Starting phenix.real_space_refine on Mon Jul 6 19:14:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9q8i_52895/07_2026/9q8i_52895.cif Found real_map, /net/cci-nas-00/data/ceres_data/9q8i_52895/07_2026/9q8i_52895.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9q8i_52895/07_2026/9q8i_52895.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9q8i_52895/07_2026/9q8i_52895.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9q8i_52895/07_2026/9q8i_52895.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9q8i_52895/07_2026/9q8i_52895.map" } resolution = 2.35 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= 0.011 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 32 7.16 5 P 11 5.49 5 S 268 5.16 5 Cl 2 4.86 5 C 24376 2.51 5 N 6223 2.21 5 O 6735 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 37648 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 840 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 1, 'TRANS': 104} Chain breaks: 1 Chain: "B" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1601 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 186} Chain breaks: 2 Chain: "C" Number of atoms: 4746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4746 Classifications: {'peptide': 587} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 550} Chain breaks: 1 Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Chain: "F" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3429 Classifications: {'peptide': 442} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 416} Chain: "G" Number of atoms: 7044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 907, 7044 Classifications: {'peptide': 907} Link IDs: {'PTRANS': 41, 'TRANS': 865} Chain: "H" Number of atoms: 2517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2517 Classifications: {'peptide': 320} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 305} Chain breaks: 1 Chain: "I" Number of atoms: 1186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1186 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 135} Chain: "J" Number of atoms: 1331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1331 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "K" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 761 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "L" Number of atoms: 4685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 4685 Classifications: {'peptide': 613} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 594} Chain: "M" Number of atoms: 3960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3960 Classifications: {'peptide': 505} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 483} Chain: "N" Number of atoms: 3673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3673 Classifications: {'peptide': 485} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 463} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 28 Ad-hoc single atom residues: {' CA': 1, ' CL': 1} Unusual residues: {'FES': 1, 'SF4': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain breaks: 2 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: "J" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "L" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 189 Unusual residues: {'3PE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "M" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 76 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 26 Chain: "N" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Ad-hoc single atom residues: {' CL': 1} Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "C" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1718 SG CYS B 129 54.974 88.319 100.275 1.00 39.70 S ATOM 1304 SG CYS B 64 55.642 94.523 101.864 1.00 42.88 S ATOM 1298 SG CYS B 63 60.540 91.482 102.565 1.00 44.59 S ATOM 1935 SG CYS B 158 58.037 91.680 96.526 1.00 39.50 S ATOM 7834 SG CYS E 92 84.709 79.095 30.731 1.00 62.42 S ATOM 7868 SG CYS E 97 87.079 80.432 29.192 1.00 66.64 S ATOM 8146 SG CYS E 133 86.566 74.416 31.603 1.00 70.42 S ATOM 8172 SG CYS E 137 89.857 75.601 30.069 1.00 68.68 S ATOM 11150 SG CYS F 354 78.641 67.527 52.449 1.00 39.64 S ATOM 11170 SG CYS F 357 79.840 71.301 48.911 1.00 42.47 S ATOM 11491 SG CYS F 398 81.285 65.132 46.959 1.00 42.48 S ATOM 11126 SG CYS F 351 75.485 67.173 46.610 1.00 40.16 S ATOM 12693 SG CYS G 112 63.690 74.245 66.315 1.00 34.62 S ATOM 12633 SG CYS G 103 64.018 81.011 67.371 1.00 37.31 S ATOM 12653 SG CYS G 106 59.233 77.910 64.513 1.00 33.34 S ATOM 13047 SG CYS G 154 66.419 67.438 58.321 1.00 41.48 S ATOM 13028 SG CYS G 151 65.110 72.694 54.920 1.00 35.87 S ATOM 13076 SG CYS G 157 61.580 67.282 54.255 1.00 34.22 S ATOM 13424 SG CYS G 201 61.188 70.340 59.612 1.00 34.33 S ATOM 13649 SG CYS G 228 43.380 57.435 67.436 1.00 37.50 S ATOM 13934 SG CYS G 263 45.563 57.272 61.110 1.00 42.22 S ATOM 13697 SG CYS G 235 47.941 53.935 66.367 1.00 37.65 S ATOM 13673 SG CYS G 231 42.315 52.611 63.320 1.00 43.13 S ATOM 12196 SG CYS G 48 76.769 61.892 62.945 1.00 39.72 S ATOM 12345 SG CYS G 67 75.412 59.887 60.813 1.00 45.78 S ATOM 12094 SG CYS G 34 72.291 62.953 58.847 1.00 36.47 S ATOM 12170 SG CYS G 45 73.220 66.161 60.389 1.00 39.13 S ATOM 21972 SG CYS I 102 60.173 89.722 88.309 1.00 45.18 S ATOM 21947 SG CYS I 99 54.241 92.523 88.670 1.00 44.59 S ATOM 21990 SG CYS I 105 57.627 91.205 83.274 1.00 43.13 S ATOM 21705 SG CYS I 70 55.425 86.293 86.319 1.00 40.38 S ATOM 22019 SG CYS I 109 58.509 91.429 74.641 1.00 37.33 S ATOM 21682 SG CYS I 66 55.089 87.689 78.380 1.00 38.95 S ATOM 21642 SG CYS I 60 52.300 90.371 73.068 1.00 36.67 S ATOM 21660 SG CYS I 63 57.158 85.896 72.768 1.00 38.58 S Time building chain proxies: 6.77, per 1000 atoms: 0.18 Number of scatterers: 37648 At special positions: 0 Unit cell: (122.408, 157.872, 281.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 32 26.01 Ca 1 19.99 Cl 2 17.00 S 268 16.00 P 11 15.00 O 6735 8.00 N 6223 7.00 C 24376 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: 3.25 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb=" FES G1004 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 48 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 67 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 34 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 45 " 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="FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb=" SF4 G1001 " pdb="FE3 SF4 G1001 " - pdb=" NE2 HIS G 99 " pdb="FE1 SF4 G1001 " - pdb=" SG CYS G 112 " pdb="FE2 SF4 G1001 " - pdb=" SG CYS G 103 " pdb="FE4 SF4 G1001 " - pdb=" SG CYS G 106 " pdb=" SF4 G1002 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 151 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 154 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 201 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 157 " pdb=" SF4 G1003 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 231 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 235 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 228 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 263 " pdb=" SF4 I 201 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 74 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " Number of angles added : 96 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8674 Finding SS restraints... Secondary structure from input PDB file: 224 helices and 26 sheets defined 62.5% alpha, 7.