Starting phenix.real_space_refine on Thu Jan 23 02:53:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7awt_11930/01_2025/7awt_11930.cif Found real_map, /net/cci-nas-00/data/ceres_data/7awt_11930/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7awt_11930/01_2025/7awt_11930.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7awt_11930/01_2025/7awt_11930.map" model { file = "/net/cci-nas-00/data/ceres_data/7awt_11930/01_2025/7awt_11930.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7awt_11930/01_2025/7awt_11930.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 10.09, per 1000 atoms: 0.53 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: 5.32 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 2.12 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: 6.49 Time building geometry restraints manager: 5.85 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: 25082 2.66 - 5.32: 857 5.32 - 7.98: 132 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 - 34.17: 11169 34.17 - 68.34: 272 68.34 - 102.50: 19 102.50 - 136.67: 0 136.67 - 170.84: 1 Dihedral angle restraints: 11461 sinusoidal: 4658 harmonic: 6803 Sorted by residual: dihedral pdb=" C10 FMN F 502 " pdb=" C1' FMN F 502 " pdb=" N10 FMN F 502 " pdb=" C2' FMN F 502 " ideal model delta sinusoidal sigma weight residual 257.59 86.75 170.84 1 2.00e+01 2.50e-03 4.77e+01 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 ... (remaining 11458 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: 3416 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 3413 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.140 Process input model: 46.590 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.070 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:11.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.690 ------------------------------------------------------------------------------- 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 : 0.012 0.176 19227 Z= 0.779 Angle : 1.119 13.297 26113 Z= 0.732 Chirality : 1.946 22.068 2808 Planarity : 0.007 0.081 3416 Dihedral : 14.797 170.840 7105 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.022 0.001 TRP F 15 HIS 0.014 0.001 HIS D 83 PHE 0.018 0.002 PHE G 130 TYR 0.023 0.002 TYR G 638 ARG 0.022 0.001 ARG G 394 *********************** 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 : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 MET cc_start: 0.6987 (ptp) cc_final: 0.6775 (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: E 164 ARG cc_start: 0.8194 (mtt180) cc_final: 0.7911 (mtm-85) 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 436 ASP cc_start: 0.7740 (p0) cc_final: 0.7471 (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: 0.8109 (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: 0.8172 (ppt90) REVERT: G 832 GLN cc_start: 0.8416 (mm-40) cc_final: 0.8189 (mp10) REVERT: G 835 MET cc_start: 0.7735 (ptp) cc_final: 0.7349 (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: 0.7351 (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: 0.5453 (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: 1.6896 time to fit residues: 671.2129 Evaluate side-chains 240 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 223 time to evaluate : 2.311 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.9990 chunk 177 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 111 