 41.752 1.00115.59 S ATOM 784 SG CYS B 158 56.774 76.118 46.112 1.00101.71 S ATOM 6507 SG CYS E 92 59.861 86.615 116.986 1.00 89.33 S ATOM 6541 SG CYS E 97 60.601 89.981 118.905 1.00 87.05 S ATOM 6819 SG CYS E 133 55.629 86.230 118.040 1.00 90.81 S ATOM 6845 SG CYS E 137 54.971 88.887 120.135 1.00 87.76 S ATOM 9784 SG CYS F 351 48.617 74.400 103.858 1.00 81.15 S ATOM 9828 SG CYS F 357 49.173 80.594 101.744 1.00 78.34 S ATOM 10149 SG CYS F 398 44.190 78.576 105.503 1.00 77.70 S ATOM 9808 SG CYS F 354 45.552 78.139 99.116 1.00 77.15 S ATOM 10837 SG CYS G 48 37.698 73.642 90.613 1.00 89.22 S ATOM 10986 SG CYS G 67 37.091 70.953 93.050 1.00 89.22 S ATOM 10735 SG CYS G 34 42.355 70.321 92.820 1.00 89.22 S ATOM 10811 SG CYS G 45 43.005 73.363 91.234 1.00 89.22 S ATOM 11688 SG CYS G 154 48.441 67.645 90.400 1.00 89.22 S ATOM 11669 SG CYS G 151 54.630 68.861 92.128 1.00 89.22 S ATOM 11717 SG CYS G 157 52.035 63.182 93.388 1.00 89.22 S ATOM 12065 SG CYS G 201 52.612 64.723 87.284 1.00 89.22 S ATOM 11274 SG CYS G 103 56.298 73.313 77.403 1.00 89.22 S ATOM 11334 SG CYS G 112 51.844 69.415 80.609 1.00 89.22 S ATOM 11294 SG CYS G 106 57.595 67.782 80.229 1.00 89.22 S ATOM 12290 SG CYS G 228 47.797 43.848 79.438 1.00 89.22 S ATOM 12575 SG CYS G 263 47.787 44.768 86.396 1.00 89.22 S ATOM 12338 SG CYS G 235 43.053 45.655 82.945 1.00 89.22 S ATOM 12314 SG CYS G 231 45.558 39.913 84.340 1.00 89.22 S ATOM 18100 SG CYS I 109 64.739 74.947 66.230 1.00 89.22 S ATOM 17763 SG CYS I 66 62.111 70.349 63.035 1.00 89.22 S ATOM 17723 SG CYS I 60 66.970 68.703 66.380 1.00 89.22 S ATOM 17741 SG CYS I 63 61.809 70.518 69.636 1.00 89.22 S ATOM 18053 SG CYS I 102 57.243 76.097 54.830 1.00 89.22 S ATOM 18028 SG CYS I 99 62.174 72.805 51.893 1.00 89.22 S ATOM 18071 SG CYS I 105 61.932 74.482 58.063 1.00 89.22 S ATOM 17786 SG CYS I 70 57.538 70.403 56.109 1.00 89.22 S ATOM 17810 SG CYS I 74 59.716 69.044 53.986 1.00 83.14 S Residues with excluded nonbonded symmetry interactions: 119 residue: pdb=" N TYR B 65 " occ=0.00 ... (10 atoms not shown) pdb=" OH TYR B 65 " occ=0.00 residue: pdb=" N VAL B 66 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL B 66 " occ=0.00 residue: pdb=" N GLU B 67 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU B 67 " occ=0.00 residue: pdb=" N MET B 68 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET B 68 " occ=0.00 residue: pdb=" N VAL B 69 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL B 69 " occ=0.00 residue: pdb=" N THR B 70 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR B 70 " occ=0.00 residue: pdb=" N SER B 71 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER B 71 " occ=0.00 residue: pdb=" N PHE B 72 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHE B 72 " occ=0.00 residue: pdb=" N ALA B 74 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA B 74 " occ=0.00 residue: pdb=" N VAL B 75 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL B 75 " occ=0.00 residue: pdb=" N HIS B 76 " occ=0.00 ... (8 atoms not shown) pdb=" NE2 HIS B 76 " occ=0.00 residue: pdb=" N ASP B 77 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASP B 77 " occ=0.00 ... (remaining 107 not shown) Time building chain proxies: 4.09, per 1000 atoms: 0.22 Number of scatterers: 18891 At special positions: 0 Unit cell: (94.34, 120.84, 155.82, 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 32 26.01 S 146 16.00 P 1 15.00 Mg 8 11.99 O 3597 8.00 N 3292 7.00 C 11815 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=0, symmetry=0 Time building additional restraints: 1.72 Conformation dependent library (CDL) restraints added in 756.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1001 " pdb="FE2 FES G1001 " - pdb=" SG CYS G 45 " pdb="FE2 FES G1001 " - pdb=" SG CYS G 34 " pdb="FE1 FES G1001 " - pdb=" SG CYS G 48 " pdb="FE1 FES G1001 " - pdb=" SG CYS G 67 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb=" SF4 F 501 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 351 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb=" SF4 G1002 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 201 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 154 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 151 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 157 " pdb=" SF4 G1003 " pdb="FE2 SF4 G1003 " - pdb=" NE2 HIS G 99 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 106 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 103 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 112 " pdb=" SF4 G1004 " pdb="FE2 SF4 G1004 " - pdb=" SG CYS G 263 " pdb="FE1 SF4 G1004 " - pdb=" SG CYS G 228 " pdb="FE3 SF4 G1004 " - pdb=" SG CYS G 235 " pdb="FE4 SF4 G1004 " - pdb=" SG CYS G 231 " pdb=" SF4 I 301 " pdb="FE3 SF4 I 301 " - pdb=" SG CYS I 60 " pdb="FE2 SF4 I 301 " - pdb=" SG CYS I 66 " pdb="FE1 SF4 I 301 " - pdb=" SG CYS I 109 " pdb="FE4 SF4 I 301 " - pdb=" SG CYS I 63 " pdb=" SF4 I 302 " pdb="FE2 SF4 I 302 " - pdb=" SG CYS I 99 " pdb="FE4 SF4 I 302 " - pdb=" SG CYS I 70 " pdb="FE3 SF4 I 302 " - pdb=" SG CYS I 105 " pdb="FE1 SF4 I 302 " - pdb=" SG CYS I 102 " pdb="FE4 SF4 I 302 " - pdb=" SG CYS I 74 " Number of angles added : 96 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4356 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 22 sheets defined 40.4% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'B' and resid 62 through 68 removed outlier: 3.870A pdb=" N VAL B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.545A pdb=" N ALA B 93 " --> pdb=" O PRO B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 117 removed outlier: 3.710A pdb=" N MET B 117 " --> pdb=" O LEU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 132 removed outlier: 3.935A pdb=" N ALA B 130 " --> pdb=" O MET B 126 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN B 131 " --> pdb=" O GLY B 127 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 126 through 132' Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 161 through 177 removed outlier: 3.563A pdb=" N SER B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 removed outlier: 4.076A pdb=" N ARG B 208 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA B 210 " --> pdb=" O GLY B 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 30 removed outlier: 3.622A pdb=" N GLY D 23 " --> pdb=" O ASP D 19 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLU D 24 " --> pdb=" O PRO D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 62 removed outlier: 3.676A pdb=" N ASP D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE D 59 " --> pdb=" O GLU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 141 Processing helix chain 'D' and resid 177 through 191 removed outlier: 3.845A pdb=" N LEU D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU D 189 " --> pdb=" O LYS D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 201 removed outlier: 3.772A pdb=" N TRP D 200 " --> pdb=" O LYS D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 258 Processing helix chain 'D' and resid 264 through 272 removed outlier: 4.571A pdb=" N GLU D 272 " --> pdb=" O THR D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 292 removed outlier: 4.248A pdb=" N TYR D 283 " --> pdb=" O ASN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 326 Processing helix chain 'D' and resid 333 through 351 removed outlier: 3.554A pdb=" N THR D 337 " --> pdb=" O PHE D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 396 removed outlier: 3.552A pdb=" N LEU D 375 " --> pdb=" O GLY D 371 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE D 379 " --> pdb=" O LEU D 375 " (cutoff:3.500A) Proline residue: D 384 - end of helix Processing helix chain 'D' and resid 397 through 404 Processing helix chain 'D' and resid 411 through 418 Processing helix chain 'D' and resid 433 through 438 Processing helix chain 'D' and resid 442 through 446 removed outlier: 3.814A pdb=" N ASN D 445 " --> pdb=" O GLY D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 483 removed outlier: 3.840A pdb=" N LEU D 470 " --> pdb=" O LYS D 466 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ARG D 471 " --> pdb=" O VAL D 467 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN D 472 " --> pdb=" O GLU D 468 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER D 473 " --> pdb=" O GLU D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 500 through 505 Processing helix chain 'D' and resid 507 through 520 Processing helix chain 'D' and resid 560 through 567 Processing helix chain 'D' and resid 567 through 572 Processing helix chain 'D' and resid 576 through 587 Processing helix chain 'D' and resid 590 through 596 Processing helix chain 'E' and resid 15 through 26 Processing helix chain 'E' and resid 31 through 34 Processing helix chain 'E' and resid 35 through 48 Processing helix chain 'E' and resid 51 through 63 removed outlier: 3.650A pdb=" N ILE E 55 " --> pdb=" O PRO E 51 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N HIS E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 76 Processing helix chain 'E' and resid 94 through 101 Processing helix chain 'E' and resid 101 through 113 removed outlier: 3.834A pdb=" N ILE E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 163 Processing helix chain 'F' and resid 13 through 17 removed outlier: 4.256A pdb=" N ARG F 16 " --> pdb=" O LEU F 13 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU F 17 " --> pdb=" O THR F 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 13 through 17' Processing helix chain 'F' and resid 25 through 32 Processing helix chain 'F' and resid 35 through 45 removed outlier: 3.573A pdb=" N LEU F 45 " --> pdb=" O ALA F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 58 removed outlier: 3.529A pdb=" N GLY F 58 " --> pdb=" O VAL F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 68 through 75 Processing helix chain 'F' and resid 99 through 108 removed outlier: 4.109A pdb=" N LEU F 103 " --> pdb=" O TYR F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 123 removed outlier: 3.781A pdb=" N LEU F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 153 Processing helix chain 'F' and resid 177 through 181 Processing helix chain 'F' and resid 182 through 191 removed outlier: 3.896A pdb=" N ILE F 187 " --> pdb=" O GLU F 183 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN F 188 " --> pdb=" O