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.18 Creating SS restraints... Processing helix chain 'A' and resid 6 through 37 removed outlier: 3.514A pdb=" N ILE A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 90 removed outlier: 4.057A pdb=" N TYR A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 120 removed outlier: 6.072A pdb=" N TRP A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N VAL A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 52 Processing helix chain 'B' and resid 63 through 73 removed outlier: 3.713A pdb=" N GLU B 67 " --> pdb=" O CYS B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 106 through 115 Processing helix chain 'B' and resid 127 through 133 Processing helix chain 'B' and resid 144 through 148 Processing helix chain 'B' and resid 161 through 177 removed outlier: 3.670A pdb=" N TYR B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N MET B 166 " --> pdb=" O PRO B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 204 Processing helix chain 'B' and resid 204 through 211 Processing helix chain 'C' and resid 19 through 30 removed outlier: 3.973A pdb=" N GLY C 23 " --> pdb=" O ASP C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 62 Processing helix chain 'C' and resid 129 through 142 removed outlier: 4.088A pdb=" N TYR C 133 " --> pdb=" O ASN C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 190 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 251 through 256 Processing helix chain 'C' and resid 264 through 269 removed outlier: 3.697A pdb=" N ASP C 269 " --> pdb=" O ILE C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 279 Processing helix chain 'C' and resid 280 through 292 Processing helix chain 'C' and resid 296 through 327 Processing helix chain 'C' and resid 334 through 351 removed outlier: 4.067A pdb=" N ASP C 338 " --> pdb=" O PHE C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 380 Processing helix chain 'C' and resid 382 through 397 Processing helix chain 'C' and resid 397 through 405 Processing helix chain 'C' and resid 411 through 418 Processing helix chain 'C' and resid 422 through 428 Processing helix chain 'C' and resid 433 through 438 Processing helix chain 'C' and resid 442 through 446 Processing helix chain 'C' and resid 458 through 483 Processing helix chain 'C' and resid 500 through 507 Processing helix chain 'C' and resid 507 through 519 Processing helix chain 'C' and resid 559 through 565 removed outlier: 4.140A pdb=" N ALA C 563 " --> pdb=" O THR C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 573 Processing helix chain 'C' and resid 576 through 587 Processing helix chain 'C' and resid 590 through 596 Processing helix chain 'E' and resid 15 through 27 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: 3.730A pdb=" N ILE E 55 " --> pdb=" O PRO E 51 " (cutoff:3.500A) removed outlier: 4.236A 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 114 removed outlier: 3.750A pdb=" N ILE E 105 " --> pdb=" O GLY E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 136 through 140 Processing helix chain 'E' and resid 154 through 156 No H-bonds generated for 'chain 'E' and resid 154 through 156' Processing helix chain 'E' and resid 157 through 164 removed outlier: 3.519A pdb=" N ARG E 164 " --> pdb=" O GLU E 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 32 Processing helix chain 'F' and resid 35 through 43 Processing helix chain 'F' and resid 46 through 58 Processing helix chain 'F' and resid 68 through 75 Processing helix chain 'F' and resid 99 through 108 removed outlier: 3.784A pdb=" N LEU F 103 " --> pdb=" O TYR F 99 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 124 removed outlier: 4.040A pdb=" N LEU F 112 " --> pdb=" O LEU F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 154 Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'F' and resid 178 through 181 Processing helix chain 'F' and resid 182 through 191 Processing helix chain 'F' and resid 208 through 212 Processing helix chain 'F' and resid 219 through 224 Processing helix chain 'F' and resid 224 through 232 removed outlier: 3.592A pdb=" N ILE F 228 " --> pdb=" O ASN F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 238 removed outlier: 3.543A pdb=" N TYR F 236 " --> pdb=" O GLY F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 277 Processing helix chain 'F' and resid 301 through 307 removed outlier: 4.055A pdb=" N ASP F 306 " --> pdb=" O ALA F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 318 Processing helix chain 'F' and resid 334 through 349 Processing helix chain 'F' and resid 354 through 373 removed outlier: 3.732A pdb=" N LEU F 361 " --> pdb=" O CYS F 357 " (cutoff:3.500A) Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 379 through 391 Processing helix chain 'F' and resid 399 through 415 removed outlier: 3.863A pdb=" N GLU F 406 " --> pdb=" O PRO F 402 " (cutoff:3.500A) Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 415 through 423 removed outlier: 3.701A pdb=" N PHE F 419 " --> pdb=" O PHE F 415 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLY F 422 " --> pdb=" O GLU F 418 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ILE F 423 " --> pdb=" O PHE F 419 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 26 Processing helix chain 'G' and resid 81 through 98 removed outlier: 4.405A 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 148 through 151 Processing helix chain 'G' and resid 155 through 164 Processing helix chain 'G' and resid 175 through 179 removed outlier: 3.827A pdb=" N VAL G 179 " --> pdb=" O HIS G 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 196 through 201 Processing helix chain 'G' and resid 209 through 213 Processing helix chain 'G' and resid 217 through 221 Processing helix chain 'G' and resid 263 through 269 Processing helix chain 'G' and resid 270 through 275 Processing helix chain 'G' and resid 294 through 308 Processing helix chain 'G' and resid 321 through 333 Processing helix chain 'G' and resid 342 through 359 Processing helix chain 'G' and resid 366 through 372 Processing helix chain 'G' and resid 381 through 386 Processing helix chain 'G' and resid 386 through 398 removed outlier: 3.538A pdb=" N ALA G 390 " --> pdb=" O GLY G 386 " (cutoff:3.500A) Processing helix chain 'G' and resid 398 through 408 removed outlier: 3.610A pdb=" N ARG G 402 " --> pdb=" O LYS G 398 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN G 408 " --> pdb=" O MET G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 423 Processing helix chain 'G' and resid 437 through 442 removed outlier: 4.282A pdb=" N ASP G 441 " --> pdb=" O ARG G 438 " (cutoff:3.500A) Processing helix chain 'G' and resid 450 through 466 Processing helix chain 'G' and resid 476 through 493 Processing helix chain 'G' and resid 506 through 523 removed outlier: 3.971A 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 559 Processing helix chain 'G' and resid 576 through 586 Processing helix chain 'G' and resid 599 through 604 Processing helix chain 'G' and resid 612 through 616 Processing helix chain 'G' and resid 647 through 662 Processing helix chain 'G' and resid 668 through 680 removed outlier: 3.517A pdb=" N VAL G 672 " --> pdb=" O GLN G 668 " (cutoff:3.500A) Processing helix chain 'G' and resid 684 through 689 Processing helix chain 'G' and resid 761 through 769 removed outlier: 3.676A pdb=" N GLN G 769 " --> pdb=" O ASN G 766 " (cutoff:3.500A) Processing helix chain 'G' and resid 822 through 828 removed outlier: 3.523A pdb=" N GLN G 826 " --> pdb=" O ASP G 822 " (cutoff:3.500A) Processing helix chain 'G' and resid 830 through 835 removed outlier: 4.581A pdb=" N ARG G 834 " --> pdb=" O VAL G 830 " (cutoff:3.500A) Processing helix chain 'G' and resid 843 through 850 Processing helix chain 'G' and resid 892 through 896 Processing helix chain 'H' and resid 5 through 44 removed outlier: 3.507A pdb=" N GLU H 10 " --> pdb=" O PRO H 6 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE H 15 " --> pdb=" O ILE H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'H' and resid 58 through 69 Processing helix chain 'H' and resid 79 through 92 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 93 through 98 Processing helix chain 'H' and resid 99 through 101 No H-bonds generated for 'chain 'H' and resid 99 through 101' Processing helix chain 'H' and resid 115 through 138 removed outlier: 4.044A pdb=" N PHE H 119 " --> pdb=" O GLY H 115 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ASN H 138 " --> pdb=" O GLY H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 158 Processing helix chain 'H' and resid 159 through 164 removed outlier: 3.669A pdb=" N LEU H 164 " --> pdb=" O LEU H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 172 Processing helix chain 'H' and resid 175 through 182 Processing helix chain 'H' and resid 192 through 207 Processing helix chain 'H' and resid 231 through 257 removed outlier: 3.716A pdb=" N PHE H 237 " --> pdb=" O LYS H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 288 Processing helix chain 'H' and resid 293 through 304 Processing helix chain 'H' and resid 304 through 324 Processing helix chain 'I' and resid 64 through 70 Processing helix chain 'I' and resid 103 through 109 Processing helix chain 'I' and resid 126 through 129 Processing helix chain 'I' and resid 133 through 