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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** 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.131705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.108649 restraints weight = 15344.488| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.55 r_work: 0.3410 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.268 19227 Z= 0.973 Angle : 2.828 50.970 26113 Z= 1.866 Chirality : 0.582 6.528 2808 Planarity : 0.005 0.052 3416 Dihedral : 7.194 167.150 2662 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.90 % Allowed : 15.55 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.16), residues: 2359 helix: -0.69 (0.17), residues: 859 sheet: -1.84 (0.31), residues: 251 loop : -2.10 (0.16), residues: 1249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 15 HIS 0.007 0.001 HIS G 176 PHE 0.025 0.001 PHE I 101 TYR 0.019 0.002 TYR I 44 ARG 0.008 0.001 ARG B 201 *********************** 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: 57 poor density : 253 time to evaluate : 2.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 163 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6579 (pp20) REVERT: B 170 MET cc_start: 0.6377 (mmt) cc_final: 0.6055 (mpp) REVERT: D 48 ILE cc_start: 0.8577 (mm) cc_final: 0.8207 (pt) REVERT: D 58 ASP cc_start: 0.7794 (t0) cc_final: 0.7535 (t0) REVERT: D 85 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8552 (mp0) REVERT: D 123 PHE cc_start: 0.7760 (OUTLIER) cc_final: 0.7062 (m-80) REVERT: D 272 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7119 (tm-30) REVERT: D 391 GLU cc_start: 0.4008 (pt0) cc_final: 0.3307 (pp20) REVERT: D 449 GLU cc_start: 0.8175 (pt0) cc_final: 0.7269 (mm-30) REVERT: D 468 GLU cc_start: 0.7391 (pt0) cc_final: 0.6849 (tp30) REVERT: D 469 GLU cc_start: 0.7630 (tt0) cc_final: 0.7341 (mt-10) REVERT: D 471 ARG cc_start: 0.6949 (mtp85) cc_final: 0.6513 (mtm-85) REVERT: D 575 SER cc_start: 0.8119 (m) cc_final: 0.7685 (t) REVERT: E 13 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: E 31 ASP cc_start: 0.8611 (t0) cc_final: 0.8389 (t0) REVERT: F 31 SER cc_start: 0.9038 (t) cc_final: 0.8794 (p) REVERT: F 48 ASP cc_start: 0.7550 (m-30) cc_final: 0.7236 (m-30) REVERT: F 94 MET cc_start: 0.7277 (OUTLIER) cc_final: 0.6956 (mtt) REVERT: F 168 GLU cc_start: 0.8179 (tt0) cc_final: 0.7965 (tt0) REVERT: F 241 LYS cc_start: 0.9305 (mmpt) cc_final: 0.8928 (mppt) REVERT: F 243 LYS cc_start: 0.8337 (ptpp) cc_final: 0.7741 (ptmm) REVERT: F 258 ASN cc_start: 0.8440 (t0) cc_final: 0.7993 (t0) REVERT: F 286 LYS cc_start: 0.8178 (mtpp) cc_final: 0.7622 (mtmt) REVERT: F 312 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7412 (tt0) REVERT: F 386 GLN cc_start: 0.7386 (tt0) cc_final: 0.7086 (tt0) REVERT: F 424 LYS cc_start: 0.8829 (mtpt) cc_final: 0.8423 (mtmm) REVERT: G 57 GLU cc_start: 0.7844 (pm20) cc_final: 0.7557 (mp0) REVERT: G 62 ARG cc_start: 0.7725 (ptt-90) cc_final: 0.7403 (ptt-90) REVERT: G 80 ASP cc_start: 0.8473 (m-30) cc_final: 0.8206 (m-30) REVERT: G 108 GLU cc_start: 0.7530 (pt0) cc_final: 0.7320 (pt0) REVERT: G 185 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.6534 (pp20) REVERT: G 190 GLU cc_start: 0.8597 (mt-10) cc_final: 0.7964 (mp0) REVERT: G 276 LYS cc_start: 0.9021 (mmtm) cc_final: 0.8776 (mmpt) REVERT: G 277 ASP cc_start: 0.8394 (p0) cc_final: 0.8186 (p0) REVERT: G 335 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7518 (mp0) REVERT: G 484 ASP cc_start: 0.7654 (m-30) cc_final: 