THR F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 219 through 232 removed outlier: 3.588A pdb=" N VAL F 225 " --> pdb=" O THR F 221 " (cutoff:3.500A) Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 232 through 238 removed outlier: 3.692A pdb=" N TYR F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 275 Processing helix chain 'F' and resid 302 through 307 removed outlier: 4.082A pdb=" N ASP F 306 " --> pdb=" O ALA F 303 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU F 307 " --> pdb=" O HIS F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 317 Processing helix chain 'F' and resid 334 through 349 removed outlier: 3.627A pdb=" N PHE F 345 " --> pdb=" O ASN F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 374 Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 380 through 391 removed outlier: 3.546A pdb=" N GLN F 386 " --> pdb=" O GLU F 382 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG F 389 " --> pdb=" O GLU F 385 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 405 Processing helix chain 'F' and resid 405 through 421 removed outlier: 3.547A pdb=" N TYR F 414 " --> pdb=" O SER F 410 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLU F 417 " --> pdb=" O LYS F 413 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLU F 418 " --> pdb=" O TYR F 414 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N PHE F 419 " --> pdb=" O PHE F 415 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 27 Processing helix chain 'G' and resid 67 through 69 No H-bonds generated for 'chain 'G' and resid 67 through 69' Processing helix chain 'G' and resid 81 through 98 removed outlier: 3.625A pdb=" N LEU G 95 " --> pdb=" O VAL G 91 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ASN G 98 " --> pdb=" O TRP G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 121 Processing helix chain 'G' and resid 147 through 151 Processing helix chain 'G' and resid 155 through 164 Processing helix chain 'G' and resid 196 through 201 Processing helix chain 'G' and resid 208 through 214 removed outlier: 4.447A pdb=" N ARG G 214 " --> pdb=" O THR G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 217 through 221 Processing helix chain 'G' and resid 264 through 269 Processing helix chain 'G' and resid 270 through 274 removed outlier: 3.585A pdb=" N ASN G 274 " --> pdb=" O GLY G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 307 Processing helix chain 'G' and resid 321 through 333 Processing helix chain 'G' and resid 342 through 358 removed outlier: 3.715A pdb=" N ARG G 348 " --> pdb=" O GLY G 344 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU G 349 " --> pdb=" O GLU G 345 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA G 352 " --> pdb=" O ARG G 348 " (cutoff:3.500A) Processing helix chain 'G' and resid 367 through 372 removed outlier: 3.549A pdb=" N TYR G 372 " --> pdb=" O ILE G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 397 removed outlier: 3.747A pdb=" N ALA G 390 " --> pdb=" O GLY G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 398 through 407 removed outlier: 3.631A pdb=" N ARG G 402 " --> pdb=" O LYS G 398 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 423 Processing helix chain 'G' and resid 452 through 467 Processing helix chain 'G' and resid 476 through 491 removed outlier: 4.088A pdb=" N LYS G 482 " --> pdb=" O GLU G 478 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL G 485 " --> pdb=" O SER G 481 " (cutoff:3.500A) Processing helix chain 'G' and resid 506 through 524 removed outlier: 3.867A pdb=" N ILE G 510 " --> pdb=" O SER G 506 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 545 Processing helix chain 'G' and resid 548 through 558 removed outlier: 3.637A pdb=" N ALA G 552 " --> pdb=" O SER G 548 " (cutoff:3.500A) Processing helix chain 'G' and resid 576 through 586 removed outlier: 3.646A pdb=" N ASN G 581 " --> pdb=" O ALA G 577 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS G 586 " --> pdb=" O ALA G 582 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 603 removed outlier: 3.784A pdb=" N ASN G 603 " --> pdb=" O ILE G 600 " (cutoff:3.500A) Processing helix chain 'G' and resid 647 through 661 Processing helix chain 'G' and resid 668 through 680 Processing helix chain 'G' and resid 681 through 684 Processing helix chain 'G' and resid 761 through 767 Processing helix chain 'G' and resid 824 through 828 Processing helix chain 'G' and resid 830 through 835 removed outlier: 3.902A pdb=" N ARG G 834 " --> pdb=" O VAL G 830 " (cutoff:3.500A) Processing helix chain 'G' and resid 843 through 848 Processing helix chain 'I' and resid 64 through 70 Processing helix chain 'I' and resid 103 through 109 Processing helix chain 'I' and resid 149 through 153 Processing sheet with id=AA1, first strand: chain 'B' and resid 56 through 59 removed outlier: 3.512A pdb=" N VAL B 97 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N MET B 96 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL B 153 " --> pdb=" O VAL B 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 36 through 37 removed outlier: 4.338A pdb=" N VAL D 45 " --> pdb=" O GLN D 37 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ALA D 112 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG D 105 " --> pdb=" O SER D 100 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N SER D 93 " --> pdb=" O GLY D 75 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY D 75 " --> pdb=" O SER D 93 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N PHE D 95 " --> pdb=" O LEU D 73 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LEU D 73 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N HIS D 97 " --> pdb=" O PHE D 71 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 119 through 121 Processing sheet with id=AA4, first strand: chain 'D' and resid 215 through 216 removed outlier: 6.655A pdb=" N VAL D 230 " --> pdb=" O CYS D 241 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N CYS D 241 " --> pdb=" O VAL D 230 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLN D 232 " --> pdb=" O VAL D 239 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 359 through 360 Processing sheet with id=AA6, first strand: chain 'D' and resid 527 through 535 removed outlier: 3.573A pdb=" N ASN D 540 " --> pdb=" O ILE D 533 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY D 538 " --> pdb=" O ALA D 535 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 128 through 131 removed outlier: 6.178A pdb=" N ILE E 89 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR E 131 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N TYR E 91 " --> pdb=" O THR E 131 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 168 through 173 removed outlier: 6.283A pdb=" N GLY F 128 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N HIS F 172 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE F 130 " --> pdb=" O HIS F 172 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU F 87 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N PHE F 131 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N CYS F 89 " --> pdb=" O PHE F 131 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 260 through 264 removed outlier: 7.192A pdb=" N ALA F 326 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLY F 251 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ALA F 328 " --> pdb=" O GLY F 251 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER F 253 " --> pdb=" O ALA F 328 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ASP F 330 " --> pdb=" O SER F 253 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 9 through 12 removed outlier: 8.485A pdb=" N ILE G 77 " --> pdb=" O THR G 3 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N HIS G 5 " --> pdb=" O ILE G 77 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE G 76 " --> pdb=" O TYR G 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 171 through 173 Processing sheet with id=AB3, first strand: chain 'G' and resid 226 through 227 removed outlier: 8.081A pdb=" N ASN G 236 " --> pdb=" O ASN G 251 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N ASN G 251 " --> pdb=" O ASN G 236 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N SER G 238 " --> pdb=" O ILE G 249 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ILE G 249 " --> pdb=" O SER G 238 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLY G 240 " --> pdb=" O ARG G 247 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 289 through 292 removed outlier: 3.598A pdb=" N ASP G 289 " --> pdb=" O ARG G 286 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 337 through 339 removed outlier: 6.171A pdb=" N GLY G 314 " --> pdb=" O TYR G 338 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 445 through 448 removed outlier: 3.710A pdb=" N TRP G 445 " --> pdb=" O LEU G 429 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL G 375 " --> pdb=" O PHE G 430 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N THR G 432 " --> pdb=" O VAL G 375 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL G 377 " --> pdb=" O THR G 432 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU G 376 " --> pdb=" O ILE G 499 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N GLY G 501 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N LEU G 378 " --> pdb=" O GLY G 501 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE G 498 " --> pdb=" O THR G 530 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE G 532 " --> pdb=" O ILE G 498 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N SER G 500 " --> pdb=" O ILE G 532 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 618 through 621 removed outlier: 3.511A pdb=" N GLN G 628 " --> pdb=" O VAL G 620 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL G 783 " --> pdb=" O ALA G 627 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 702 through 703 removed outlier: 6.907A pdb=" N LEU G 702 " --> pdb=" O THR G 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'G' and resid 881 through 886 Processing sheet with id=AC1, first strand: chain 'G' and resid 840 through 842 removed outlier: 3.584A pdb=" N GLU G 872 " --> pdb=" O ILE G 840 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 866 through 869 removed outlier: 3.792A pdb=" N ASP G 902 " --> pdb=" O SER G 861 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 47 through 50 removed outlier: 3.683A pdb=" N THR I 117 " --> pdb=" O ARG I 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 75 through 81 removed outlier: 6.893A pdb=" N SER I 76 " --> pdb=" O PHE I 92 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE I 92 " --> pdb=" O SER I 76 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLN I 78 " --> pdb=" O GLU I 90 " (cutoff:3.500A) 649 hydrogen bonds defined for protein. 