137 Processing helix chain 'I' and resid 149 through 153 Processing helix chain 'J' and resid 2 through 22 Processing helix chain 'J' and resid 24 through 46 Processing helix chain 'J' and resid 48 through 58 removed outlier: 3.710A pdb=" N ILE J 56 " --> pdb=" O GLY J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 74 Processing helix chain 'J' and resid 79 through 85 Processing helix chain 'J' and resid 86 through 88 No H-bonds generated for 'chain 'J' and resid 86 through 88' Processing helix chain 'J' and resid 89 through 113 removed outlier: 5.197A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 125 through 134 Processing helix chain 'J' and resid 137 through 160 removed outlier: 3.653A pdb=" N MET J 146 " --> pdb=" O GLU J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 175 Processing helix chain 'K' and resid 3 through 25 Processing helix chain 'K' and resid 27 through 54 Processing helix chain 'K' and resid 56 through 88 Processing helix chain 'K' and resid 91 through 95 Processing helix chain 'L' and resid 5 through 22 Proline residue: L 11 - end of helix removed outlier: 3.889A pdb=" N ARG L 22 " --> pdb=" O LEU L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 26 through 55 removed outlier: 3.550A pdb=" N VAL L 38 " --> pdb=" O GLY L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 107 removed outlier: 3.797A pdb=" N TRP L 105 " --> pdb=" O MET L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 112 through 133 Processing helix chain 'L' and resid 135 through 155 removed outlier: 4.317A pdb=" N GLY L 142 " --> pdb=" O LEU L 138 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLY L 145 " --> pdb=" O LEU L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 193 removed outlier: 3.619A pdb=" N GLY L 164 " --> pdb=" O ASP L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 196 through 208 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 212 through 230 removed outlier: 3.729A pdb=" N TRP L 217 " --> pdb=" O ASN L 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 245 removed outlier: 3.633A pdb=" N GLY L 245 " --> pdb=" O ALA L 242 " (cutoff:3.500A) Processing helix chain 'L' and resid 246 through 254 Processing helix chain 'L' and resid 260 through 269 Processing helix chain 'L' and resid 269 through 274 Processing helix chain 'L' and resid 276 through 300 removed outlier: 3.580A pdb=" N VAL L 300 " --> pdb=" O PHE L 296 " (cutoff:3.500A) Processing helix chain 'L' and resid 303 through 325 Processing helix chain 'L' and resid 327 through 356 removed outlier: 3.833A pdb=" N ALA L 343 " --> pdb=" O ALA L 339 " (cutoff:3.500A) Processing helix chain 'L' and resid 367 through 372 removed outlier: 4.213A pdb=" N SER L 371 " --> pdb=" O GLY L 367 " (cutoff:3.500A) Processing helix chain 'L' and resid 372 through 387 Processing helix chain 'L' and resid 393 through 409 removed outlier: 4.172A pdb=" N PHE L 397 " --> pdb=" O THR L 393 " (cutoff:3.500A) Processing helix chain 'L' and resid 411 through 437 removed outlier: 3.531A pdb=" N MET L 432 " --> pdb=" O TYR L 428 " (cutoff:3.500A) Processing helix chain 'L' and resid 453 through 464 removed outlier: 3.631A pdb=" N LEU L 457 " --> pdb=" O HIS L 453 " (cutoff:3.500A) Processing helix chain 'L' and resid 465 through 471 Processing helix chain 'L' and resid 486 through 513 Processing helix chain 'L' and resid 516 through 525 removed outlier: 3.641A pdb=" N THR L 520 " --> pdb=" O ARG L 516 " (cutoff:3.500A) Processing helix chain 'L' and resid 525 through 537 Processing helix chain 'L' and resid 540 through 549 Processing helix chain 'L' and resid 549 through 561 Processing helix chain 'L' and resid 563 through 569 Processing helix chain 'L' and resid 570 through 584 Processing helix chain 'L' and resid 585 through 587 No H-bonds generated for 'chain 'L' and resid 585 through 587' Processing helix chain 'L' and resid 590 through 612 Processing helix chain 'M' and resid 2 through 20 removed outlier: 3.881A pdb=" N ILE M 7 " --> pdb=" O LEU M 3 " (cutoff:3.500A) Proline residue: M 10 - end of helix Processing helix chain 'M' and resid 21 through 24 Processing helix chain 'M' and resid 27 through 48 Processing helix chain 'M' and resid 49 through 50 No H-bonds generated for 'chain 'M' and resid 49 through 50' Processing helix chain 'M' and resid 51 through 55 Processing helix chain 'M' and resid 73 through 76 Processing helix chain 'M' and resid 84 through 105 removed outlier: 3.516A pdb=" N SER M 105 " --> pdb=" O ALA M 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 112 through 133 Processing helix chain 'M' and resid 135 through 146 Processing helix chain 'M' and resid 146 through 157 removed outlier: 3.629A pdb=" N MET M 150 " --> pdb=" O MET M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 200 Processing helix chain 'M' and resid 206 through 211 Processing helix chain 'M' and resid 216 through 235 removed outlier: 3.756A pdb=" N ALA M 230 " --> pdb=" O GLY M 226 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LYS M 234 " --> pdb=" O ALA M 230 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET M 235 " --> pdb=" O PHE M 231 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 251 removed outlier: 4.035A pdb=" N ASP M 246 " --> pdb=" O GLY M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 255 through 263 removed outlier: 3.715A pdb=" N LEU M 263 " --> pdb=" O LEU M 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 265 through 274 removed outlier: 3.649A pdb=" N TYR M 269 " --> pdb=" O LYS M 265 " (cutoff:3.500A) Processing helix chain 'M' and resid 274 through 279 Processing helix chain 'M' and resid 279 through 307 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 310 through 331 removed outlier: 3.709A pdb=" N VAL M 320 " --> pdb=" O ALA M 316 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE M 325 " --> pdb=" O SER M 321 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL M 326 " --> pdb=" O HIS M 322 " (cutoff:3.500A) Processing helix chain 'M' and resid 334 through 367 Processing helix chain 'M' and resid 370 through 374 Processing helix chain 'M' and resid 376 through 380 Processing helix chain 'M' and resid 383 through 396 Processing helix chain 'M' and resid 402 through 418 removed outlier: 3.608A pdb=" N GLN M 416 " --> pdb=" O PHE M 412 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL M 417 " --> pdb=" O GLY M 413 " (cutoff:3.500A) Processing helix chain 'M' and resid 418 through 427 removed outlier: 3.557A pdb=" N PHE M 427 " --> pdb=" O VAL M 423 " (cutoff:3.500A) Processing helix chain 'M' and resid 427 through 444 Processing helix chain 'M' and resid 451 through 455 removed outlier: 3.745A pdb=" N GLN M 455 " --> pdb=" O ILE M 452 " (cutoff:3.500A) Processing helix chain 'M' and resid 461 through 481 Processing helix chain 'M' and resid 482 through 505 removed outlier: 3.646A pdb=" N THR M 488 " --> pdb=" O PRO M 484 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N SER M 491 " --> pdb=" O ASP M 487 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ALA M 492 " --> pdb=" O THR M 488 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 10 removed outlier: 3.552A pdb=" N ALA N 10 " --> pdb=" O GLN N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 11 through 31 Processing helix chain 'N' and resid 33 through 59 removed outlier: 4.469A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE N 54 " --> pdb=" O VAL N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 70 through 96 Proline residue: N 93 - end of helix Processing helix chain 'N' and resid 102 through 122 removed outlier: 4.202A pdb=" N TYR N 106 " --> pdb=" O LYS N 102 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 144 Proline residue: N 138 - end of helix removed outlier: 3.762A pdb=" N GLY N 141 " --> pdb=" O LEU N 137 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 182 Processing helix chain 'N' and resid 185 through 189 Processing helix chain 'N' and resid 200 through 218 removed outlier: 3.615A pdb=" N GLY N 213 " --> pdb=" O LEU N 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 226 through 234 Processing helix chain 'N' and resid 235 through 244 removed outlier: 3.785A pdb=" N PHE N 241 " --> pdb=" O PRO N 237 " (cutoff:3.500A) Processing helix chain 'N' and resid 244 through 261 Processing helix chain 'N' and resid 262 through 265 Processing helix chain 