0.7100 (m-30) REVERT: G 488 GLN cc_start: 0.7553 (tt0) cc_final: 0.7105 (mt0) REVERT: G 494 LYS cc_start: 0.8073 (mtmt) cc_final: 0.7288 (mmtm) REVERT: G 544 MET cc_start: 0.8191 (ttm) cc_final: 0.7814 (ttm) REVERT: G 591 MET cc_start: 0.8201 (mtp) cc_final: 0.7974 (ttm) REVERT: G 642 LYS cc_start: 0.8823 (pttp) cc_final: 0.8469 (ptpp) REVERT: G 715 MET cc_start: 0.8956 (ptt) cc_final: 0.8591 (ptm) REVERT: G 771 GLU cc_start: 0.7882 (pt0) cc_final: 0.7582 (pt0) REVERT: G 787 GLU cc_start: 0.8087 (pm20) cc_final: 0.7691 (mp0) REVERT: G 849 LYS cc_start: 0.8781 (ttpt) cc_final: 0.8464 (ttpp) REVERT: G 881 GLN cc_start: 0.7946 (mt0) cc_final: 0.7585 (mt0) REVERT: G 888 MET cc_start: 0.7705 (tpp) cc_final: 0.7178 (mmm) REVERT: I 83 LYS cc_start: 0.8122 (tppt) cc_final: 0.7703 (mptt) REVERT: I 122 MET cc_start: 0.6367 (mmp) cc_final: 0.5184 (ptm) REVERT: I 153 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7222 (mmm) REVERT: I 165 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7516 (mt-10) REVERT: I 171 LYS cc_start: 0.8548 (mttt) cc_final: 0.7949 (mptt) outliers start: 57 outliers final: 21 residues processed: 289 average time/residue: 1.6757 time to fit residues: 535.6868 Evaluate side-chains 249 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 218 time to evaluate : 2.303 ------------------------------------------------------------------------------- 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 364 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 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 312 GLU Chi-restraints excluded: chain G residue 185 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 66 optimal weight: 6.9990 chunk 136 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 233 optimal weight: 0.0980 chunk 180 optimal weight: 2.9990 chunk 159 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 226 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 123 HIS ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 653 HIS G 769 GLN G 804 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.135823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.110607 restraints weight = 16441.924| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.60 r_work: 0.3428 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.249 19227 Z= 0.926 Angle : 2.813 50.622 26113 Z= 1.859 Chirality : 0.586 6.406 2808 Planarity : 0.005 0.054 3416 Dihedral : 6.678 168.185 2640 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 2.90 % Allowed : 16.26 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.17), residues: 2359 helix: -0.15 (0.18), residues: 869 sheet: -1.45 (0.31), residues: 260 loop : -1.85 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 15 HIS 0.007 0.001 HIS G 176 PHE 0.015 0.001 PHE D 352 TYR 0.014 0.001 TYR I 44 ARG 0.007 0.000 ARG G 712 *********************** 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 296 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 239 time to evaluate : 2.