1797 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.40: 7971 1.40 - 1.67: 10984 1.67 - 1.93: 180 1.93 - 2.19: 7 2.19 - 2.46: 85 Bond restraints: 19227 Sorted by residual: bond pdb=" CA SER G 317 " pdb=" C SER G 317 " ideal model delta sigma weight residual 1.524 1.411 0.113 1.26e-02 6.30e+03 8.07e+01 bond pdb=" C ARG G 394 " pdb=" O ARG G 394 " ideal model delta sigma weight residual 1.237 1.138 0.099 1.17e-02 7.31e+03 7.09e+01 bond pdb=" C VAL G 91 " pdb=" O VAL G 91 " ideal model delta sigma weight residual 1.237 1.140 0.097 1.17e-02 7.31e+03 6.87e+01 bond pdb=" CA ALA G 703 " pdb=" C ALA G 703 " ideal model delta sigma weight residual 1.524 1.428 0.095 1.25e-02 6.40e+03 5.82e+01 bond pdb=" C ILE G 621 " pdb=" O ILE G 621 " ideal model delta sigma weight residual 1.236 1.153 0.083 1.09e-02 8.42e+03 5.79e+01 ... (remaining 19222 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.66: 25064 2.66 - 5.32: 870 5.32 - 7.98: 137 7.98 - 10.64: 34 10.64 - 13.30: 8 Bond angle restraints: 26113 Sorted by residual: angle pdb=" N ALA G 44 " pdb=" CA ALA G 44 " pdb=" C ALA G 44 " ideal model delta sigma weight residual 111.07 123.71 -12.64 1.07e+00 8.73e-01 1.40e+02 angle pdb=" N TRP F 353 " pdb=" CA TRP F 353 " pdb=" C TRP F 353 " ideal model delta sigma weight residual 111.07 121.84 -10.77 1.07e+00 8.73e-01 1.01e+02 angle pdb=" N ARG B 205 " pdb=" CA ARG B 205 " pdb=" C ARG B 205 " ideal model delta sigma weight residual 111.28 122.16 -10.88 1.09e+00 8.42e-01 9.97e+01 angle pdb=" N ARG G 834 " pdb=" CA ARG G 834 " pdb=" C ARG G 834 " ideal model delta sigma weight residual 111.36 121.60 -10.24 1.09e+00 8.42e-01 8.82e+01 angle pdb=" N CYS E 137 " pdb=" CA CYS E 137 " pdb=" C CYS E 137 " ideal model delta sigma weight residual 111.28 121.41 -10.13 1.09e+00 8.42e-01 8.64e+01 ... (remaining 26108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 10303 17.86 - 35.72: 895 35.72 - 53.58: 199 53.58 - 71.44: 52 71.44 - 89.30: 14 Dihedral angle restraints: 11463 sinusoidal: 4660 harmonic: 6803 Sorted by residual: dihedral pdb=" C HIS F 431 " pdb=" N HIS F 431 " pdb=" CA HIS F 431 " pdb=" CB HIS F 431 " ideal model delta harmonic sigma weight residual -122.60 -138.53 15.93 0 2.50e+00 1.60e-01 4.06e+01 dihedral pdb=" N HIS F 431 " pdb=" C HIS F 431 " pdb=" CA HIS F 431 " pdb=" CB HIS F 431 " ideal model delta harmonic sigma weight residual 122.80 138.57 -15.77 0 2.50e+00 1.60e-01 3.98e+01 dihedral pdb=" N GLU E 70 " pdb=" C GLU E 70 " pdb=" CA GLU E 70 " pdb=" CB GLU E 70 " ideal model delta harmonic sigma weight residual 122.80 137.38 -14.58 0 2.50e+00 1.60e-01 3.40e+01 ... (remaining 11460 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.414: 2784 4.414 - 8.827: 0 8.827 - 13.241: 0 13.241 - 17.654: 0 17.654 - 22.068: 24 Chirality restraints: 2808 Sorted by residual: chirality pdb="FE4 SF4 I 302 " pdb=" S1 SF4 I 302 " pdb=" S2 SF4 I 302 " pdb=" S3 SF4 I 302 " both_signs ideal model delta sigma weight residual False 10.55 -11.51 22.07 2.00e-01 2.50e+01 1.22e+04 chirality pdb="FE3 SF4 B 301 " pdb=" S1 SF4 B 301 " pdb=" S2 SF4 B 301 " pdb=" S4 SF4 B 301 " both_signs ideal model delta sigma weight residual False -10.55 10.64 -21.19 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE1 SF4 B 301 " pdb=" S2 SF4 B 301 " pdb=" S3 SF4 B 301 " pdb=" S4 SF4 B 301 " both_signs ideal model delta sigma weight residual False -10.55 10.61 -21.17 2.00e-01 2.50e+01 1.12e+04 ... (remaining 2805 not shown) Planarity restraints: 3417 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU G 660 " -0.024 2.00e-02 2.50e+03 4.96e-02 2.46e+01 pdb=" C LEU G 660 " 0.086 2.00e-02 2.50e+03 pdb=" O LEU G 660 " -0.033 2.00e-02 2.50e+03 pdb=" N SER G 661 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE G 819 " 0.024 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C PHE G 819 " -0.085 2.00e-02 2.50e+03 pdb=" O PHE G 819 " 0.032 2.00e-02 2.50e+03 pdb=" N GLY G 820 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER G 317 " 0.020 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" C SER G 317 " -0.068 2.00e-02 2.50e+03 pdb=" O SER G 317 " 0.026 2.00e-02 2.50e+03 pdb=" N PRO G 318 " 0.022 2.00e-02 2.50e+03 ... (remaining 3414 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.27: 47 2.27 - 2.93: 8791 2.93 - 3.59: 26292 3.59 - 4.24: 47145 4.24 - 4.90: 81666 Nonbonded interactions: 163941 Sorted by model distance: nonbonded pdb=" OD1 ASP G 177 " pdb=" O HOH G1101 " model vdw 1.618 3.040 nonbonded pdb=" OE2 GLU F 135 " pdb=" O HOH F 601 " model vdw 1.654 3.040 nonbonded pdb=" OE2 GLU D 115 " pdb=" NH2 ARG G 698 " model vdw 1.815 3.120 nonbonded pdb=" OE2 GLU D 85 " pdb=" O HOH D 601 " model vdw 1.841 3.040 nonbonded pdb=" OE2 GLU G 380 " pdb=" ND2 ASN G 503 " model vdw 1.857 3.120 ... (remaining 163936 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.95 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.460 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 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 : 0.013 0.665 19264 Z= 0.778 Angle : 1.331 44.966 26209 Z= 0.735 Chirality : 1.946 22.068 2808 Planarity : 0.007 0.081 3417 Dihedral : 14.634 89.303 7107 Min Nonbonded Distance : 1.618 Molprobity Statistics. All-atom Clashscore : 15.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 1.58 % Allowed : 11.23 % Favored : 87.20 % Cbeta Deviations : 0.37 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.38 (0.15), residues: 2359 helix: -1.89 (0.15), residues: 861 sheet: -2.23 (0.32), residues: 228 loop : -2.53 (0.15), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG G 394 TYR 0.023 0.002 TYR G 638 PHE 0.018 0.002 PHE G 130 TRP 0.022 0.001 TRP F 15 HIS 0.014 0.001 HIS D 83 Details of bonding type rmsd covalent geometry : bond 0.01180 (19227) covalent geometry : angle 1.12616 (26113) hydrogen bonds : bond 0.20091 ( 649) hydrogen bonds : angle 7.89380 ( 1797) metal coordination : bond 0.11683 ( 37) metal coordination : angle 11.78570 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 337 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 MET cc_start: 0.6987 (ptp) cc_final: 0.6774 (ptp) REVERT: B 208 ARG cc_start: -0.3261 (OUTLIER) cc_final: -0.3581 (ptm160) REVERT: D 105 ARG cc_start: 0.7669 (mmt90) cc_final: 0.7360 (mpt180) REVERT: D 123 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.6936 (m-80) REVERT: D 272 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.6921 (tm-30) REVERT: D 273 TYR cc_start: 0.7462 (p90) cc_final: 0.7212 (p90) REVERT: D 390 TYR cc_start: 0.7325 (t80) cc_final: 0.6850 (t80) REVERT: D 449 GLU cc_start: 0.7951 (pt0) cc_final: 0.7254 (mm-30) REVERT: D 468 GLU cc_start: 0.7379 (pt0) cc_final: 0.6839 (tp30) REVERT: D 471 ARG cc_start: 0.6733 (mtp85) cc_final: 0.6449 (mtp-110) REVERT: D 575 SER cc_start: 0.8140 (m) cc_final: 0.7707 (t) REVERT: E 31 ASP cc_start: 0.8617 (t0) cc_final: 0.8390 (t0) REVERT: E 60 ASP cc_start: 0.7876 (m-30) cc_final: 0.7646 (m-30) REVERT: F 48 ASP cc_start: 0.7392 (m-30) cc_final: 0.7148 (m-30) REVERT: F 135 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6782 (mp0) REVERT: F 158 LYS cc_start: 0.7657 (mmpt) cc_final: 0.7068 (mmpt) REVERT: F 168 GLU cc_start: 0.7984 (tt0) cc_final: 0.7756 (tt0) REVERT: F 183 GLU cc_start: 0.8702 (tt0) cc_final: 0.8411 (tt0) REVERT: F 241 LYS cc_start: 0.9210 (mmpt) cc_final: 0.8949 (mppt) REVERT: F 258 ASN cc_start: 0.8313 (t0) cc_final: 0.7841 (t0) REVERT: F 275 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7894 (mt-10) REVERT: F 386 GLN cc_start: 0.7466 (tt0) cc_final: 0.7137 (mt0) REVERT: F 424 LYS cc_start: 0.8771 (mtpt) cc_final: 0.8423 (mtmm) REVERT: G 72 SER cc_start: 0.8345 (m) cc_final: 0.8142 (p) REVERT: G 80 ASP cc_start: 0.8481 (m-30) cc_final: 0.8241 (m-30) REVERT: G 276 LYS cc_start: 0.8860 (mmtm) cc_final: 0.8646 (mmpt) REVERT: G 277 ASP cc_start: 0.8207 (p0) cc_final: 0.7989 (p0) REVERT: G 335 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7431 (mp0) REVERT: G 435 ASP cc_start: 0.8481 (t0) cc_final: 0.8248 (t70) REVERT: G 436 ASP cc_start: 0.7740 (p0) cc_final: 0.7203 (p0) REVERT: G 488 GLN cc_start: 0.7700 (tt0) cc_final: 0.7255 (mt0) REVERT: G 494 LYS cc_start: 0.8021 (mtmt) cc_final: 0.7299 (mmtm) REVERT: G 544 MET cc_start: 0.8406 (ttm) cc_final: 0.8108 (ttp) REVERT: G 586 LYS cc_start: 0.8038 (ptpt) cc_final: 0.7772 (ptmt) REVERT: G 642 LYS cc_start: 0.8835 (pttp) cc_final: 0.8539 (ptpp) REVERT: G 725 ARG cc_start: 0.7469 (ptm160) cc_final: 0.7233 (ptm160) REVERT: G 748 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8173 (ppt90) REVERT: G 832 GLN cc_start: 0.8416 (mm-40) cc_final: 0.8184 (mp10) REVERT: G 835 MET cc_start: 0.7735 (ptp) cc_final: 0.7292 (ptm) REVERT: G 849 LYS cc_start: 0.8757 (ttpt) cc_final: 0.8430 (ttpp) REVERT: G 881 GLN cc_start: 0.7818 (mt0) cc_final: 0.7512 (mt0) REVERT: G 888 MET cc_start: 0.7943 (tpp) cc_final: 0.7345 (mmm) REVERT: G 902 ASP cc_start: 0.8080 (t0) cc_final: 0.6511 (p0) REVERT: I 57 GLU cc_start: 0.6696 (mm-30) cc_final: 0.6461 (mm-30) REVERT: I 83 LYS cc_start: 0.7980 (tppt) cc_final: 0.7705 (mptt) REVERT: I 122 MET cc_start: 0.6243 (mmp) cc_final: 0.5452 (ptm) REVERT: I 145 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7808 (m-80) REVERT: I 171 LYS cc_start: 0.8324 (mttt) cc_final: 0.7733 (mptt) outliers start: 31 outliers final: 11 residues processed: 361 average time/residue: 0.7242 time to fit residues: 287.5029 Evaluate side-chains 241 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 224 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 208 ARG Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 337 THR Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain F residue 126 TYR Chi-restraints excluded: chain F residue 135 GLU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain G residue 698 ARG Chi-restraints excluded: chain G residue 738 MET