'N' and resid 266 through 289 removed outlier: 3.744A pdb=" N ASN N 285 " --> pdb=" O ILE N 281 " (cutoff:3.500A) Processing helix chain 'N' and resid 293 through 315 removed outlier: 3.563A pdb=" N VAL N 311 " --> pdb=" O GLY N 307 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA N 312 " --> pdb=" O TYR N 308 " (cutoff:3.500A) Processing helix chain 'N' and resid 316 through 319 removed outlier: 3.722A pdb=" N GLY N 319 " --> pdb=" O LEU N 316 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 316 through 319' Processing helix chain 'N' and resid 320 through 348 removed outlier: 4.084A pdb=" N GLU N 324 " --> pdb=" O GLU N 320 " (cutoff:3.500A) Processing helix chain 'N' and resid 358 through 363 Processing helix chain 'N' and resid 364 through 368 Processing helix chain 'N' and resid 369 through 385 Processing helix chain 'N' and resid 389 through 405 removed outlier: 3.649A pdb=" N ILE N 393 " --> pdb=" O THR N 389 " (cutoff:3.500A) Processing helix chain 'N' and resid 407 through 432 removed outlier: 3.878A pdb=" N TYR N 423 " --> pdb=" O ALA N 419 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR N 424 " --> pdb=" O ILE N 420 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU N 432 " --> pdb=" O VAL N 428 " (cutoff:3.500A) Processing helix chain 'N' and resid 447 through 470 Processing helix chain 'N' and resid 471 through 481 Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 64 Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 26 Processing sheet with id=AA3, first strand: chain 'B' and resid 56 through 60 removed outlier: 3.790A pdb=" N ALA B 99 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N VAL B 123 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N ILE B 155 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N SER B 125 " --> pdb=" O ILE B 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 34 through 37 removed outlier: 4.150A pdb=" N VAL C 45 " --> pdb=" O GLN C 37 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL C 46 " --> pdb=" O LYS C 110 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ALA C 112 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N ILE C 48 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE C 99 " --> pdb=" O LEU C 70 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N LEU C 70 " --> pdb=" O ILE C 99 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 119 through 121 Processing sheet with id=AA6, first strand: chain 'C' and resid 210 through 215 removed outlier: 3.617A pdb=" N ARG C 228 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ASP C 234 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE C 238 " --> pdb=" O ASP C 234 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 359 through 360 Processing sheet with id=AA8, first strand: chain 'C' and resid 527 through 534 removed outlier: 3.506A pdb=" N GLN C 531 " --> pdb=" O TYR C 542 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 126 through 131 Processing sheet with id=AB1, first strand: chain 'F' and resid 157 through 160 removed outlier: 5.256A pdb=" N LYS F 158 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE F 167 " --> pdb=" O LYS F 158 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N PHE F 165 " --> pdb=" O ILE F 160 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 260 through 265 removed outlier: 7.379A pdb=" N ALA F 326 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLY F 251 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ALA F 328 " --> pdb=" O GLY F 251 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N SER F 253 " --> pdb=" O ALA F 328 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ASP F 330 " --> pdb=" O SER F 253 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 9 through 13 removed outlier: 3.881A pdb=" N THR G 75 " --> pdb=" O THR G 3 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE G 76 " --> pdb=" O TYR G 53 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 144 through 146 Processing sheet with id=AB5, first strand: chain 'G' and resid 171 through 173 Processing sheet with id=AB6, first strand: chain 'G' and resid 222 through 223 Processing sheet with id=AB7, first strand: chain 'G' and resid 222 through 223 removed outlier: 3.540A pdb=" N GLU G 250 " --> pdb=" O SER G 238 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ARG G 242 " --> pdb=" O LEU G 246 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N LEU G 246 " --> pdb=" O ARG G 242 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 289 through 292 removed outlier: 3.621A pdb=" N ASP G 594 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N VAL G 564 " --> pdb=" O MET G 591 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL G 593 " --> pdb=" O VAL G 564 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL G 566 " --> pdb=" O VAL G 593 " (cutoff:3.500A) removed outlier: 8.306A pdb=" N TYR G 338 " --> pdb=" O VAL G 312 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLY G 314 " --> pdb=" O TYR G 338 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 445 through 448 removed outlier: 7.030A pdb=" N LEU G 429 " --> pdb=" O TRP G 445 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N TYR G 447 " --> pdb=" O LEU G 429 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL G 431 " --> pdb=" O TYR G 447 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA G 374 " --> pdb=" O LEU G 497 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE G 499 " --> pdb=" O ALA G 374 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU G 376 " --> pdb=" O ILE G 499 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N GLY G 501 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N LEU G 378 " --> pdb=" O GLY G 501 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 618 through 621 Processing sheet with id=AC2, first strand: chain 'G' and resid 702 through 703 removed outlier: 6.734A pdb=" N LEU G 702 " --> pdb=" O THR G 735 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'G' and resid 899 through 900 removed outlier: 3.505A pdb=" N LEU G 884 " --> pdb=" O ALA G 813 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE G 840 " --> pdb=" O GLU G 872 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 48 through 50 Processing sheet with id=AC5, first strand: chain 'I' and resid 75 through 81 removed outlier: 4.012A pdb=" N PHE I 91 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ALA I 80 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 60 through 70 removed outlier: 5.330A pdb=" N SER L 61 " --> pdb=" O LEU L 81 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU L 81 " --> pdb=" O SER L 61 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU L 79 " --> pdb=" O PRO L 63 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP L 65 " --> pdb=" O PHE L 77 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ILE L 75 " --> pdb=" O TRP L 67 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER L 69 " --> pdb=" O PHE L 73 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N PHE L 73 " --> pdb=" O SER L 69 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 65 through 72 removed outlier: 4.156A pdb=" N SER M 65 " --> pdb=" O ILE M 83 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 61 through 64 removed outlier: 6.596A pdb=" N MET N 67 " --> pdb=" O VAL N 63 " (cutoff:3.500A) 2169 hydrogen bonds defined for protein. 