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 75 VAL cc_start: 0.3271 (OUTLIER) cc_final: 0.2984 (t) REVERT: B 163 GLU cc_start: 0.7245 (OUTLIER) cc_final: 0.6628 (pp20) REVERT: B 166 MET cc_start: 0.7167 (tpp) cc_final: 0.6941 (tpt) REVERT: D 48 ILE cc_start: 0.8613 (mm) cc_final: 0.8257 (pt) REVERT: D 58 ASP cc_start: 0.7957 (t0) cc_final: 0.7641 (t0) REVERT: D 123 PHE cc_start: 0.7812 (OUTLIER) cc_final: 0.7248 (m-80) REVERT: D 272 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7298 (tm-30) REVERT: D 273 TYR cc_start: 0.7734 (p90) cc_final: 0.7408 (p90) REVERT: D 391 GLU cc_start: 0.3999 (pt0) cc_final: 0.2689 (pp20) REVERT: D 449 GLU cc_start: 0.8179 (pt0) cc_final: 0.7310 (mm-30) REVERT: D 468 GLU cc_start: 0.7320 (pt0) cc_final: 0.6757 (tp30) REVERT: D 469 GLU cc_start: 0.7611 (tt0) cc_final: 0.7388 (mt-10) REVERT: D 471 ARG cc_start: 0.7022 (mtp85) cc_final: 0.6321 (mmt90) REVERT: D 575 SER cc_start: 0.8100 (m) cc_final: 0.7663 (t) REVERT: E 31 ASP cc_start: 0.8677 (t0) cc_final: 0.8458 (t0) REVERT: E 111 LYS cc_start: 0.8568 (tmmm) cc_final: 0.8259 (ttpp) REVERT: E 156 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7246 (mp0) REVERT: E 163 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: F 31 SER cc_start: 0.9008 (t) cc_final: 0.8781 (p) REVERT: F 48 ASP cc_start: 0.7523 (m-30) cc_final: 0.7249 (m-30) REVERT: F 152 GLU cc_start: 0.8305 (tm-30) cc_final: 0.8105 (tm-30) REVERT: F 158 LYS cc_start: 0.8051 (mmpt) cc_final: 0.7646 (mmpt) REVERT: F 183 GLU cc_start: 0.8915 (tt0) cc_final: 0.8641 (tt0) REVERT: F 241 LYS cc_start: 0.9226 (mmpt) cc_final: 0.8908 (mmtm) REVERT: F 243 LYS cc_start: 0.8356 (ptpp) cc_final: 0.7709 (ptmm) REVERT: F 258 ASN cc_start: 0.8472 (t0) cc_final: 0.7724 (t0) REVERT: F 286 LYS cc_start: 0.8272 (mtpp) cc_final: 0.7726 (mtmt) REVERT: F 312 GLU cc_start: 0.7975 (tt0) cc_final: 0.7486 (tt0) REVERT: F 386 GLN cc_start: 0.7371 (tt0) cc_final: 0.7082 (tt0) REVERT: F 424 LYS cc_start: 0.8876 (mtpt) cc_final: 0.8433 (mtmm) REVERT: G 57 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7487 (mp0) REVERT: G 62 ARG cc_start: 0.7875 (ptt-90) cc_final: 0.7617 (ptt-90) REVERT: G 80 ASP cc_start: 0.8469 (m-30) cc_final: 0.8200 (m-30) REVERT: G 108 GLU cc_start: 0.7517 (pt0) cc_final: 0.7300 (pt0) REVERT: G 185 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.6659 (pp20) REVERT: G 190 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8041 (mp0) REVERT: G 209 LYS cc_start: 0.7746 (mttt) cc_final: 0.7215 (mttp) REVERT: G 276 LYS cc_start: 0.9041 (mmtm) cc_final: 0.8819 (mmpt) REVERT: G 335 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7598 (mp0) REVERT: G 484 ASP cc_start: 0.7575 (m-30) cc_final: 0.6947 (m-30) REVERT: G 488 GLN cc_start: 0.7674 (tt0) cc_final: 0.7218 (mt0) REVERT: G 494 LYS cc_start: 0.8122 (mtmt) cc_final: 0.7368 (mmtm) REVERT: G 531 MET cc_start: 0.8830 (mmt) cc_final: 0.8286 (mmt) REVERT: G 544 MET cc_start: 0.8381 (ttm) cc_final: 0.7858 (ttm) REVERT: G 642 LYS cc_start: 0.8912 (pttp) cc_final: 0.8505 (ptpp) REVERT: G 715 MET cc_start: 0.8930 (ptt) cc_final: 0.8617 (ptm) REVERT: G 725 ARG cc_start: 0.7518 (OUTLIER) cc_final: 0.7062 (ptm160) REVERT: G 787 GLU cc_start: 0.7991 (pm20) cc_final: 0.7665 (mp0) REVERT: G 849 LYS cc_start: 0.8743 (ttpt) cc_final: 0.8439 (ttmt) REVERT: G 881 GLN cc_start: 0.7928 (mt0) cc_final: 0.7537 (mt0) REVERT: G 888 MET cc_start: 0.7801 (tpp) cc_final: 0.7249 (mmm) REVERT: I 83 LYS cc_start: 0.8135 (tppt) cc_final: 0.7740 (mptt) REVERT: I 122 MET cc_start: 0.6240 (mmp) cc_final: 0.5066 (ptm) REVERT: I 165 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7586 (mt-10) REVERT: I 171 LYS cc_start: 0.8554 (mttt) cc_final: 0.7935 (mptt) outliers start: 57 outliers final: 15 residues processed: 280 average time/residue: 1.6071 time to fit residues: 497.9545 Evaluate side-chains 242 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 