Chi-restraints excluded: chain G residue 748 ARG Chi-restraints excluded: chain I residue 145 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.0980 chunk 103 optimal weight: 0.6980 chunk 200 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN D 129 ASN D 315 HIS ** D 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN F 196 ASN G 101 HIS ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 671 HIS G 707 HIS G 726 GLN G 769 GLN G 804 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.132796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.109704 restraints weight = 15357.726| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.55 r_work: 0.3417 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.275 19264 Z= 0.518 Angle : 3.294 55.577 26209 Z= 1.871 Chirality : 0.580 6.648 2808 Planarity : 0.005 0.054 3417 Dihedral : 6.274 58.589 2664 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.69 % Allowed : 15.40 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.30 (0.16), residues: 2359 helix: -0.65 (0.17), residues: 859 sheet: -1.84 (0.31), residues: 251 loop : -2.13 (0.16), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 201 TYR 0.020 0.001 TYR I 44 PHE 0.026 0.001 PHE I 101 TRP 0.017 0.001 TRP F 15 HIS 0.007 0.001 HIS G 176 Details of bonding type rmsd covalent geometry : bond 0.01523 (19227) covalent geometry : angle 2.83092 (26113) hydrogen bonds : bond 0.03934 ( 649) hydrogen bonds : angle 5.77664 ( 1797) metal coordination : bond 0.03832 ( 37) metal coordination : angle 27.97759 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 257 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.6572 (pp20) REVERT: B 170 MET cc_start: 0.6345 (mmt) cc_final: 0.6041 (mpp) REVERT: D 48 ILE cc_start: 0.8563 (mm) cc_final: 0.8202 (pt) REVERT: D 85 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8536 (mp0) REVERT: D 123 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7066 (m-80) REVERT: D 272 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7152 (tm-30) REVERT: D 391 GLU cc_start: 0.4223 (tt0) cc_final: 0.3460 (pp20) REVERT: D 449 GLU cc_start: 0.8176 (pt0) cc_final: 0.7266 (mm-30) REVERT: D 468 GLU cc_start: 0.7378 (pt0) cc_final: 0.6847 (tp30) REVERT: D 469 GLU cc_start: 0.7609 (tt0) cc_final: 0.7330 (mt-10) REVERT: D 471 ARG cc_start: 0.6931 (mtp85) cc_final: 0.6500 (mtm-85) REVERT: D 575 SER cc_start: 0.8103 (m) cc_final: 0.7664 (t) REVERT: E 13 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7317 (tm-30) REVERT: E 31 ASP cc_start: 0.8656 (t0) cc_final: 0.8436 (t0) REVERT: E 164 ARG cc_start: 0.8329 (mtt90) cc_final: 0.8043 (mtm-85) REVERT: F 31 SER cc_start: 0.9034 (t) cc_final: 0.8791 (p) REVERT: F 48 ASP cc_start: 0.7535 (m-30) cc_final: 0.7228 (m-30) REVERT: F 168 GLU cc_start: 0.8157 (tt0) cc_final: 0.7949 (tt0) REVERT: F 233 VAL cc_start: 0.7469 (p) cc_final: 0.7265 (t) REVERT: F 241 LYS cc_start: 0.9309 (mmpt) cc_final: 0.8919 (mppt) REVERT: F 243 LYS cc_start: 0.8287 (ptpp) cc_final: 0.7622 (ptmm) REVERT: F 258 ASN cc_start: 0.8420 (t0) cc_final: 0.7964 (t0) REVERT: F 286 LYS cc_start: 0.8187 (mtpp) cc_final: 0.7619 (mtmt) REVERT: F 312 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7405 (tt0) REVERT: F 386 GLN cc_start: 0.7354 (tt0) cc_final: 0.7049 (tt0) REVERT: F 424 LYS cc_start: 0.8834 (mtpt) cc_final: 0.8413 (mtmm) REVERT: G 57 GLU cc_start: 0.7803 (pm20) cc_final: 0.7512 (mp0) REVERT: G 62 ARG cc_start: 0.7615 (ptt-90) cc_final: 0.7409 (ptt-90) REVERT: G 80 ASP cc_start: 0.8450 (m-30) cc_final: 0.8179 (m-30) REVERT: G 108 GLU cc_start: 0.7456 (pt0) cc_final: 0.7231 (pt0) REVERT: G 190 GLU cc_start: 0.8592 (mt-10) cc_final: 0.7960 (mp0) REVERT: G 276 LYS cc_start: 0.8996 (mmtm) cc_final: 0.8777 (mmpt) REVERT: G 277 ASP cc_start: 0.8392 (p0) cc_final: 0.8189 (p0) REVERT: G 335 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7514 (mp0) REVERT: G 436 ASP cc_start: 0.7920 (p0) cc_final: 0.7686 (p0) REVERT: G 484 ASP cc_start: 0.7636 (m-30) cc_final: 0.7077 (m-30) REVERT: G 488 GLN cc_start: 0.7571 (tt0) cc_final: 0.7112 (mt0) REVERT: G 494 LYS cc_start: 0.8075 (mtmt) cc_final: 0.7292 (mmtm) REVERT: G 544 MET cc_start: 0.8216 (ttm) cc_final: 0.7847 (ttm) REVERT: G 591 MET cc_start: 0.8169 (mtp) cc_final: 0.7941 (ttm) REVERT: G 642 LYS cc_start: 0.8845 (pttp) cc_final: 0.8474 (ptpp) REVERT: G 715 MET cc_start: 0.8953 (ptt) cc_final: 0.8576 (ptm) REVERT: G 771 GLU cc_start: 0.7857 (pt0) cc_final: 0.7562 (pt0) REVERT: G 787 GLU cc_start: 0.8090 (pm20) cc_final: 0.7660 (mp0) REVERT: G 849 LYS cc_start: 0.8776 (ttpt) cc_final: 0.8446 (ttpp) REVERT: G 881 GLN cc_start: 0.7904 (mt0) cc_final: 0.7528 (mt0) REVERT: G 888 MET cc_start: 0.7769 (tpp) cc_final: 0.7265 (mmm) REVERT: I 83 LYS cc_start: 0.8109 (tppt) cc_final: 0.7693 (mptt) REVERT: I 122 MET cc_start: 0.6216 (mmp) cc_final: 0.5073 (ptm) REVERT: I 153 MET cc_start: 0.7783 (OUTLIER) cc_final: 0.7147 (mmm) REVERT: I 165 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7506 (mt-10) REVERT: I 171 LYS cc_start: 0.8544 (mttt) cc_final: 0.7945 (mptt) outliers start: 53 outliers final: 20 residues processed: 289 average time/residue: 0.7041 time to fit residues: 224.6737 Evaluate side-chains 247 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 219 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 312 GLU Chi-restraints excluded: chain G residue 738 MET Chi-restraints excluded: chain G residue 769 GLN Chi-restraints excluded: chain G residue 833 SER Chi-restraints excluded: chain G residue 850 LEU Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 867 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 165 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 150 optimal weight: 0.9990 chunk 194 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 176 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 1 optimal weight: 20.0000 chunk 225 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 566 GLN E 142 ASN F 224 ASN ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 804 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.131376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.105879 restraints weight = 16509.979| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.59 r_work: 0.3374 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3273 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.247 19264 Z= 0.526 Angle : 3.287 57.599 26209 Z= 1.868 Chirality : 0.589 6.469 2808 Planarity : 0.005 0.056 3417 Dihedral : 5.979 58.622 2641 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 3.30 % Allowed : 16.06 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.84 (0.17), residues: 2359 helix: -0.28 (0.18), residues: 863 sheet: -1.47 (0.32), residues: 249 loop : -1.87 (0.17), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 712 TYR 0.016 0.002 TYR F 178 PHE 0.017 0.002 PHE F 167 TRP 0.018 0.002 TRP F 15 HIS 0.007 0.001 HIS D 493 Details of bonding type rmsd covalent geometry : bond 0.01523 (19227) covalent geometry : angle 2.82906 (26113) hydrogen bonds : bond 0.04191 ( 649) hydrogen bonds : angle 5.42609 ( 1797) metal coordination : bond 0.03802 ( 37) metal coordination : angle 27.80596 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 230 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: B 163 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6646 (pp20) REVERT: B 166 MET cc_start: 0.7207 (tpp) cc_final: 0.6976 (tpt) REVERT: D 58 ASP cc_start: 0.7795 (t0) cc_final: 0.7588 (t0) REVERT: D 85 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8588 (mp0) REVERT: D 123 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7501 (m-80) REVERT: D 272 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7344 (tm-30) REVERT: D 273 TYR cc_start: 0.7826 (p90) cc_final: 0.7507 (p90) REVERT: D 391 GLU cc_start: 0.4200 (tt0) cc_final: 0.3349 (pp20) REVERT: D 438 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7641 (mtt180) REVERT: D 449 GLU cc_start: 0.8214 (pt0) cc_final: 0.7368 (mm-30) REVERT: D 468 GLU cc_start: 0.7414 (pt0) cc_final: 0.6821 (tp30) REVERT: D 471 ARG cc_start: 0.7120 (mtp85) cc_final: 0.6625 (mtt90) REVERT: D 575 SER cc_start: 0.8223 (m) cc_final: 0.7788 (t) REVERT: E 156 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7245 (mp0) REVERT: E 160 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7806 (tm-30) REVERT: E 163 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7368 (mp0) REVERT: E 164 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7694 (mtm180) REVERT: F 31 SER cc_start: 0.8932 (t) cc_final: 0.8673 (p) REVERT: F 152 GLU cc_start: 0.8314 (tm-30) cc_final: 0.8078 (tm-30) REVERT: F 158 LYS cc_start: 0.8074 (mmpt) cc_final: 0.7578 (mmpt) REVERT: F 168 GLU cc_start: 0.8204 (tt0) cc_final: 0.7933 (tt0) REVERT: F 183 GLU cc_start: 0.9030 (tt0) cc_final: 0.8781 (tt0) REVERT: F 241 LYS cc_start: 0.9247 (mmpt) cc_final: 0.8895 (mmtm) REVERT: F 243 LYS cc_start: 0.8480 (ptpp) cc_final: 0.7799 (ptmm) REVERT: F 275 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8113 (mt-10) REVERT: F 286 LYS cc_start: 0.8278 (mtpp) cc_final: 0.7752 (mtmt) REVERT: F 312 GLU cc_start: 0.7993 (tt0) cc_final: 0.7471 (tt0) REVERT: F 386 GLN cc_start: 0.7457 (tt0) cc_final: 0.7199 (tt0) REVERT: F 424 LYS cc_start: 0.8888 (mtpt) cc_final: 0.8375 (mtpp) REVERT: G 57 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: G 80 ASP cc_start: 0.8505 (m-30) cc_final: 0.8269 (m-30) REVERT: G 108 GLU cc_start: 0.7742 (pt0) cc_final: 0.7502 (pt0) REVERT: G 185 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.6649 (pp20) REVERT: G 276 LYS cc_start: 0.9027 (mmtm) cc_final: 0.8808 (mmpt) REVERT: G 335 GLU cc_start: 0.8026 (mm-30) cc_final: 0.7577 (mp0) REVERT: G 484 ASP cc_start: 0.7597 (m-30) cc_final: 0.6958 (m-30) REVERT: G 488 GLN cc_start: 0.7743 (tt0) cc_final: 0.7271 (mt0) REVERT: G 494 LYS cc_start: 0.8123 (mtmt) cc_final: 0.7381 (mmtm) REVERT: G 544 MET cc_start: 0.8359 (ttm) cc_final: 0.7802 (ttm) REVERT: G 642 LYS cc_start: 0.8879 (pttp) cc_final: 0.8536 (ptpp) REVERT: G 715 MET cc_start: 0.8948 (ptt) cc_final: 0.8576 (ptm) REVERT: G 787 GLU cc_start: 0.7997 (pm20) cc_final: 0.7690 (mp0) REVERT: G 849 LYS cc_start: 0.8729 (ttpt) cc_final: 0.8418 (ttpp) REVERT: G 881 GLN cc_start: 0.8184 (mt0) cc_final: 0.7720 (mt0) REVERT: G 888 MET cc_start: 0.7907 (tpp) cc_final: 