6180 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: 8.45 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 15739 1.42 - 1.64: 22223 1.64 - 1.86: 411 1.86 - 2.08: 0 2.08 - 2.30: 92 Bond restraints: 38465 Sorted by residual: bond pdb=" N ILE G 680 " pdb=" CA ILE G 680 " ideal model delta sigma weight residual 1.458 1.495 -0.037 7.70e-03 1.69e+04 2.37e+01 bond pdb=" N ILE B 155 " pdb=" CA ILE B 155 " ideal model delta sigma weight residual 1.458 1.493 -0.036 7.70e-03 1.69e+04 2.14e+01 bond pdb=" N VAL G 751 " pdb=" CA VAL G 751 " ideal model delta sigma weight residual 1.458 1.493 -0.035 7.70e-03 1.69e+04 2.12e+01 bond pdb=" N ILE C 450 " pdb=" CA ILE C 450 " ideal model delta sigma weight residual 1.460 1.493 -0.033 7.60e-03 1.73e+04 1.86e+01 bond pdb=" N ILE B 149 " pdb=" CA ILE B 149 " ideal model delta sigma weight residual 1.457 1.496 -0.038 9.00e-03 1.23e+04 1.82e+01 ... (remaining 38460 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.07: 51658 4.07 - 8.14: 534 8.14 - 12.22: 4 12.22 - 16.29: 0 16.29 - 20.36: 1 Bond angle restraints: 52197 Sorted by residual: angle pdb=" C CYS I 109 " pdb=" CA CYS I 109 " pdb=" CB CYS I 109 " ideal model delta sigma weight residual 109.42 89.06 20.36 1.57e+00 4.06e-01 1.68e+02 angle pdb=" N PRO I 110 " pdb=" CA PRO I 110 " pdb=" C PRO I 110 " ideal model delta sigma weight residual 114.68 106.12 8.56 1.28e+00 6.10e-01 4.48e+01 angle pdb=" N ILE M 134 " pdb=" CA ILE M 134 " pdb=" C ILE M 134 " ideal model delta sigma weight residual 113.10 107.13 5.97 9.70e-01 1.06e+00 3.79e+01 angle pdb=" C TYR I 145 " pdb=" CA TYR I 145 " pdb=" CB TYR I 145 " ideal model delta sigma weight residual 110.08 116.97 -6.89 1.15e+00 7.56e-01 3.59e+01 angle pdb=" CA GLY N 59 " pdb=" C GLY N 59 " pdb=" O GLY N 59 " ideal model delta sigma weight residual 122.45 118.30 4.15 7.20e-01 1.93e+00 3.33e+01 ... (remaining 52192 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.94: 21644 24.94 - 49.88: 729 49.88 - 74.82: 290 74.82 - 99.76: 3 99.76 - 124.70: 4 Dihedral angle restraints: 22670 sinusoidal: 9110 harmonic: 13560 Sorted by residual: dihedral pdb=" C CYS I 109 " pdb=" N CYS I 109 " pdb=" CA CYS I 109 " pdb=" CB CYS I 109 " ideal model delta harmonic sigma weight residual -122.60 -100.63 -21.97 0 2.50e+00 1.60e-01 7.73e+01 dihedral pdb=" CD ARG E 90 " pdb=" NE ARG E 90 " pdb=" CZ ARG E 90 " pdb=" NH1 ARG E 90 " ideal model delta sinusoidal sigma weight residual 0.00 -55.02 55.02 1 1.00e+01 1.00e-02 4.10e+01 dihedral pdb=" CA VAL M 238 " pdb=" C VAL M 238 " pdb=" N PRO M 239 " pdb=" CA PRO M 239 " ideal model delta harmonic sigma weight residual 0.00 26.89 -26.89 0 5.00e+00 4.00e-02 2.89e+01 ... (remaining 22667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.251: 5792 4.251 - 8.501: 0 8.501 - 12.752: 0 12.752 - 17.002: 0 17.002 - 21.253: 28 Chirality restraints: 5820 Sorted by residual: chirality pdb="FE1 SF4 F 501 " pdb=" S2 SF4 F 501 " pdb=" S3 SF4 F 501 " pdb=" S4 SF4 F 501 " both_signs ideal model delta sigma weight residual False -10.55 10.70 -21.25 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.70 -21.25 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE4 SF4 I 201 " pdb=" S1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.69 21.24 2.00e-01 2.50e+01 1.13e+04 ... (remaining 5817 not shown) Planarity restraints: 6552 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 90 " 0.910 9.50e-02 1.11e+02 4.08e-01 1.01e+02 pdb=" NE ARG E 90 " -0.054 2.00e-02 2.50e+03 pdb=" CZ ARG E 90 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG E 90 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG E 90 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN F 502 " -0.037 2.00e-02 2.50e+03 3.00e-02 4.05e+01 pdb=" C10 FMN F 502 " 0.004 2.00e-02 2.50e+03 pdb=" C2 FMN F 502 " -0.013 2.00e-02 2.50e+03 pdb=" C4 FMN F 502 " 0.011 2.00e-02 2.50e+03 pdb=" C4A FMN F 502 " 0.017 2.00e-02 2.50e+03 pdb=" C5A FMN F 502 " 0.032 2.00e-02 2.50e+03 pdb=" C6 FMN F 502 " 0.006 2.00e-02 2.50e+03 pdb=" C7 FMN F 502 " -0.015 2.00e-02 2.50e+03 pdb=" C7M FMN F 502 " -0.091 2.00e-02 2.50e+03 pdb=" C8 FMN F 502 " 0.010 2.00e-02 2.50e+03 pdb=" C8M FMN F 502 " 0.026 2.00e-02 2.50e+03 pdb=" C9 FMN F 502 " 0.029 2.00e-02 2.50e+03 pdb=" C9A FMN F 502 " 0.031 2.00e-02 2.50e+03 pdb=" N1 FMN F 502 " -0.006 2.00e-02 2.50e+03 pdb=" N10 FMN F 502 " 0.003 2.00e-02 2.50e+03 pdb=" N3 FMN F 502 " -0.005 2.00e-02 2.50e+03 pdb=" N5 FMN F 502 " 0.029 2.00e-02 2.50e+03 pdb=" O2 FMN F 502 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 61 " -0.280 9.50e-02 1.11e+02 1.26e-01 9.69e+00 pdb=" NE ARG A 61 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 61 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 61 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 61 " -0.010 2.00e-02 2.50e+03 ... (remaining 6549 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.87: 13886 2.87 - 3.38: 38087 3.38 - 3.89: 69613 3.89 - 4.39: 82955 4.39 - 4.90: 132572 Nonbonded interactions: 337113 Sorted by model distance: nonbonded pdb=" O LEU L 252 " pdb=" OG1 THR L 257 " model vdw 2.366 3.040 nonbonded pdb=" OD2 ASP L 82 " pdb=" NH1 ARG L 268 " model vdw 2.370 3.120 nonbonded pdb=" O LEU H 160 " pdb=" OG SER H 163 " model vdw 2.387 3.040 nonbonded pdb=" O LEU C 425 " pdb=" OG1 THR C 428 " model vdw 2.392 3.040 nonbonded pdb=" O GLY N 299 " pdb=" OG SER N 302 " model vdw 2.396 3.040 ... (remaining 337108 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=1.00 max=1.00 mean=1.00 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: 4.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 37.010 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 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 : 0.014 1.063 38502 Z= 0.969 Angle : 1.559 59.598 52293 Z= 1.144 Chirality : 1.472 21.253 5820 Planarity : 0.013 0.408 6552 Dihedral : 13.508 124.700 13996 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.72 % Favored : 96.20 % Rotamer: Outliers : 1.06 % Allowed : 5.18 % Favored : 93.76 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 6.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.11), residues: 4710 helix: 0.09 (0.09), residues: 2633 sheet: -0.92 (0.29), residues: 285 loop : -1.17 (0.14), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 250 TYR 0.020 0.002 TYR L 428 PHE 0.019 0.002 PHE L 341 TRP 0.018 0.002 TRP G 651 HIS 0.008 0.002 HIS C 163 Details of bonding type rmsd/Z covalent geometry : bond 0.01278 / 0.96 (38465) covalent geometry : angle 1.46672 / 1.14 (52197) hydrogen bonds : bond 0.19481 / 13.02 ( 2167) hydrogen bonds : angle 7.42069 / 5.24 ( 6180) metal coordination : bond 0.18327 / 15.49 ( 37) metal coordination : angle 12.43822 / 9.23 ( 96) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 655 time to evaluate : 1.418 Fit side-chains revert: symmetry clash REVERT: A 126 THR cc_start: 0.6570 (OUTLIER) cc_final: 0.5851 (t) REVERT: B 17 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.7396 (t80) REVERT: B 45 MET cc_start: 0.8883 (ttp) cc_final: 0.8655 (ttp) REVERT: B 126 MET cc_start: 0.9017 (ttt) cc_final: 0.8757 (ttt) REVERT: B 135 MET cc_start: 0.9358 (ptm) cc_final: 0.9101 (ptm) REVERT: B 219 GLU cc_start: 0.8267 (mm-30) cc_final: 0.7929 (mm-30) REVERT: C 324 GLN cc_start: 0.8533 (tt0) cc_final: 0.8212 (tt0) REVERT: C 336 PHE cc_start: 0.6892 (t80) cc_final: 0.6223 (t80) REVERT: C 383 MET cc_start: 0.8803 (mmm) cc_final: 0.8561 (mmm) REVERT: C 387 LEU cc_start: 0.8942 (tp) cc_final: 0.8633 (tt) REVERT: C 524 MET cc_start: 0.9206 (mmt) cc_final: 0.8921 (mmt) REVERT: C 532 MET cc_start: 0.9171 (ptp) cc_final: 0.8954 (ptp) REVERT: C 591 MET cc_start: 0.9279 (mmm) cc_final: 0.8835 (mmm) REVERT: E 86 ARG cc_start: 0.8960 (mtm-85) cc_final: 0.8726 (mtm-85) REVERT: E 120 THR cc_start: 0.9024 (p) cc_final: 0.8753 (m) REVERT: F 309 MET cc_start: 0.9179 (mmt) cc_final: 0.8929 (mmt) REVERT: F 335 MET cc_start: 0.9072 (mmm) cc_final: 0.8789 (mmm) REVERT: G 299 MET cc_start: 0.9098 (mmp) cc_final: 0.8728 (mmp) REVERT: G 888 MET cc_start: 0.8220 (mmm) cc_final: 0.7960 (tpp) REVERT: G 902 ASP cc_start: 0.7362 (t70) cc_final: 0.7091 (p0) REVERT: H 71 GLU cc_start: 0.8837 (tt0) cc_final: 0.8634 (tt0) REVERT: H 80 ARG cc_start: 0.8009 (ttp-110) cc_final: 0.7304 (tmt170) REVERT: H 211 PRO cc_start: 0.9277 (OUTLIER) cc_final: 0.9059 (Cg_endo) REVERT: J 1 MET cc_start: 0.7753 (ttt) cc_final: 0.7545 (ttp) REVERT: J 73 MET cc_start: 0.9027 (mtp) cc_final: 0.8825 (mtp) REVERT: J 146 MET cc_start: 0.9271 (mmt) cc_final: 0.9011 (mmm) REVERT: L 221 MET cc_start: 0.9259 (mmp) cc_final: 0.9055 (mmt) REVERT: L 313 MET cc_start: 0.9073 (ttm) cc_final: 0.8743 (ttp) REVERT: L 365 MET cc_start: 0.8667 (mtt) cc_final: 0.8462 (mtp) REVERT: L 449 LYS cc_start: 0.8645 (pttt) cc_final: 0.8316 (tptp) REVERT: L 562 ARG cc_start: 0.8269 (mtp180) cc_final: 0.7987 (mtt90) REVERT: L 610 MET cc_start: 0.9172 (mmp) cc_final: 0.8964 (mmp) REVERT: M 22 ARG cc_start: 0.8685 (ptm160) cc_final: 0.7291 (mmt180) REVERT: M 136 MET cc_start: 0.9140 (mmm) cc_final: 0.8887 (mmm) REVERT: M 303 TRP cc_start: 0.9329 (OUTLIER) cc_final: 0.8623 (m-10) REVERT: M 345 MET cc_start: 0.9237 (mtp) cc_final: 0.8988 (mtm) REVERT: M 371 MET cc_start: 0.9237 (mtm) cc_final: 0.8941 (mtp) REVERT: N 30 TRP cc_start: 0.8607 (t-100) cc_final: 0.8372 (t-100) outliers start: 41 outliers final: 9 residues processed: 