217 time to evaluate : 2.019 ------------------------------------------------------------------------------- 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 101 THR Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain D residue 35 THR 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 269 ASP 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 156 GLU Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 252 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 185 GLU Chi-restraints excluded: chain G residue 589 LEU Chi-restraints excluded: chain G residue 725 ARG Chi-restraints excluded: chain G residue 738 MET Chi-restraints excluded: chain G residue 852 VAL Chi-restraints excluded: chain G residue 867 VAL Chi-restraints excluded: chain I residue 165 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 90 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 173 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 206 optimal weight: 0.4980 chunk 68 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 804 GLN G 908 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.133246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.107770 restraints weight = 16512.421| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.60 r_work: 0.3397 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.252 19227 Z= 0.937 Angle : 2.818 50.616 26113 Z= 1.861 Chirality : 0.588 6.452 2808 Planarity : 0.005 0.056 3416 Dihedral : 6.514 167.633 2636 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.25 % Allowed : 16.77 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.17), residues: 2359 helix: 0.02 (0.18), residues: 872 sheet: -1.36 (0.31), residues: 254 loop : -1.77 (0.17), residues: 1233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 651 HIS 0.007 0.001 HIS G 176 PHE 0.017 0.001 PHE F 167 TYR 0.014 0.002 TYR I 44 ARG 0.008 0.000 ARG G 712 *********************** 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 284 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 220 time to evaluate : 2.047 Fit side-chains revert: symmetry clash REVERT: B 163 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6675 (pp20) REVERT: D 48 ILE cc_start: 0.8518 (mm) cc_final: 0.8176 (pt) REVERT: D 58 ASP cc_start: 0.8006 (t0) cc_final: 0.7704 (t0) REVERT: D 123 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7298 (m-80) REVERT: D 191 GLU cc_start: -0.0818 (OUTLIER) cc_final: -0.1128 (tp30) REVERT: D 272 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7497 (tm-30) REVERT: D 273 TYR cc_start: 0.7904 (p90) cc_final: 0.7619 (p90) REVERT: D 391 GLU cc_start: 0.4039 (pt0) cc_final: 0.2952 (pp20) REVERT: D 449 GLU cc_start: 0.8172 (pt0) cc_final: 0.7342 (mm-30) REVERT: D 468 GLU cc_start: 0.7360 (pt0) cc_final: 0.6853 (tp30) REVERT: D 471 ARG cc_start: 0.7077 (mtp85) cc_final: 0.6490 (mpt-90) REVERT: D 575 SER cc_start: 0.8236 (m) cc_final: 0.7773 (t) REVERT: E 13 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7329 (tm-30) REVERT: E 111 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8277 (tttp) REVERT: E 156 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: E 163 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: F 31 SER cc_start: 0.8910 (t) cc_final: 0.8655 (p) REVERT: F 152 GLU cc_start: 0.8311 (tm-30) cc_final: 0.8025 (tm-30) REVERT: F 158 LYS cc_start: 0.8056 (mmpt) cc_final: 0.7577 (mmpt) REVERT: F 182 