0.7235 (mmm) REVERT: I 83 LYS cc_start: 0.8202 (tppt) cc_final: 0.7787 (mptt) REVERT: I 122 MET cc_start: 0.6593 (mmp) cc_final: 0.5387 (ptm) REVERT: I 171 LYS cc_start: 0.8560 (mttt) cc_final: 0.7932 (mptt) outliers start: 65 outliers final: 25 residues processed: 274 average time/residue: 0.7014 time to fit residues: 212.4510 Evaluate side-chains 246 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 211 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 ILE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 438 ARG Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 557 VAL Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 164 ARG Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 589 LEU Chi-restraints excluded: chain G residue 738 MET Chi-restraints excluded: chain G residue 833 SER Chi-restraints excluded: chain G residue 850 LEU Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 867 VAL Chi-restraints excluded: chain I residue 49 VAL Chi-restraints excluded: chain I residue 136 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 123 optimal weight: 0.9990 chunk 121 optimal weight: 0.4980 chunk 177 optimal weight: 0.0980 chunk 173 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 190 optimal weight: 4.9990 chunk 35 optimal weight: 0.0570 chunk 106 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 227 optimal weight: 0.9980 chunk 184 optimal weight: 5.9990 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 98 HIS G 216 ASN G 236 ASN G 628 GLN G 653 HIS G 769 GLN G 804 GLN G 908 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.135881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.110629 restraints weight = 16461.103| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.60 r_work: 0.3428 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.252 19264 Z= 0.496 Angle : 3.271 52.990 26209 Z= 1.861 Chirality : 0.585 6.383 2808 Planarity : 0.005 0.053 3417 Dihedral : 5.626 59.796 2641 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.15 % Allowed : 17.38 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.51 (0.17), residues: 2359 helix: 0.10 (0.18), residues: 865 sheet: -1.31 (0.31), residues: 254 loop : -1.76 (0.17), residues: 1240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG G 712 TYR 0.016 0.001 TYR I 44 PHE 0.013 0.001 PHE D 352 TRP 0.011 0.001 TRP G 651 HIS 0.008 0.001 HIS G 176 Details of bonding type rmsd covalent geometry : bond 0.01469 (19227) covalent geometry : angle 2.81011 (26113) hydrogen bonds : bond 0.03248 ( 649) hydrogen bonds : angle 5.11827 ( 1797) metal coordination : bond 0.02406 ( 37) metal coordination : angle 27.81785 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 229 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6670 (pp20) REVERT: B 166 MET cc_start: 0.7232 (tpp) cc_final: 0.7019 (tpt) REVERT: D 48 ILE cc_start: 0.8568 (mm) cc_final: 0.8229 (pt) REVERT: D 58 ASP cc_start: 0.7961 (t0) cc_final: 0.7563 (t0) REVERT: D 123 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.7296 (m-80) REVERT: D 191 GLU cc_start: -0.0698 (OUTLIER) cc_final: -0.0949 (tp30) REVERT: D 272 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7502 (tm-30) REVERT: D 391 GLU cc_start: 0.4171 (tt0) cc_final: 0.3415 (pp20) REVERT: D 449 GLU cc_start: 0.8159 (pt0) cc_final: 0.7334 (mm-30) REVERT: D 468 GLU cc_start: 0.7325 (pt0) cc_final: 0.6856 (tp30) REVERT: D 471 ARG cc_start: 0.7014 (mtp85) cc_final: 0.6443 (mpt-90) REVERT: D 575 SER cc_start: 0.8239 (m) cc_final: 0.7768 (t) REVERT: E 111 LYS cc_start: 0.8545 (OUTLIER) cc_final: 0.8266 (tttp) REVERT: E 156 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7261 (mp0) REVERT: E 160 GLU cc_start: 0.8013 (tm-30) cc_final: 0.7803 (tm-30) REVERT: E 163 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: F 31 SER cc_start: 0.9009 (t) cc_final: 0.8782 (p) REVERT: F 152 GLU cc_start: 0.8298 (tm-30) cc_final: 0.8019 (tm-30) REVERT: F 158 LYS cc_start: 0.8164 (mmpt) cc_final: 0.7766 (mmpt) REVERT: F 168 GLU cc_start: 0.8151 (tt0) cc_final: 0.7917 (tt0) REVERT: F 182 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8029 (tp30) REVERT: F 241 LYS cc_start: 0.9283 (mmpt) cc_final: 0.8955 (mmtm) REVERT: F 243 LYS cc_start: 0.8475 (ptpp) cc_final: 0.7797 (ptmm) REVERT: F 275 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8123 (mt-10) REVERT: F 286 LYS cc_start: 0.8308 (mtpp) cc_final: 0.7773 (mtmt) REVERT: F 312 GLU cc_start: 0.7980 (tt0) cc_final: 0.7421 (tt0) REVERT: F 386 GLN cc_start: 0.7312 (tt0) cc_final: 0.6995 (tt0) REVERT: F 424 LYS cc_start: 0.8878 (mtpt) cc_final: 0.8381 (mtpp) REVERT: G 57 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: G 80 ASP cc_start: 0.8498 (m-30) cc_final: 0.8271 (m-30) REVERT: G 209 LYS cc_start: 0.7802 (mttt) cc_final: 0.7253 (mttp) REVERT: G 221 MET cc_start: 0.9032 (tpp) cc_final: 0.8717 (mmm) REVERT: G 276 LYS cc_start: 0.9025 (mmtm) cc_final: 0.8812 (mmpt) REVERT: G 335 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7543 (pm20) REVERT: G 484 ASP cc_start: 0.7576 (m-30) cc_final: 0.6940 (m-30) REVERT: G 488 GLN cc_start: 0.7685 (tt0) cc_final: 0.7222 (mt0) REVERT: G 494 LYS cc_start: 0.8181 (mtmt) cc_final: 0.7454 (mmtm) REVERT: G 531 MET cc_start: 0.8822 (mmt) cc_final: 0.8222 (mmt) REVERT: G 544 MET cc_start: 0.8388 (ttm) cc_final: 0.7978 (ttm) REVERT: G 642 LYS cc_start: 0.8824 (pttp) cc_final: 0.8434 (ptpp) REVERT: G 715 MET cc_start: 0.8901 (ptt) cc_final: 0.8577 (ptm) REVERT: G 787 GLU cc_start: 0.7988 (pm20) cc_final: 0.7688 (mp0) REVERT: G 849 LYS cc_start: 0.8723 (ttpt) cc_final: 0.8437 (ttmt) REVERT: G 881 GLN cc_start: 0.7983 (mt0) cc_final: 0.7578 (mt0) REVERT: G 888 MET cc_start: 0.7763 (tpp) cc_final: 0.7281 (mmm) REVERT: I 83 LYS cc_start: 0.8203 (tppt) cc_final: 0.7840 (mptt) REVERT: I 122 MET cc_start: 0.6436 (mmp) cc_final: 0.5213 (ptm) REVERT: I 153 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7028 (mmm) REVERT: I 165 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7593 (mt-10) REVERT: I 171 LYS cc_start: 0.8548 (mttt) cc_final: 0.7914 (mptt) outliers start: 62 outliers final: 20 residues processed: 266 average time/residue: 0.7075 time to fit residues: 208.6679 Evaluate side-chains 243 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 212 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain D residue 116 ASN Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 332 VAL Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 589 LEU Chi-restraints excluded: chain G residue 738 MET Chi-restraints excluded: chain G residue 840 ILE Chi-restraints excluded: chain G residue 850 LEU Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 867 VAL Chi-restraints excluded: chain I residue 44 TYR Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 153 MET Chi-restraints excluded: chain I residue 165 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 205 optimal weight: 0.6980 chunk 209 optimal weight: 9.9990 chunk 19 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 109 optimal weight: 0.6980 chunk 112 optimal weight: 0.0980 chunk 21 optimal weight: 0.0770 chunk 82 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 769 GLN G 804 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.131505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.106987 restraints weight = 15728.085| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.70 r_work: 0.3287 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.246 19264 Z= 0.494 Angle : 3.271 51.219 26209 Z= 1.860 Chirality : 0.585 6.401 2808 Planarity : 0.004 0.052 3417 Dihedral : 5.111 58.119 2635 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 3.20 % Allowed : 17.94 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.27 (0.17), residues: 2359 helix: 0.33 (0.18), residues: 872 sheet: -1.28 (0.30), residues: 272 loop : -1.63 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 712 TYR 0.026 0.001 TYR D 273 PHE 0.012 0.001 PHE D 71 TRP 0.010 0.001 TRP G 651 HIS 0.007 0.001 HIS G 176 Details of bonding type rmsd covalent geometry : bond 0.01467 (19227) covalent geometry : angle 2.80738 (26113) hydrogen bonds : bond 0.03094 ( 649) hydrogen bonds : angle 4.91867 ( 1797) metal coordination : bond 0.02192 ( 37) metal coordination : angle 27.86714 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 222 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6735 (pp20) REVERT: D 48 ILE cc_start: 0.8390 (mm) cc_final: 0.8043 (pt) REVERT: D 58 ASP cc_start: 0.7758 (t0) cc_final: 0.7467 (t0) REVERT: D 123 PHE cc_start: 0.7618 (OUTLIER) cc_final: 0.7075 (m-80) REVERT: D 191 GLU cc_start: -0.0601 (OUTLIER) cc_final: -0.0903 (tp30) REVERT: D 272 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7343 (tm-30) REVERT: D 273 TYR cc_start: 0.7778 (p90) cc_final: 0.7523 (p90) REVERT: D 430 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8050 (mp) REVERT: D 449 GLU cc_start: 0.8081 (pt0) cc_final: 0.7182 (mm-30) REVERT: D 468 GLU cc_start: 0.7003 (pt0) cc_final: 0.6694 (OUTLIER) REVERT: D 471 ARG cc_start: 0.6659 (mtp85) cc_final: 0.6395 (mtp-110) REVERT: D 575 SER cc_start: 0.8200 (m) cc_final: 0.7685 (t) REVERT: E 47 ARG cc_start: 0.7915 (mtp85) cc_final: 0.7615 (mtp85) REVERT: E 111 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8055 (tttp) REVERT: E 156 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7298 (mp0) REVERT: E 163 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7549 (mm-30) REVERT: F 31 SER cc_start: 0.8929 (t) cc_final: 0.8692 (p) REVERT: F 152 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7901 (tm-30) REVERT: F 158 LYS cc_start: 0.8134 (mmpt) cc_final: 0.7739 (mmpt) REVERT: F 168 GLU cc_start: 0.8092 (tt0) cc_final: 0.7850 (tt0) REVERT: F 241 LYS cc_start: 0.9289 (mmpt) cc_final: 0.8894 (mmtm) REVERT: F 275 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8040 (mt-10) REVERT: F 286 LYS cc_start: 0.8075 (mtpp) cc_final: 0.7535 (mtmt) REVERT: F 312 GLU cc_start: 0.7819 (tt0) cc_final: 0.7400 (tt0) REVERT: F 386 GLN cc_start: 0.7070 (tt0) cc_final: 0.6746 (tt0) REVERT: F 420 GLU cc_start: 0.6909 (mm-30) cc_final: 0.6465 (mm-30) REVERT: F 424 LYS cc_start: 0.8788 (mtpt) cc_final: 0.8293 (mtpp) REVERT: G 57 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: G 80 ASP cc_start: 0.8387 (m-30) cc_final: 0.8184 (m-30) REVERT: G 