692 average time/residue: 0.8156 time to fit residues: 663.2705 Evaluate side-chains 502 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 489 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain B residue 17 TYR Chi-restraints excluded: chain B residue 63 CYS Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain G residue 106 CYS Chi-restraints excluded: chain G residue 231 CYS Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain H residue 211 PRO Chi-restraints excluded: chain I residue 109 CYS Chi-restraints excluded: chain M residue 303 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 432 optimal weight: 0.9980 chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 0.6980 chunk 455 optimal weight: 0.9980 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 190 GLN B 196 ASN C 158 GLN C 248 HIS C 397 ASN C 482 ASN C 540 ASN E 46 GLN E 82 GLN E 100 ASN E 150 HIS F 53 GLN F 409 GLN G 113 HIS G 135 HIS G 176 HIS G 671 HIS G 804 GLN H 152 GLN H 170 GLN H 208 HIS H 226 HIS J 24 ASN J 115 ASN K 27 ASN K 82 GLN L 62 GLN L 78 ASN L 121 ASN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 196 ASN L 232 GLN ** L 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 357 HIS L 446 HIS M 19 GLN ** M 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 250 GLN M 281 ASN M 322 HIS N 180 GLN N 472 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.075596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.062114 restraints weight = 48087.940| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.20 r_work: 0.2932 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.253 38502 Z= 0.392 Angle : 2.528 55.500 52293 Z= 1.442 Chirality : 0.439 6.448 5820 Planarity : 0.004 0.082 6552 Dihedral : 8.557 104.657 5584 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.93 % Allowed : 10.08 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.12), residues: 4710 helix: 1.56 (0.10), residues: 2639 sheet: -0.67 (0.29), residues: 292 loop : -0.58 (0.15), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 293 TYR 0.029 0.002 TYR M 435 PHE 0.039 0.002 PHE L 341 TRP 0.029 0.001 TRP C 382 HIS 0.006 0.001 HIS G 99 Details of bonding type rmsd/Z covalent geometry : bond 0.01130 / 0.39 (38465) covalent geometry : angle 2.18792 / 1.44 (52197) hydrogen bonds : bond 0.05556 / 3.70 ( 2167) hydrogen bonds : angle 5.03668 / 3.56 ( 6180) metal coordination : bond 0.04669 / 3.59 ( 37) metal coordination : angle 29.65624 / 22.24 ( 96) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 506 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 THR cc_start: 0.6104 (OUTLIER) cc_final: 0.5892 (p) REVERT: B 45 MET cc_start: 0.8989 (ttp) cc_final: 0.8687 (ttp) REVERT: B 89 SER cc_start: 0.8332 (t) cc_final: 0.8004 (p) REVERT: B 126 MET cc_start: 0.9292 (ttt) cc_final: 0.9044 (ttt) REVERT: C 76 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8829 (tpp) REVERT: C 324 GLN cc_start: 0.8639 (tt0) cc_final: 0.8296 (tt0) REVERT: C 336 PHE cc_start: 0.6408 (t80) cc_final: 0.5783 (t80) REVERT: C 383 MET cc_start: 0.8701 (mmm) cc_final: 0.8490 (mmm) REVERT: C 524 MET cc_start: 0.9292 (mmt) cc_final: 0.9058 (mmt) REVERT: C 591 MET cc_start: 0.9269 (mmm) cc_final: 0.8792 (mmm) REVERT: E 47 ARG cc_start: 0.8886 (mmt180) cc_final: 0.8588 (mpt180) REVERT: E 86 ARG cc_start: 0.8918 (mtm-85) cc_final: 0.8658 (mtm-85) REVERT: E 90 ARG cc_start: 0.8864 (mtm-85) cc_final: 0.8444 (mtt180) REVERT: E 116 LYS cc_start: 0.8924 (mtpt) cc_final: 0.8652 (mmtp) REVERT: E 126 PHE cc_start: 0.8876 (m-80) cc_final: 0.8662 (m-80) REVERT: F 335 MET cc_start: 0.9151 (mmm) cc_final: 0.8921 (mmm) REVERT: F 369 ARG cc_start: 0.8552 (mtm-85) cc_final: 0.8209 (mtp85) REVERT: G 9 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8294 (mppt) REVERT: G 299 MET cc_start: 0.8874 (mmp) cc_final: 0.8654 (mmp) REVERT: G 888 MET cc_start: 0.8037 (mmm) cc_final: 0.7780 (mmm) REVERT: H 34 PHE cc_start: 0.8521 (t80) cc_final: 0.8287 (t80) REVERT: H 80 ARG cc_start: 0.8163 (ttp-110) cc_final: 0.7352 (tmt170) REVERT: H 139 ASN cc_start: 0.8763 (t0) cc_final: 0.8480 (t0) REVERT: H 213 ASP cc_start: 0.8304 (p0) cc_final: 0.7521 (OUTLIER) REVERT: H 291 ARG cc_start: 0.8142 (ttm-80) cc_final: 0.7493 (mtt90) REVERT: I 36 GLU cc_start: 0.8663 (tt0) cc_final: 0.8395 (tp30) REVERT: I 174 ASP cc_start: 0.8998 (t70) cc_final: 0.8780 (t0) REVERT: J 73 MET cc_start: 0.8859 (mtp) cc_final: 0.8636 (mtp) REVERT: J 146 MET cc_start: 0.9227 (mmt) cc_final: 0.8996 (mmm) REVERT: K 87 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.7843 (mtm-85) REVERT: L 313 MET cc_start: 0.9010 (ttm) cc_final: 0.8557 (ttp) REVERT: L 365 MET cc_start: 0.8558 (mtt) cc_final: 0.8291 (mtp) REVERT: L 449 LYS cc_start: 0.8651 (pttt) cc_final: 0.8243 (tptp) REVERT: L 529 ARG cc_start: 0.8003 (mtt180) cc_final: 0.7619 (mtm180) REVERT: L 562 ARG cc_start: 0.8190 (mtp180) cc_final: 0.7913 (ptt90) REVERT: L 610 MET cc_start: 0.9212 (mmp) cc_final: 0.8964 (mmp) REVERT: M 22 ARG cc_start: 0.8828 (ptm160) cc_final: 0.7056 (mmp-170) REVERT: M 136 MET cc_start: 0.9174 (mmm) cc_final: 0.8850 (mmm) REVERT: M 224 MET cc_start: 0.8992 (tmm) cc_final: 0.8466 (tmm) REVERT: M 264 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8843 (mm) REVERT: M 345 MET cc_start: 0.9116 (mtp) cc_final: 0.8881 (mtm) REVERT: M 371 MET cc_start: 0.9205 (mtm) cc_final: 0.9005 (mtp) REVERT: N 30 TRP cc_start: 0.8606 (t-100) cc_final: 0.8347 (t-100) outliers start: 75 outliers final: 22 residues processed: 544 average time/residue: 0.7641 time to fit residues: 490.5106 Evaluate side-chains 488 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 462 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 432 LEU Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain K residue 87 ARG Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 373 MET Chi-restraints excluded: chain N residue 443 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 417 optimal weight: 0.9980 chunk 307 optimal weight: 3.9990 chunk 379 optimal weight: 2.9990 chunk 289 optimal weight: 0.4980 chunk 67 optimal weight: 3.9990 chunk 271 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 156 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 130 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 186 GLN C 355 HIS C 397 ASN F 409 GLN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 671 HIS J 115 ASN K 89 ASN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 411 HIS L 446 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.073293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.059644 restraints weight = 50133.073| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.23 r_work: 0.2879 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9079 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.246 38502 Z= 0.401 Angle : 2.512 54.209 52293 Z= 1.435 Chirality : 0.443 6.485 5820 Planarity : 0.005 0.079 6552 Dihedral : 8.376 102.505 5569 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.86 % Allowed : 11.42 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.12), residues: 4710 helix: 1.70 (0.10), residues: 2654 sheet: -0.56 (0.28), residues: 315 loop : -0.39 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 373 TYR 0.027 0.002 TYR M 435 PHE 0.033 0.002 PHE L 341 TRP 0.019 0.001 TRP C 382 HIS 0.008 0.001 HIS G 99 Details of bonding type rmsd/Z covalent geometry : bond 0.01154 / 0.40 (38465) covalent geometry : angle 2.17576 / 1.43 (52197) hydrogen bonds : bond 0.05308 / 3.53 ( 2167) hydrogen bonds : angle 4.75919 / 3.35 ( 6180) metal coordination : bond 0.04171 / 3.07 ( 37) metal coordination : angle 29.37091 / 22.03 ( 96) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 481 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.8995 (ttp) cc_final: 0.8694 (ttp) REVERT: B 89 SER cc_start: 0.8367 (t) cc_final: 0.8031 (p) REVERT: B 126 MET cc_start: 0.9303 (ttt) cc_final: 0.9064 (ttt) REVERT: C 76 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8805 (tpp) REVERT: C 250 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.7720 (ptp-170) REVERT: C 324 GLN cc_start: 0.8726 (tt0) cc_final: 0.8377 (tt0) REVERT: C 383 MET cc_start: 0.8629 (mmm) cc_final: 0.8378 (mmm) REVERT: C 524 MET cc_start: 0.9270 (mmt) cc_final: 0.9019 (mmt) REVERT: C 591 MET cc_start: 0.9265 (mmm) cc_final: 0.8846 (mmm) REVERT: E 86 ARG cc_start: 0.8999 (mtm-85) cc_final: 