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8095 (tp30) REVERT: F 241 LYS cc_start: 0.9289 (mmpt) cc_final: 0.8958 (mmtm) REVERT: F 243 LYS cc_start: 0.8478 (ptpp) cc_final: 0.7799 (ptmm) REVERT: F 286 LYS cc_start: 0.8303 (mtpp) cc_final: 0.7773 (mtmt) REVERT: F 312 GLU cc_start: 0.7981 (tt0) cc_final: 0.7480 (tt0) REVERT: F 386 GLN cc_start: 0.7412 (tt0) cc_final: 0.7081 (tt0) REVERT: F 424 LYS cc_start: 0.8893 (mtpt) cc_final: 0.8406 (mtpp) REVERT: G 57 GLU cc_start: 0.7846 (pm20) cc_final: 0.7521 (mp0) REVERT: G 80 ASP cc_start: 0.8446 (m-30) cc_final: 0.8216 (m-30) REVERT: G 185 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.6647 (pp20) REVERT: G 221 MET cc_start: 0.9028 (tpp) cc_final: 0.8726 (mmm) REVERT: G 276 LYS cc_start: 0.9036 (mmtm) cc_final: 0.8806 (mmpt) REVERT: G 305 ILE cc_start: 0.8428 (tp) cc_final: 0.8103 (tp) REVERT: G 335 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7641 (mp0) REVERT: G 484 ASP cc_start: 0.7591 (m-30) cc_final: 0.6971 (m-30) REVERT: G 488 GLN cc_start: 0.7813 (tt0) cc_final: 0.7391 (mt0) REVERT: G 494 LYS cc_start: 0.8201 (mtmt) cc_final: 0.7474 (mmtm) REVERT: G 544 MET cc_start: 0.8395 (ttm) cc_final: 0.7981 (ttm) REVERT: G 589 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7856 (mt) REVERT: G 642 LYS cc_start: 0.8871 (pttp) cc_final: 0.8480 (ptpp) REVERT: G 715 MET cc_start: 0.8920 (ptt) cc_final: 0.8585 (ptm) REVERT: G 787 GLU cc_start: 0.8032 (pm20) cc_final: 0.7741 (mp0) REVERT: G 849 LYS cc_start: 0.8736 (ttpt) cc_final: 0.8441 (ttmt) REVERT: G 881 GLN cc_start: 0.8137 (mt0) cc_final: 0.7704 (mt0) REVERT: G 888 MET cc_start: 0.7860 (tpp) cc_final: 0.7338 (mmm) REVERT: I 83 LYS cc_start: 0.8208 (tppt) cc_final: 0.7823 (mptt) REVERT: I 122 MET cc_start: 0.6553 (mmp) cc_final: 0.5026 (ttm) REVERT: I 153 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7068 (mmm) REVERT: I 171 LYS cc_start: 0.8540 (mttt) cc_final: 0.7936 (mptt) outliers start: 64 outliers final: 26 residues processed: 264 average time/residue: 1.5696 time to fit residues: 461.9072 Evaluate side-chains 248 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 116 ASN Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 138 TRP 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 280 GLU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 332 VAL 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 13 GLU Chi-restraints excluded: chain E residue 111 LYS Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 252 PHE 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 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 44 TYR Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 153 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 234 random chunks: chunk 152 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 197 optimal weight: 0.9990 chunk 212 optimal weight: 0.7980 chunk 182 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 chunk 3 optimal weight: 10.