185 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.6408 (pp20) REVERT: G 221 MET cc_start: 0.8910 (tpp) cc_final: 0.8491 (mmm) REVERT: G 276 LYS cc_start: 0.8998 (mmtm) cc_final: 0.8781 (mmpt) REVERT: G 335 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7565 (pm20) REVERT: G 484 ASP cc_start: 0.7430 (m-30) cc_final: 0.6797 (m-30) REVERT: G 488 GLN cc_start: 0.7641 (tt0) cc_final: 0.7181 (mt0) REVERT: G 494 LYS cc_start: 0.8111 (mtmt) cc_final: 0.7299 (mmtm) REVERT: G 531 MET cc_start: 0.8685 (mmt) cc_final: 0.8078 (mmt) REVERT: G 544 MET cc_start: 0.8104 (ttm) cc_final: 0.7718 (ttm) REVERT: G 551 GLU cc_start: 0.7595 (OUTLIER) cc_final: 0.7361 (mp0) REVERT: G 642 LYS cc_start: 0.8726 (pttp) cc_final: 0.8303 (ptpp) REVERT: G 715 MET cc_start: 0.8691 (ptt) cc_final: 0.8483 (ptm) REVERT: G 787 GLU cc_start: 0.7926 (pm20) cc_final: 0.7647 (mp0) REVERT: G 849 LYS cc_start: 0.8601 (ttpt) cc_final: 0.8341 (ttmt) REVERT: G 881 GLN cc_start: 0.7669 (mt0) cc_final: 0.7162 (mt0) REVERT: G 888 MET cc_start: 0.7493 (tpp) cc_final: 0.7102 (mmm) REVERT: I 83 LYS cc_start: 0.8133 (tppt) cc_final: 0.7704 (mptt) REVERT: I 121 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: I 122 MET cc_start: 0.6318 (mmp) cc_final: 0.4793 (ttm) REVERT: I 153 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.6705 (mmm) REVERT: I 171 LYS cc_start: 0.8500 (mttt) cc_final: 0.7796 (mptt) outliers start: 63 outliers final: 24 residues processed: 266 average time/residue: 0.6880 time to fit residues: 203.0913 Evaluate side-chains 247 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 211 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 551 GLU Chi-restraints excluded: chain G residue 589 LEU Chi-restraints excluded: chain G residue 665 ASP Chi-restraints excluded: chain G residue 738 MET Chi-restraints excluded: chain G residue 769 GLN Chi-restraints excluded: chain G residue 833 SER Chi-restraints excluded: chain G residue 850 LEU Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 867 VAL Chi-restraints excluded: chain I residue 44 TYR Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 153 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 171 optimal weight: 0.7980 chunk 178 optimal weight: 0.5980 chunk 113 optimal weight: 0.7980 chunk 224 optimal weight: 1.9990 chunk 97 optimal weight: 0.0770 chunk 202 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 219 optimal weight: 0.2980 chunk 165 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 804 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.132273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.107724 restraints weight = 15622.642| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.70 r_work: 0.3299 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.248 19264 Z= 0.493 Angle : 3.268 50.901 26209 Z= 1.860 Chirality : 0.585 6.391 2808 Planarity : 0.004 0.053 3417 Dihedral : 5.016 57.395 2635 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.05 % Allowed : 18.60 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.12 (0.17), residues: 2359 helix: 0.50 (0.18), residues: 866 sheet: -1.20 (0.30), residues: 278 loop : -1.57 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 712 TYR 0.019 0.001 TYR D 273 PHE 0.011 0.001 PHE F 167 TRP 0.010 0.001 TRP G 651 HIS 0.006 0.001 HIS G 176 Details of bonding type rmsd covalent geometry : bond 0.01466 (19227) covalent geometry : angle 2.80657 (26113) hydrogen bonds : bond 0.03075 ( 649) hydrogen bonds : angle 4.83458 ( 1797) metal coordination : bond 0.02238 ( 37) metal coordination : angle 27.80921 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 221 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6690 (pp20) REVERT: D 48 ILE cc_start: 0.8364 (mm) cc_final: 0.7985 (pt) REVERT: D 58 ASP cc_start: 0.7799 (t0) cc_final: 0.7484 (t0) REVERT: D 123 PHE cc_start: 0.7592 (OUTLIER) cc_final: 0.7009 (m-80) REVERT: D 191 GLU cc_start: -0.0632 (OUTLIER) cc_final: -0.1021 (tp30) REVERT: D 272 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7499 (tm-30) REVERT: D 273 TYR cc_start: 0.7839 (p90) cc_final: 0.7595 (p90) REVERT: D 383 MET cc_start: 0.8048 (mmt) cc_final: 0.7501 (mmm) REVERT: D 391 GLU cc_start: 0.4116 (pt0) cc_final: 0.3183 (pp20) REVERT: D 449 GLU cc_start: 0.8073 (pt0) cc_final: 0.7182 (mm-30) REVERT: D 468 GLU cc_start: 0.6932 (pt0) cc_final: 0.6709 (OUTLIER) REVERT: D 471 ARG cc_start: 0.6673 (mtp85) cc_final: 0.6340 (mtt90) REVERT: D 575 SER cc_start: 0.8154 (m) cc_final: 0.7637 (t) REVERT: E 13 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7209 (tm-30) REVERT: E 25 GLU cc_start: 0.7360 (tp30) cc_final: 0.7105 (tp30) REVERT: E 111 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8017 (tttp) REVERT: E 119 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7905 (mt0) REVERT: F 31 SER cc_start: 0.8941 (t) cc_final: 0.8709 (p) REVERT: F 152 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7929 (tm-30) REVERT: F 158 LYS cc_start: 0.8110 (mmpt) cc_final: 0.7703 (mmpt) REVERT: F 168 GLU cc_start: 0.8059 (tt0) cc_final: 0.7833 (tt0) REVERT: F 241 LYS cc_start: 0.9289 (mmpt) cc_final: 0.8886 (mmtm) REVERT: F 275 GLU cc_start: 0.8283 (mt-10) cc_final: 0.8048 (mt-10) REVERT: F 286 LYS cc_start: 0.8108 (mtpp) cc_final: 0.7612 (mtmt) REVERT: F 312 GLU cc_start: 0.7828 (tt0) cc_final: 0.7427 (tt0) REVERT: F 386 GLN cc_start: 0.7072 (tt0) cc_final: 0.6747 (tt0) REVERT: F 420 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6461 (mt-10) REVERT: F 424 LYS cc_start: 0.8768 (mtpt) cc_final: 0.8286 (mtpp) REVERT: G 57 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7387 (mp0) REVERT: G 80 ASP cc_start: 0.8404 (m-30) cc_final: 0.8190 (m-30) REVERT: G 185 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6401 (pp20) REVERT: G 190 GLU cc_start: 0.8528 (mt-10) cc_final: 0.7901 (mp0) REVERT: G 216 ASN cc_start: 0.8609 (p0) cc_final: 0.8376 (p0) REVERT: G 221 MET cc_start: 0.8877 (tpp) cc_final: 0.8463 (mmm) REVERT: G 276 LYS cc_start: 0.8999 (mmtm) cc_final: 0.8788 (mmpt) REVERT: G 335 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7572 (pm20) REVERT: G 484 ASP cc_start: 0.7421 (m-30) cc_final: 0.6788 (m-30) REVERT: G 488 GLN cc_start: 0.7638 (tt0) cc_final: 0.7187 (mt0) REVERT: G 494 LYS cc_start: 0.8034 (mtmt) cc_final: 0.7196 (mmtm) REVERT: G 531 MET cc_start: 0.8699 (mmt) cc_final: 0.8136 (mmt) REVERT: G 544 MET cc_start: 0.8094 (ttm) cc_final: 0.7784 (ttm) REVERT: G 551 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7369 (mp0) REVERT: G 642 LYS cc_start: 0.8707 (pttp) cc_final: 0.8280 (ptpp) REVERT: G 787 GLU cc_start: 0.7924 (pm20) cc_final: 0.7632 (mp0) REVERT: G 849 LYS cc_start: 0.8573 (ttpt) cc_final: 0.8342 (ttmt) REVERT: G 881 GLN cc_start: 0.7683 (mt0) cc_final: 0.7308 (mt0) REVERT: G 888 MET cc_start: 0.7685 (tpp) cc_final: 0.7389 (mmm) REVERT: G 901 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7959 (tp30) REVERT: I 83 LYS cc_start: 0.8148 (tppt) cc_final: 0.7725 (mptt) REVERT: I 121 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7565 (mp0) REVERT: I 122 MET cc_start: 0.6302 (mmp) cc_final: 0.4807 (ttm) REVERT: I 153 MET cc_start: 0.7487 (OUTLIER) cc_final: 0.6610 (mmm) REVERT: I 171 LYS cc_start: 0.8511 (mttt) cc_final: 0.7795 (mptt) outliers start: 60 outliers final: 26 residues processed: 262 average time/residue: 0.6786 time to fit residues: 197.4688 Evaluate side-chains 246 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 208 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 465 LEU Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 551 GLU Chi-restraints excluded: chain G residue 665 ASP Chi-restraints excluded: chain G residue 738 MET Chi-restraints excluded: chain G residue 833 SER Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 867 VAL Chi-restraints excluded: chain G residue 901 GLU Chi-restraints excluded: chain G residue 902 ASP Chi-restraints excluded: chain I residue 44 TYR Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 153 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 207 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 36 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 185 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 196 optimal weight: 5.9990 chunk 190 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 308 GLN G 804 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.130443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.105721 restraints weight = 15706.195| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.70 r_work: 0.3269 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.253 19264 Z= 0.499 Angle : 3.271 52.634 26209 Z= 1.861 Chirality : 0.586 6.398 2808 Planarity : 0.004 0.055 3417 Dihedral : 5.044 56.362 2635 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.00 % Allowed : 18.90 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.07 (0.17), residues: 2359 helix: 0.54 (0.18), residues: 868 sheet: -1.16 (0.31), residues: 272 loop : -1.55 (0.17), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 712 TYR 0.013 0.001 TYR D 273 PHE 0.013 0.001 PHE F 167 TRP 0.010 0.001 TRP G 651 HIS 0.006 0.001 HIS G 176 Details of bonding type rmsd covalent geometry : bond 0.01474 (19227) covalent geometry : angle 2.81018 (26113) hydrogen bonds : bond 0.03223 ( 649) hydrogen bonds : angle 4.82733 ( 1797) metal coordination : bond 0.02543 ( 37) metal coordination : angle 27.81549 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 216 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6766 (pp20) REVERT: B 170 MET cc_start: 0.5863 (OUTLIER) cc_final: 0.5657 (mmt) REVERT: D 48 ILE cc_start: 0.8380 (mm) cc_final: 0.7978 (pt) REVERT: D 58 ASP cc_start: 0.7830 (t0) cc_final: 0.7507 (t0) REVERT: D 123 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.6974 (m-80) REVERT: D 272 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7552 (tm-30) REVERT: D 383 MET cc_start: 0.8045 (mmt) cc_final: 0.7498 (mmm) REVERT: D 449 GLU cc_start: 0.8081 (pt0) cc_final: 0.7180 (mm-30) REVERT: D 468 GLU cc_start: 0.6946 (pt0) cc_final: 0.6708 (OUTLIER) REVERT: D 471 ARG cc_start: 0.6701 (mtp85) cc_final: 0.6444 (mtp-110) REVERT: D 575 SER cc_start: 0.8155 (m) cc_final: 0.7637 (t) REVERT: E 25 GLU cc_start: 0.7318 (tp30) cc_final: 0.7062 (tp30) REVERT: E 111 