0.8639 (mtm-85) REVERT: E 90 ARG cc_start: 0.8909 (mtm-85) cc_final: 0.8618 (mtm-85) REVERT: E 103 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8386 (mp10) REVERT: E 116 LYS cc_start: 0.8998 (mmpt) cc_final: 0.8689 (mmtp) REVERT: F 76 MET cc_start: 0.9411 (tpt) cc_final: 0.9164 (mmm) REVERT: F 335 MET cc_start: 0.9096 (mmm) cc_final: 0.8848 (mmm) REVERT: F 369 ARG cc_start: 0.8534 (mtm-85) cc_final: 0.8319 (mtp85) REVERT: G 3 THR cc_start: 0.9373 (OUTLIER) cc_final: 0.9074 (t) REVERT: G 9 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8302 (mppt) REVERT: G 888 MET cc_start: 0.8055 (mmm) cc_final: 0.7844 (mmm) REVERT: G 902 ASP cc_start: 0.6927 (p0) cc_final: 0.6546 (p0) REVERT: H 34 PHE cc_start: 0.8413 (t80) cc_final: 0.8122 (t80) REVERT: H 36 GLU cc_start: 0.8811 (tt0) cc_final: 0.8299 (tm-30) REVERT: H 38 ARG cc_start: 0.8739 (mtp180) cc_final: 0.8462 (mtp180) REVERT: H 80 ARG cc_start: 0.8114 (ttp-110) cc_final: 0.7453 (tmt170) REVERT: H 213 ASP cc_start: 0.8291 (p0) cc_final: 0.8084 (p0) REVERT: J 73 MET cc_start: 0.8999 (mtp) cc_final: 0.8765 (mtp) REVERT: J 146 MET cc_start: 0.9228 (mmt) cc_final: 0.8978 (mmm) REVERT: J 160 ARG cc_start: 0.8332 (ptt-90) cc_final: 0.8115 (ptt90) REVERT: L 313 MET cc_start: 0.9022 (ttm) cc_final: 0.8626 (ttp) REVERT: L 365 MET cc_start: 0.8548 (mtt) cc_final: 0.8285 (mtp) REVERT: L 449 LYS cc_start: 0.8628 (pttt) cc_final: 0.8219 (tptp) REVERT: L 495 ILE cc_start: 0.9358 (OUTLIER) cc_final: 0.9066 (mp) REVERT: L 529 ARG cc_start: 0.8013 (mtt180) cc_final: 0.7635 (mtm180) REVERT: L 562 ARG cc_start: 0.8194 (mtp180) cc_final: 0.7837 (mtt90) REVERT: M 22 ARG cc_start: 0.8878 (ptm160) cc_final: 0.7042 (mmp-170) REVERT: M 110 GLU cc_start: 0.7167 (pm20) cc_final: 0.6801 (pp20) REVERT: M 136 MET cc_start: 0.9197 (mmm) cc_final: 0.8864 (mmm) REVERT: M 264 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8945 (mm) REVERT: M 303 TRP cc_start: 0.9525 (OUTLIER) cc_final: 0.7973 (m-10) REVERT: M 371 MET cc_start: 0.9221 (mtm) cc_final: 0.8996 (mtp) REVERT: M 455 GLN cc_start: 0.8688 (pt0) cc_final: 0.8080 (pt0) REVERT: N 30 TRP cc_start: 0.8731 (t-100) cc_final: 0.8476 (t-100) REVERT: N 197 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8049 (mtp) REVERT: N 427 ARG cc_start: 0.8279 (mtm110) cc_final: 0.8009 (ttp-110) outliers start: 72 outliers final: 32 residues processed: 523 average time/residue: 0.7685 time to fit residues: 475.0310 Evaluate side-chains 502 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 461 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 305 MET Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 185 GLU Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 833 SER Chi-restraints excluded: chain G residue 866 THR Chi-restraints excluded: chain H residue 232 MET Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 495 ILE Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain L residue 568 MET Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 263 LEU Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 318 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 339 optimal weight: 3.9990 chunk 47 optimal weight: 0.0970 chunk 371 optimal weight: 0.0570 chunk 466 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 195 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 395 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 186 GLN C 355 HIS F 409 GLN G 653 HIS J 115 ASN K 40 ASN K 82 GLN K 89 ASN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 446 HIS M 117 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.074916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.061346 restraints weight = 50148.313| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.24 r_work: 0.2921 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9046 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.245 38502 Z= 0.383 Angle : 2.500 53.630 52293 Z= 1.430 Chirality : 0.440 6.424 5820 Planarity : 0.004 0.056 6552 Dihedral : 8.072 105.775 5568 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.06 % Allowed : 12.09 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.12), residues: 4710 helix: 1.89 (0.10), residues: 2649 sheet: -0.24 (0.28), residues: 309 loop : -0.34 (0.15), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 293 TYR 0.027 0.001 TYR M 435 PHE 0.031 0.001 PHE L 341 TRP 0.020 0.001 TRP C 382 HIS 0.007 0.001 HIS L 446 Details of bonding type rmsd/Z covalent geometry : bond 0.01123 / 0.38 (38465) covalent geometry : angle 2.16257 / 1.43 (52197) hydrogen bonds : bond 0.04391 / 2.91 ( 2167) hydrogen bonds : angle 4.52491 / 3.19 ( 6180) metal coordination : bond 0.02645 / 1.88 ( 37) metal coordination : angle 29.37589 / 22.05 ( 96) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 473 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.9016 (ttp) cc_final: 0.8729 (ttp) REVERT: B 89 SER cc_start: 0.8278 (t) cc_final: 0.7965 (p) REVERT: B 117 MET cc_start: 0.9189 (mtp) cc_final: 0.8911 (mtp) REVERT: B 126 MET cc_start: 0.9284 (ttt) cc_final: 0.9063 (ttt) REVERT: C 74 HIS cc_start: 0.9313 (OUTLIER) cc_final: 0.8989 (t-90) REVERT: C 76 MET cc_start: 0.9078 (OUTLIER) cc_final: 0.8762 (tpp) REVERT: C 199 GLU cc_start: 0.8094 (mp0) cc_final: 0.7806 (mp0) REVERT: C 324 GLN cc_start: 0.8742 (tt0) cc_final: 0.8425 (tt0) REVERT: C 383 MET cc_start: 0.8644 (mmm) cc_final: 0.8442 (mmm) REVERT: C 591 MET cc_start: 0.9284 (mmm) cc_final: 0.8883 (mmm) REVERT: E 47 ARG cc_start: 0.8737 (mmt-90) cc_final: 0.8425 (mpt180) REVERT: E 86 ARG cc_start: 0.9047 (mtm-85) cc_final: 0.8622 (mtm-85) REVERT: E 90 ARG cc_start: 0.8852 (mtm-85) cc_final: 0.8545 (mtm-85) REVERT: E 103 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8356 (mp10) REVERT: E 116 LYS cc_start: 0.8992 (mmpt) cc_final: 0.8686 (mmtp) REVERT: E 126 PHE cc_start: 0.8868 (m-80) cc_final: 0.8645 (m-80) REVERT: F 76 MET cc_start: 0.9410 (tpt) cc_final: 0.8967 (mmm) REVERT: F 335 MET cc_start: 0.9057 (mmm) cc_final: 0.8838 (mmm) REVERT: G 3 THR cc_start: 0.9359 (OUTLIER) cc_final: 0.9061 (t) REVERT: G 9 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8275 (mppt) REVERT: G 902 ASP cc_start: 0.6833 (p0) cc_final: 0.6414 (p0) REVERT: H 34 PHE cc_start: 0.8172 (t80) cc_final: 0.7969 (t80) REVERT: H 36 GLU cc_start: 0.8952 (tt0) cc_final: 0.8456 (tm-30) REVERT: H 38 ARG cc_start: 0.8784 (mtp180) cc_final: 0.8399 (mtp180) REVERT: H 72 ASP cc_start: 0.7704 (t70) cc_final: 0.7352 (t70) REVERT: H 80 ARG cc_start: 0.8158 (ttp-110) cc_final: 0.7496 (tmt170) REVERT: H 140 LYS cc_start: 0.8608 (tptt) cc_final: 0.8157 (tptp) REVERT: H 214 GLN cc_start: 0.8418 (mt0) cc_final: 0.8143 (pt0) REVERT: J 73 MET cc_start: 0.8903 (mtp) cc_final: 0.8677 (mtp) REVERT: J 146 MET cc_start: 0.9232 (mmt) cc_final: 0.9024 (mmm) REVERT: L 194 THR cc_start: 0.8289 (p) cc_final: 0.8087 (t) REVERT: L 243 MET cc_start: 0.9040 (mmp) cc_final: 0.8743 (mmp) REVERT: L 313 MET cc_start: 0.8952 (ttm) cc_final: 0.8552 (ttp) REVERT: L 365 MET cc_start: 0.8320 (mtt) cc_final: 0.8058 (mtp) REVERT: L 449 LYS cc_start: 0.8412 (pttt) cc_final: 0.8001 (tptp) REVERT: L 476 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8379 (pt0) REVERT: L 529 ARG cc_start: 0.7959 (mtt180) cc_final: 0.7575 (mtm180) REVERT: L 562 ARG cc_start: 0.8133 (mtp180) cc_final: 0.7773 (mtt90) REVERT: M 22 ARG cc_start: 0.8839 (ptm160) cc_final: 0.7018 (mmp-170) REVERT: M 121 MET cc_start: 0.9214 (mmp) cc_final: 0.8924 (mmm) REVERT: M 136 MET cc_start: 0.9170 (mmm) cc_final: 0.8871 (mmm) REVERT: M 234 LYS cc_start: 0.8817 (tttt) cc_final: 0.8530 (tmtm) REVERT: M 264 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8822 (mm) REVERT: M 303 TRP cc_start: 0.9505 (OUTLIER) cc_final: 0.7774 (m-10) REVERT: M 408 PHE cc_start: 0.9253 (OUTLIER) cc_final: 0.8750 (m-80) REVERT: M 455 GLN cc_start: 0.8678 (pt0) cc_final: 0.8091 (pt0) REVERT: N 30 TRP cc_start: 0.8750 (t-100) cc_final: 0.8509 (t-100) REVERT: N 197 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.8099 (mtp) REVERT: N 427 ARG cc_start: 0.8248 (mtm110) cc_final: 0.7985 (ttp-110) outliers start: 80 outliers final: 32 residues processed: 526 average time/residue: 0.7761 time to fit residues: 484.6239 Evaluate side-chains 498 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 456 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 833 SER Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 