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.128625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.103876 restraints weight = 15667.345| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.69 r_work: 0.3245 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.249 19227 Z= 0.928 Angle : 2.813 50.653 26113 Z= 1.860 Chirality : 0.586 6.434 2808 Planarity : 0.005 0.055 3416 Dihedral : 6.416 168.405 2635 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 3.46 % Allowed : 17.53 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.17), residues: 2359 helix: 0.18 (0.18), residues: 873 sheet: -1.28 (0.31), residues: 260 loop : -1.70 (0.17), residues: 1226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 651 HIS 0.007 0.001 HIS G 176 PHE 0.014 0.001 PHE F 167 TYR 0.013 0.001 TYR I 44 ARG 0.010 0.000 ARG G 712 *********************** 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 287 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 219 time to evaluate : 2.209 Fit side-chains revert: symmetry clash REVERT: B 163 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6627 (pp20) REVERT: D 48 ILE cc_start: 0.8376 (mm) cc_final: 0.7991 (pt) REVERT: D 58 ASP cc_start: 0.7848 (t70) cc_final: 0.7546 (t0) REVERT: D 123 PHE cc_start: 0.7650 (OUTLIER) cc_final: 0.7043 (m-80) REVERT: D 272 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7414 (tm-30) REVERT: D 273 TYR cc_start: 0.7722 (p90) cc_final: 0.7479 (p90) REVERT: D 449 GLU cc_start: 0.8110 (pt0) cc_final: 0.7210 (mm-30) REVERT: D 468 GLU cc_start: 0.7170 (pt0) cc_final: 0.6671 (OUTLIER) REVERT: D 575 SER cc_start: 0.8196 (m) cc_final: 0.7687 (t) REVERT: E 111 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8138 (tttp) REVERT: E 119 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7867 (mt0) REVERT: E 156 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7307 (mp0) REVERT: E 163 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: F 31 SER cc_start: 0.8978 (t) cc_final: 0.8732 (p) REVERT: F 152 GLU cc_start: 0.8200 (tm-30) cc_final: 0.7900 (tm-30) REVERT: F 158 LYS cc_start: 0.8016 (mmpt) cc_final: 0.7601 (mmpt) REVERT: F 182 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7897 (tp30) REVERT: F 241 LYS cc_start: 0.9296 (mmpt) cc_final: 0.8883 (mppt) REVERT: F 243 LYS cc_start: 0.8450 (ptpp) cc_final: 0.7760 (ptmm) REVERT: F 286 LYS cc_start: 0.8087 (mtpp) cc_final: 0.7552 (mtmt) REVERT: F 312 GLU cc_start: 0.7820 (tt0) cc_final: 0.7299 (tt0) REVERT: F 386 GLN cc_start: 0.7163 (tt0) cc_final: 0.6816 (tt0) REVERT: F 424 LYS cc_start: 0.8801 (mtpt) cc_final: 0.8304 (mtpp) REVERT: G 57 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7470 (mp0) REVERT: G 62 ARG cc_start: 0.7665 (ptt-90) cc_final: 0.7446 (ptt-90) REVERT: G 80 ASP cc_start: 0.8372 (m-30) cc_final: 0.8154 (m-30) REVERT: G 185 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6426 (pp20) REVERT: G 216 ASN cc_start: 0.8678 (p0) cc_final: 0.8434 (p0) REVERT: G 221 MET cc_start: 0.8900 (tpp) cc_final: 0.8396 (mmm) REVERT: G 276 LYS cc_start: 0.8989 (mmtm) cc_final: 0.8769 (mmpt) REVERT: G 305 ILE cc_start: 0.8318 (tp) cc_final: 0.8064 (tp) REVERT: G 335 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7500 (pm20) REVERT: G 484 ASP cc_start: 0.7457 (m-30) cc_final: 0.6822 (m-30) REVERT: G 488 GLN cc_start: 0.7669 (tt0) cc_final: 0.7223 (mt0) REVERT: G 494 LYS cc_start: 0.8114 (mtmt) cc_final: 0.7330 (mmtm) REVERT: G 531 MET cc_start: 0.8744 (mmt) cc_final: 0.8104 (mmt) REVERT: G 544 MET cc_start: 0.8156 (ttm) cc_final: 0.7758 (ttm) REVERT: G 589 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7636 (tp) REVERT: G 642 LYS cc_start: 0.8738 (pttp) cc_final: 0.8315 (ptpp) REVERT: G 715 MET cc_start: 0.8832 (ptt) cc_final: 0.8472 (ptm) REVERT: G 787 GLU cc_start: 0.7989 (pm20) cc_final: 0.7723 (mp0) REVERT: G 849 LYS cc_start: 0.8649 (ttpt) cc_final: 0.8376 (ttmt) REVERT: G 881 GLN cc_start: 0.7999 (mt0) cc_final: 0.7516 (mt0) REVERT: G 888 MET cc_start: 0.7710 (tpp) cc_final: 0.7111 (mmm) REVERT: I 83 LYS cc_start: 0.8167 (tppt) cc_final: 0.7725 (mptt) REVERT: I 122 MET cc_start: 0.6514 (mmp) cc_final: 0.5046 (ttm) REVERT: I 153 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.6765 (mmm) REVERT: I 165 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7566 (mt-10) REVERT: I 171 LYS cc_start: 0.8523 (mttt) cc_final: 0.7834 (mptt) outliers start: 68 outliers final: 27 residues processed: 267 average time/residue: 1.5574 time to fit residues: 462.5258 Evaluate side-chains 247 residues out of total 1968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 2.297 ------------------------------------------------------------------------------- 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 B residue 176 ILE Chi-restraints excluded: chain D residue 35 THR 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 280 GLU Chi-restraints excluded: chain D residue 326 VAL Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 557 VAL 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 134 LEU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 161 LEU Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 285 LEU Chi-restraints excluded: chain F residue 307 LEU Chi-restraints excluded: chain F residue 327 MET 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 44 TYR Chi-restraints excluded: chain I residue 53 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.1515 > 50: distance: 58 - 62: 4.054 distance: 62 - 63: 5.044 distance: 63 - 64: 6.257 distance: 63 - 66: 3.394 distance: 64 - 65: 6.812 distance: 64 - 68: 8.178 distance: 66 - 67: 6.421 distance: 68 - 69: 8.157 distance: 69 - 70: 9.240 distance: 69 - 72: 3.831 distance: 70 - 71: 12.684 distance: 70 - 77: 15.180 distance: 72 - 73: 4.443 distance: 73 - 74: 17.699 distance: 74 - 75: 13.397 distance: 74 - 76: 11.838 distance: 77 - 78: 4.463 distance: 79 - 80: 5.958 distance: 79 - 88: 5.794 distance: 81 - 82: 5.605 distance: 82 - 83: 11.095 distance: 82 - 84: 10.601 distance: 83 - 85: 16.981 distance: 84 - 86: 12.266 distance: 85 - 87: 4.019 distance: 86 - 87: 6.699 distance: 89 - 92: 12.942 distance: 90 - 91: 7.203 distance: 90 - 94: 4.591 distance: 92 - 93: 11.669 distance: 94 - 95: 4.013 distance: 95 - 96: 4.456 distance: 96 - 97: 16.820 distance: 96 - 98: 23.953 distance: 98 - 99: 6.313 distance: 99 - 100: 8.538 distance: 99 - 102: 11.171 distance: 100 - 101: 18.923 distance: 100 - 106: 11.160 distance: 101 - 130: 16.672 distance: 102 - 103: 9.904 distance: 103 - 104: 13.329 distance: 103 - 105: 10.185 distance: 106 - 107: 8.976 distance: 107 - 108: 11.056 distance: 107 - 110: 8.185 distance: 108 - 109: 23.997 distance: 108 - 114: 12.928 distance: 109 - 138: 7.299 distance: 110 - 111: 13.817 distance: 111 - 113: 26.333 distance: 115 - 116: 10.709 distance: 115 - 118: 26.518 distance: 116 - 117: 17.122 distance: 116 - 121: 15.461 distance: 118 - 119: 3.721 distance: 118 - 120: 14.312 distance: 121 - 122: 4.857 distance: 122 - 123: 13.080 distance: 122 - 125: 5.475 distance: 123 - 124: 8.386 distance: 123 - 130: 18.733 distance: 125 - 126: 21.869 distance: 126 - 127: 28.835 distance: 127 - 128: 9.266 distance: 127 - 129: 38.642 distance: 130 - 131: 12.164 distance: 131 - 132: 7.650 distance: 131 - 134: 7.901 distance: 132 - 133: 12.489 distance: 132 - 138: 5.138 distance: 134 - 135: 12.439 distance: 134 - 136: 13.759 distance: 135 - 137: 9.666