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.8026 (tttp) REVERT: E 119 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.7938 (mt0) REVERT: F 31 SER cc_start: 0.8947 (t) cc_final: 0.8713 (p) REVERT: F 152 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7890 (tm-30) REVERT: F 158 LYS cc_start: 0.8091 (mmpt) cc_final: 0.7651 (mmpt) REVERT: F 168 GLU cc_start: 0.8026 (tt0) cc_final: 0.7783 (tt0) REVERT: F 241 LYS cc_start: 0.9287 (mmpt) cc_final: 0.8873 (mppt) REVERT: F 275 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8063 (mm-30) REVERT: F 286 LYS cc_start: 0.8240 (mtpp) cc_final: 0.7755 (mtmt) REVERT: F 312 GLU cc_start: 0.7841 (tt0) cc_final: 0.7450 (tt0) REVERT: F 386 GLN cc_start: 0.7195 (tt0) cc_final: 0.6853 (tt0) REVERT: F 420 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6378 (mt-10) REVERT: F 424 LYS cc_start: 0.8781 (mtpt) cc_final: 0.8303 (mtpp) REVERT: G 57 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: G 185 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6423 (pp20) REVERT: G 190 GLU cc_start: 0.8545 (mt-10) cc_final: 0.7922 (mp0) REVERT: G 216 ASN cc_start: 0.8643 (p0) cc_final: 0.8383 (p0) REVERT: G 221 MET cc_start: 0.8893 (tpp) cc_final: 0.8648 (mtp) REVERT: G 276 LYS cc_start: 0.9000 (mmtm) cc_final: 0.8791 (mmpt) REVERT: G 335 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7623 (pm20) REVERT: G 484 ASP cc_start: 0.7439 (m-30) cc_final: 0.6808 (m-30) REVERT: G 488 GLN cc_start: 0.7650 (tt0) cc_final: 0.7191 (mt0) REVERT: G 494 LYS cc_start: 0.8064 (mtmt) cc_final: 0.7215 (mmtm) REVERT: G 531 MET cc_start: 0.8700 (mmt) cc_final: 0.8095 (mmt) REVERT: G 544 MET cc_start: 0.8135 (ttm) cc_final: 0.7821 (ttm) REVERT: G 642 LYS cc_start: 0.8706 (pttp) cc_final: 0.8280 (ptpp) REVERT: G 715 MET cc_start: 0.8739 (ptm) cc_final: 0.8488 (ptp) REVERT: G 787 GLU cc_start: 0.7970 (pm20) cc_final: 0.7682 (mp0) REVERT: G 849 LYS cc_start: 0.8567 (ttpt) cc_final: 0.8336 (ttmt) REVERT: G 881 GLN cc_start: 0.7888 (mt0) cc_final: 0.7349 (mt0) REVERT: G 888 MET cc_start: 0.7619 (tpp) cc_final: 0.7363 (mmm) REVERT: G 901 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7932 (tp30) REVERT: I 83 LYS cc_start: 0.8168 (tppt) cc_final: 0.7747 (mptt) REVERT: I 121 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7656 (mp0) REVERT: I 122 MET cc_start: 0.6410 (mmp) cc_final: 0.4810 (ttm) REVERT: I 153 MET cc_start: 0.7584 (OUTLIER) cc_final: 0.6733 (mmm) REVERT: I 171 LYS cc_start: 0.8524 (mttt) cc_final: 0.7799 (mptt) outliers start: 59 outliers final: 25 residues processed: 255 average time/residue: 0.7023 time to fit residues: 198.3078 Evaluate side-chains 247 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 170 MET Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 272 GLU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 94 MET Chi-restraints excluded: chain F residue 266 PHE Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain G residue 409 LYS Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 738 MET Chi-restraints excluded: chain G residue 833 SER Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 858 VAL Chi-restraints excluded: chain G residue 901 GLU Chi-restraints excluded: chain G residue 902 ASP Chi-restraints excluded: chain I residue 44 TYR Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 153 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 109 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 32 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 218 optimal weight: 3.9990 chunk 228 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 GLN G 804 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.127661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.102896 restraints weight = 15543.565| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.68 r_work: 0.3230 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.251 19264 Z= 0.509 Angle : 3.277 54.108 26209 Z= 1.864 Chirality : 0.587 6.453 2808 Planarity : 0.005 0.059 3417 Dihedral : 5.231 55.200 2635 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.54 % Allowed : 19.51 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.17), residues: 2359 helix: 0.50 (0.18), residues: 867 sheet: -1.06 (0.31), residues: 266 loop : -1.55 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 712 TYR 0.015 0.002 TYR E 165 PHE 0.016 0.001 PHE F 167 TRP 0.014 0.001 TRP D 382 HIS 0.006 0.001 HIS E 98 Details of bonding type rmsd covalent geometry : bond 0.01492 (19227) covalent geometry : angle 2.81849 (26113) hydrogen bonds : bond 0.03601 ( 649) hydrogen bonds : angle 4.91850 ( 1797) metal coordination : bond 0.03089 ( 37) metal coordination : angle 27.77550 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 212 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6703 (pp20) REVERT: D 48 ILE cc_start: 0.8335 (mm) cc_final: 0.7940 (pt) REVERT: D 58 ASP cc_start: 0.7821 (t0) cc_final: 0.7478 (t0) REVERT: D 272 GLU cc_start: 0.8173 (tm-30) cc_final: 0.7605 (tm-30) REVERT: D 273 TYR cc_start: 0.7723 (p90) cc_final: 0.7521 (p90) REVERT: D 383 MET cc_start: 0.8091 (mmt) cc_final: 0.7490 (mmm) REVERT: D 449 GLU cc_start: 0.8085 (pt0) cc_final: 0.7196 (mm-30) REVERT: D 468 GLU cc_start: 0.6994 (pt0) cc_final: 0.6719 (OUTLIER) REVERT: D 471 ARG cc_start: 0.6813 (mtp85) cc_final: 0.6566 (mtp-110) REVERT: D 575 SER cc_start: 0.8270 (m) cc_final: 0.7755 (t) REVERT: E 111 LYS cc_start: 0.8336 (OUTLIER) cc_final: 0.8030 (tttp) REVERT: E 119 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7915 (mt0) REVERT: F 31 SER cc_start: 0.8972 (t) cc_final: 0.8732 (p) REVERT: F 152 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7921 (tm-30) REVERT: F 158 LYS cc_start: 0.7976 (mmpt) cc_final: 0.7473 (mmpt) REVERT: F 168 GLU cc_start: 0.7961 (tt0) cc_final: 0.7732 (tt0) REVERT: F 241 LYS cc_start: 0.9303 (mmpt) cc_final: 0.8897 (mppt) REVERT: F 275 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7999 (mm-30) REVERT: F 286 LYS cc_start: 0.8209 (mtpp) cc_final: 0.7675 (mtmt) REVERT: F 312 GLU cc_start: 0.7854 (tt0) cc_final: 0.7459 (tt0) REVERT: F 386 GLN cc_start: 0.7218 (tt0) cc_final: 0.6886 (tt0) REVERT: F 420 GLU cc_start: 0.6891 (mm-30) cc_final: 0.6392 (mt-10) REVERT: F 424 LYS cc_start: 0.8785 (mtpt) cc_final: 0.8302 (mtpp) REVERT: G 57 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: G 185 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.6392 (pp20) REVERT: G 216 ASN cc_start: 0.8677 (p0) cc_final: 0.8444 (p0) REVERT: G 335 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7619 (pm20) REVERT: G 484 ASP cc_start: 0.7432 (m-30) cc_final: 0.6819 (m-30) REVERT: G 488 GLN cc_start: 0.7671 (tt0) cc_final: 0.7210 (mt0) REVERT: G 494 LYS cc_start: 0.8054 (mtmt) cc_final: 0.7228 (mmtm) REVERT: G 544 MET cc_start: 0.8127 (ttm) cc_final: 0.7720 (ttm) REVERT: G 589 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7284 (tp) REVERT: G 642 LYS cc_start: 0.8677 (pttp) cc_final: 0.8262 (ptpp) REVERT: G 787 GLU cc_start: 0.8033 (pm20) cc_final: 0.7753 (mp0) REVERT: G 849 LYS cc_start: 0.8584 (ttpt) cc_final: 0.8356 (ttmt) REVERT: G 881 GLN cc_start: 0.8115 (mt0) cc_final: 0.7515 (mt0) REVERT: G 888 MET cc_start: 0.7579 (tpp) cc_final: 0.7085 (mmm) REVERT: I 83 LYS cc_start: 0.8275 (tppt) cc_final: 0.7802 (mptt) REVERT: I 122 MET cc_start: 0.6455 (mmp) cc_final: 0.5136 (ttm) REVERT: I 153 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.6748 (mmm) REVERT: I 171 LYS cc_start: 0.8524 (mttt) cc_final: 0.7799 (mptt) outliers start: 50 outliers final: 27 residues processed: 246 average time/residue: 0.6710 time to fit residues: 183.8787 Evaluate side-chains 239 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 138 TRP Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain G residue 409 LYS Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 589 LEU Chi-restraints excluded: chain G residue 738 MET Chi-restraints excluded: chain G residue 833 SER Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 858 VAL Chi-restraints excluded: chain G residue 902 ASP Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 153 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 77 optimal weight: 0.9990 chunk 232 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 144 optimal weight: 0.0970 chunk 5 optimal weight: 0.9980 chunk 220 optimal weight: 0.8980 chunk 225 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN G 47 GLN G 308 GLN G 804 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.130309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.105604 restraints weight = 15615.109| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 1.69 r_work: 0.3270 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.252 19264 Z= 0.496 Angle : 3.274 52.622 26209 Z= 1.861 Chirality : 0.585 6.397 2808 Planarity : 0.005 0.062 3417 Dihedral : 4.978 54.203 2632 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 2.03 % Allowed : 20.12 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.96 (0.17), residues: 2359 helix: 0.63 (0.18), residues: 867 sheet: -1.12 (0.30), residues: 278 loop : -1.49 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 712 TYR 0.015 0.001 TYR I 44 PHE 0.012 0.001 PHE F 167 TRP 0.012 0.001 TRP D 382 HIS 0.006 0.001 HIS G 176 Details of bonding type rmsd covalent geometry : bond 0.01468 (19227) covalent geometry : angle 2.81163 (26113) hydrogen bonds : bond 0.03205 ( 649) hydrogen bonds : angle 4.82270 ( 1797) metal coordination : bond 0.02359 ( 37) metal coordination : angle 27.84593 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 106 MET cc_start: 0.6647 (mtp) cc_final: 0.6408 (mtp) REVERT: B 163 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6746 (pp20) REVERT: D 48 ILE cc_start: 0.8253 (mm) cc_final: 0.7884 (pt) REVERT: D 58 ASP cc_start: 0.7810 (t0) cc_final: 0.7481 (t0) REVERT: D 228 ARG cc_start: 0.7423 (ttt-90) cc_final: 0.7183 (ttt180) REVERT: D 272 GLU cc_start: 0.8138 (tm-30) cc_final: 0.7617 (tm-30) REVERT: D 383 MET cc_start: 0.8077 (mmt) cc_final: 0.7457 (mmm) REVERT: D 449 GLU cc_start: 0.8026 (pt0) cc_final: 0.7137 (mm-30) REVERT: D 468 GLU cc_start: 0.6944 (pt0) cc_final: 0.6705 (OUTLIER) REVERT: D 471 ARG cc_start: 0.6799 (mtp85) cc_final: 0.6566 (mtp-110) REVERT: D 575 SER cc_start: 0.8311 (m) cc_final: 0.7749 (t) REVERT: E 111 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7940 (tttp) REVERT: E 119 GLN cc_start: 0.8352 (OUTLIER) cc_final: 0.7936 (mt0) REVERT: F 31 SER cc_start: 0.8933 (t) cc_final: 0.8695 (p) REVERT: F 152 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7925 (tm-30) REVERT: F 158 LYS cc_start: 0.7966 (mmpt) cc_final: 0.7451 (mmpt) REVERT: F 168 GLU cc_start: 0.7939 (tt0) cc_final: 0.7722 (tt0) REVERT: F 241 LYS cc_start: 0.9303 (mmpt) cc_final: 0.8882 (mppt) REVERT: F 275 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8059 (mm-30) REVERT: F 286 LYS cc_start: 0.8217 (mtpp) cc_final: 0.7678 (mtmt) REVERT: F 312 GLU cc_start: 0.7826 (tt0) cc_final: 0.7432 (tt0) REVERT: F 386 GLN cc_start: 0.7157 (tt0) cc_final: 0.6826 (tt0) REVERT: F 420 GLU cc_start: 0.6879 (mm-30) cc_final: 0.6384 (mt-10) REVERT: F 424 LYS cc_start: 0.8779 (mtpt) cc_final: 0.8290 (mtpp) REVERT: G 57 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7409 (mp0) REVERT: G 185 GLU cc_start: 0.7432 (OUTLIER) cc_final: 0.6358 (pp20) REVERT: G 190 GLU cc_start: 0.8506 (mt-10) cc_final: 0.7858 (mp0) REVERT: G 335 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7611 (pm20) REVERT: G 484 ASP cc_start: 0.7399 (m-30) cc_final: 0.6784 (m-30) REVERT: G 488 GLN cc_start: 0.7605 (tt0) cc_final: 0.7153 (mt0) REVERT: G 494 LYS cc_start: 0.8130 (mtmt) cc_final: 0.7275 (mmtm) REVERT: G 531 MET cc_start: 0.8654 (mmt) cc_final: 0.8147 (mmt) REVERT: G 544 MET cc_start: 0.8051 (ttm) cc_final: 0.7731 (ttm) REVERT: G 642 LYS cc_start: 0.8647 (pttp) cc_final: 0.8231 (ptpp) REVERT: G 787 GLU cc_start: 0.8024 (pm20) cc_final: 0.7753 (mp0) REVERT: G 849 LYS cc_start: 0.8545 (ttpt) cc_final: 0.8325 (ttmt) REVERT: G 875 GLU cc_start: 0.7942 (mp0) cc_final: 0.7654 (mp0) REVERT: G 881 GLN cc_start: 0.8036 (mt0) cc_final: 0.7488 (mt0) REVERT: G 901 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7959 (tp30) REVERT: I 83 LYS cc_start: 0.8251 (tppt) cc_final: 0.7849 (mptt) REVERT: I 122 MET cc_start: 0.6258 (mmp) cc_final: 0.5031 (ttm) REVERT: I 171 LYS cc_start: 0.8518 (mttt) cc_final: 0.7788 (mptt) outliers start: 40 outliers final: 22 residues processed: 241 average time/residue: 0.6904 time to fit residues: 184.5465 Evaluate side-chains 231 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 204 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 135 MET Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 211 PHE Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain G residue 409 LYS Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 738 MET Chi-restraints excluded: chain G residue 833 SER Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 858 VAL Chi-restraints excluded: chain G residue 901 GLU Chi-restraints excluded: chain I residue 136 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 210 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 198 optimal weight: 0.0370 chunk 146 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 213 optimal weight: 0.0020 chunk 175 optimal weight: 2.9990 chunk 132 optimal weight: 0.0970 chunk 83 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 overall best weight: 0.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 47 GLN G 216 ASN G 769 GLN G 804 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.133055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.108396 restraints weight = 15721.789| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.71 r_work: 0.3308 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.250 19264 Z= 0.493 Angle : 3.272 51.386 26209 Z= 1.860 Chirality : 0.585 6.387 2808 Planarity : 0.004 0.056 3417 Dihedral : 4.730 52.957 2630 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.83 % Allowed : 20.43 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.17), residues: 2359 helix: 0.74 (0.19), residues: 869 sheet: -1.00 (0.30), residues: 278 loop : -1.40 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG G 712 TYR 0.014 0.001 TYR I 44 PHE 0.011 0.001 PHE F 167 TRP 0.017 0.001 TRP D 382 HIS 0.006 0.001 HIS G 176 Details of bonding type rmsd covalent geometry : bond 0.01464 (19227) covalent geometry : angle 2.80907 (26113) hydrogen bonds : bond 0.03006 ( 649) hydrogen bonds : angle 4.71655 ( 1797) metal coordination : bond 0.01949 ( 37) metal coordination : angle 27.85588 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4718 Ramachandran restraints generated. 2359 Oldfield, 0 Emsley, 2359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 221 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 MET cc_start: 0.6768 (mtp) cc_final: 0.6557 (mtp) REVERT: B 163 GLU cc_start: 0.7218 (OUTLIER) cc_final: 0.6727 (pp20) REVERT: D 48 ILE cc_start: 0.8319 (mm) cc_final: 0.8000 (pt) REVERT: D 58 ASP cc_start: 0.7832 (t0) cc_final: 0.7505 (t0) REVERT: D 228 ARG cc_start: 0.7435 (ttt-90) cc_final: 0.7234 (ttt180) REVERT: D 272 GLU cc_start: 0.8169 (tm-30) cc_final: 0.7472 (tm-30) REVERT: D 383 MET cc_start: 0.8045 (mmt) cc_final: 0.7329 (mmm) REVERT: D 401 LYS cc_start: 0.5682 (mtpp) cc_final: 0.5479 (mtpp) REVERT: D 449 GLU cc_start: 0.8016 (pt0) cc_final: 0.7135 (mm-30) REVERT: D 471 ARG cc_start: 0.6707 (mtp85) cc_final: 0.6475 (mtp-110) REVERT: D 575 SER cc_start: 0.8266 (m) cc_final: 0.7675 (t) REVERT: E 25 GLU cc_start: 0.7275 (tp30) cc_final: 0.7035 (tp30) REVERT: E 47 ARG cc_start: 0.7227 (mtt-85) cc_final: 0.7025 (mtp85) REVERT: E 111 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7835 (tttp) REVERT: E 119 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7832 (mt0) REVERT: E 148 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.7784 (p0) REVERT: E 164 ARG cc_start: 0.8248 (mtm-85) cc_final: 0.7978 (mtm180) REVERT: F 31 SER cc_start: 0.8957 (t) cc_final: 0.8734 (p) REVERT: F 48 ASP cc_start: 0.7482 (m-30) cc_final: 0.7121 (p0) REVERT: F 152 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7934 (tm-30) REVERT: F 158 LYS cc_start: 0.8293 (mmpt) cc_final: 0.7748 (mmpt) REVERT: F 168 GLU cc_start: 0.7999 (tt0) cc_final: 0.7798 (tt0) REVERT: F 241 LYS cc_start: 0.9278 (mmpt) cc_final: 0.8830 (mppt) REVERT: F 275 GLU cc_start: 0.8278 (mt-10) cc_final: 0.8072 (mm-30) REVERT: F 286 LYS cc_start: 0.8290 (mtpp) cc_final: 0.7757 (mtmt) REVERT: F 386 GLN cc_start: 0.7135 (tt0) cc_final: 0.6793 (tt0) REVERT: F 420 GLU cc_start: 0.6874 (mm-30) cc_final: 0.6380 (mt-10) REVERT: F 424 LYS cc_start: 0.8795 (mtpt) cc_final: 0.8319 (mtpp) REVERT: G 57 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7411 (mp0) REVERT: G 190 GLU cc_start: 0.8543 (mt-10) cc_final: 0.7919 (mp0) REVERT: G 221 MET cc_start: 0.8922 (tpp) cc_final: 0.8535 (mmm) REVERT: G 335 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7611 (pm20) REVERT: G 467 ASN cc_start: 0.7688 (m-40) cc_final: 0.7326 (t0) REVERT: G 484 ASP cc_start: 0.7429 (m-30) cc_final: 0.6813 (m-30) REVERT: G 488 GLN cc_start: 0.7609 (tt0) cc_final: 0.7171 (mt0) REVERT: G 494 LYS cc_start: 0.8136 (mtmt) cc_final: 0.7286 (mmtm) REVERT: G 531 MET cc_start: 0.8642 (mmt) cc_final: 0.8252 (mmt) REVERT: G 544 MET cc_start: 0.8090 (ttm) cc_final: 0.7795 (ttm) REVERT: G 642 LYS cc_start: 0.8656 (pttp) cc_final: 0.8215 (ptpp) REVERT: G 712 ARG cc_start: 0.7618 (ttp-110) cc_final: 0.7302 (ttt90) REVERT: G 725 ARG cc_start: 0.7624 (ptm160) cc_final: 0.6573 (ttt-90) REVERT: G 787 GLU cc_start: 0.8044 (pm20) cc_final: 0.7755 (mp0) REVERT: G 849 LYS cc_start: 0.8505 (ttpt) cc_final: 0.8292 (ttmt) REVERT: G 875 GLU cc_start: 0.7943 (mp0) cc_final: 0.7620 (mp0) REVERT: G 881 GLN cc_start: 0.7963 (mt0) cc_final: 0.7578 (mt0) REVERT: G 901 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.8109 (tp30) REVERT: I 83 LYS cc_start: 0.8251 (tppt) cc_final: 0.7861 (mptt) REVERT: I 122 MET cc_start: 0.6046 (mmp) cc_final: 0.5093 (ptm) REVERT: I 153 MET cc_start: 0.7446 (mmm) cc_final: 0.7085 (mmt) REVERT: I 171 LYS cc_start: 0.8514 (mttt) cc_final: 0.7779 (mptt) outliers start: 36 outliers final: 19 residues processed: 247 average time/residue: 0.6952 time to fit residues: 190.5782 Evaluate side-chains 230 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 205 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 468 GLU Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 119 GLN Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 148 ASP Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain G residue 57 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 409 LYS Chi-restraints excluded: chain G residue 414 GLN Chi-restraints excluded: chain G residue 535 SER Chi-restraints excluded: chain G residue 576 SER Chi-restraints excluded: chain G residue 833 SER Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 858 VAL Chi-restraints excluded: chain G residue 901 GLU Chi-restraints excluded: chain I residue 136 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 12 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 chunk 179 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 169 optimal weight: 0.9980 chunk 82 optimal weight: 0.0980 chunk 174 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 176 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN G 769 GLN G 804 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.132866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.108255 restraints weight = 15742.822| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.70 r_work: 0.3303 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.251 19264 Z= 0.494 Angle : 3.273 51.293 26209 Z= 1.861 Chirality : 0.585 6.392 2808 Planarity : 0.004 0.062 3417 Dihedral : 4.461 28.514 2625 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.58 % Allowed : 21.24 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.75 (0.18), residues: 2359 helix: 0.80 (0.19), residues: 869 sheet: -0.93 (0.31), residues: 278 loop : -1.37 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 712 TYR 0.013 0.001 TYR I 44 PHE 0.011 0.001 PHE F 167 TRP 0.024 0.001 TRP D 382 HIS 0.006 0.001 HIS G 176 Details of bonding type rmsd covalent geometry : bond 0.01468 (19227) covalent geometry : angle 2.81089 (26113) hydrogen bonds : bond 0.03193 ( 649) hydrogen bonds : angle 4.73763 ( 1797) metal coordination : bond 0.02038 ( 37) metal coordination : angle 27.83463 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6606.63 seconds wall clock time: 112 minutes 58.39 seconds (6778.39 seconds total)