476 GLN Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 408 PHE Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 443 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 461 optimal weight: 0.9980 chunk 382 optimal weight: 0.7980 chunk 349 optimal weight: 0.8980 chunk 399 optimal weight: 0.8980 chunk 197 optimal weight: 2.9990 chunk 253 optimal weight: 0.8980 chunk 245 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 212 optimal weight: 5.9990 chunk 377 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 58 ASN C 186 GLN F 237 GLN F 425 GLN G 853 ASN J 115 ASN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.073815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.060166 restraints weight = 50101.449| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.24 r_work: 0.2895 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9065 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.246 38502 Z= 0.390 Angle : 2.502 52.883 52293 Z= 1.431 Chirality : 0.441 6.421 5820 Planarity : 0.004 0.056 6552 Dihedral : 7.992 104.396 5568 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.19 % Allowed : 12.14 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.12), residues: 4710 helix: 1.88 (0.10), residues: 2652 sheet: -0.35 (0.28), residues: 312 loop : -0.29 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 373 TYR 0.025 0.002 TYR M 435 PHE 0.028 0.001 PHE L 341 TRP 0.016 0.001 TRP C 382 HIS 0.005 0.001 HIS G 99 Details of bonding type rmsd/Z covalent geometry : bond 0.01137 / 0.39 (38465) covalent geometry : angle 2.16610 / 1.43 (52197) hydrogen bonds : bond 0.04604 / 3.05 ( 2167) hydrogen bonds : angle 4.50766 / 3.18 ( 6180) metal coordination : bond 0.03199 / 2.33 ( 37) metal coordination : angle 29.32839 / 22.02 ( 96) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 462 time to evaluate : 1.473 Fit side-chains revert: symmetry clash REVERT: B 45 MET cc_start: 0.9016 (ttp) cc_final: 0.8732 (ttp) REVERT: B 89 SER cc_start: 0.8356 (t) cc_final: 0.8016 (p) REVERT: B 126 MET cc_start: 0.9288 (ttt) cc_final: 0.9073 (ttt) REVERT: C 76 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8789 (tpp) REVERT: C 250 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.7526 (ptp-170) REVERT: C 324 GLN cc_start: 0.8754 (tt0) cc_final: 0.8463 (tt0) REVERT: C 336 PHE cc_start: 0.7045 (t80) cc_final: 0.6256 (t80) REVERT: C 338 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8267 (m-30) REVERT: C 383 MET cc_start: 0.8569 (mmm) cc_final: 0.8345 (mmm) REVERT: C 591 MET cc_start: 0.9295 (mmm) cc_final: 0.8900 (mmm) REVERT: E 47 ARG cc_start: 0.8750 (mmt-90) cc_final: 0.8478 (mpt180) REVERT: E 86 ARG cc_start: 0.9055 (mtm-85) cc_final: 0.8731 (mtm-85) REVERT: E 90 ARG cc_start: 0.8875 (mtm-85) cc_final: 0.8561 (mtm-85) REVERT: E 103 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8369 (mp10) REVERT: E 116 LYS cc_start: 0.8999 (mmpt) cc_final: 0.8691 (mmtp) REVERT: E 126 PHE cc_start: 0.8884 (m-80) cc_final: 0.8633 (m-80) REVERT: E 166 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8124 (mmtp) REVERT: F 6 ARG cc_start: 0.8508 (mtm-85) cc_final: 0.8244 (ttm-80) REVERT: F 76 MET cc_start: 0.9412 (OUTLIER) cc_final: 0.8948 (mmm) REVERT: F 335 MET cc_start: 0.9017 (mmm) cc_final: 0.8806 (mmm) REVERT: G 3 THR cc_start: 0.9359 (OUTLIER) cc_final: 0.9098 (t) REVERT: G 9 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8278 (mppt) REVERT: G 853 ASN cc_start: 0.8710 (m-40) cc_final: 0.8479 (m110) REVERT: G 902 ASP cc_start: 0.6714 (p0) cc_final: 0.6455 (p0) REVERT: H 34 PHE cc_start: 0.8298 (t80) cc_final: 0.8078 (t80) REVERT: H 36 GLU cc_start: 0.8944 (tt0) cc_final: 0.8457 (tm-30) REVERT: H 38 ARG cc_start: 0.8798 (mtp180) cc_final: 0.8368 (mtp180) REVERT: H 72 ASP cc_start: 0.7720 (t70) cc_final: 0.7372 (t70) REVERT: H 80 ARG cc_start: 0.8188 (ttp-110) cc_final: 0.7511 (tmt170) REVERT: H 285 ILE cc_start: 0.9223 (mt) cc_final: 0.8993 (mp) REVERT: H 295 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8285 (m-30) REVERT: J 73 MET cc_start: 0.8935 (mtp) cc_final: 0.8704 (mtp) REVERT: J 146 MET cc_start: 0.9233 (mmt) cc_final: 0.8959 (mmm) REVERT: L 313 MET cc_start: 0.8979 (ttm) cc_final: 0.8573 (ttp) REVERT: L 365 MET cc_start: 0.8387 (mtt) cc_final: 0.8111 (mtp) REVERT: L 449 LYS cc_start: 0.8452 (pttt) cc_final: 0.8062 (tptm) REVERT: L 476 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8380 (pt0) REVERT: L 495 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.9098 (mp) REVERT: L 529 ARG cc_start: 0.7966 (mtt180) cc_final: 0.7578 (mtm180) REVERT: L 562 ARG cc_start: 0.8152 (mtp180) cc_final: 0.7773 (mtt90) REVERT: M 22 ARG cc_start: 0.8864 (ptm160) cc_final: 0.7069 (mmt180) REVERT: M 136 MET cc_start: 0.9191 (mmm) cc_final: 0.8855 (mmm) REVERT: M 234 LYS cc_start: 0.8830 (tttt) cc_final: 0.8558 (tmtt) REVERT: M 264 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8776 (mm) REVERT: M 303 TRP cc_start: 0.9513 (OUTLIER) cc_final: 0.7814 (m-10) REVERT: M 408 PHE cc_start: 0.9268 (OUTLIER) cc_final: 0.8711 (m-80) REVERT: M 455 GLN cc_start: 0.8698 (pt0) cc_final: 0.8108 (pt0) REVERT: N 30 TRP cc_start: 0.8774 (t-100) cc_final: 0.8532 (t-100) REVERT: N 197 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8056 (mtp) REVERT: N 207 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8250 (t80) REVERT: N 443 ASP cc_start: 0.7676 (OUTLIER) cc_final: 0.7456 (m-30) outliers start: 85 outliers final: 36 residues processed: 514 average time/residue: 0.7673 time to fit residues: 468.1885 Evaluate side-chains 510 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 457 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 21 GLU Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 276 LYS Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 826 GLN Chi-restraints excluded: chain G residue 833 SER Chi-restraints excluded: chain G residue 866 THR Chi-restraints excluded: chain G residue 868 THR Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 476 GLN Chi-restraints excluded: chain L residue 495 ILE Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 408 PHE Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 443 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 297 optimal weight: 1.9990 chunk 261 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 chunk 230 optimal weight: 0.8980 chunk 362 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 175 optimal weight: 0.1980 chunk 383 optimal weight: 1.9990 chunk 319 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 152 optimal weight: 0.2980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 74 HIS C 186 GLN F 237 GLN J 115 ASN K 82 GLN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.074390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.060801 restraints weight = 50001.824| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 1.24 r_work: 0.2911 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9051 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.244 38502 Z= 0.385 Angle : 2.496 50.602 52293 Z= 1.429 Chirality : 0.441 6.459 5820 Planarity : 0.004 0.053 6552 Dihedral : 7.815 105.255 5568 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.91 % Allowed : 12.81 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.12), residues: 4710 helix: 1.96 (0.10), residues: 2649 sheet: -0.24 (0.28), residues: 320 loop : -0.28 (0.15), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 373 TYR 0.024 0.001 TYR M 435 PHE 0.028 0.001 PHE L 341 TRP 0.017 0.001 TRP C 382 HIS 0.004 0.001 HIS C 74 Details of bonding type rmsd/Z covalent geometry : bond 0.01128 / 0.38 (38465) covalent geometry : angle 2.16162 / 1.43 (52197) hydrogen bonds : bond 0.04317 / 2.86 ( 2167) hydrogen bonds : angle 4.42473 / 3.12 ( 6180) metal coordination : bond 0.02636 / 1.84 ( 37) metal coordination : angle 29.22703 / 21.92 ( 96) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 473 time to evaluate : 1.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.9005 (ttp) cc_final: 0.8669 (ttp) REVERT: B 62 SER cc_start: 0.8080 (m) cc_final: 0.7827 (t) REVERT: B 89 SER cc_start: 0.8320 (t) cc_final: 0.7980 (p) REVERT: B 126 MET cc_start: 0.9294 (ttt) cc_final: 0.9076 (ttt) REVERT: C 76 MET cc_start: 0.9071 (OUTLIER) cc_final: 0.8739 (tpp) REVERT: C 199 GLU cc_start: 0.8174 (mp0) cc_final: 0.7734 (mp0) REVERT: C 324 GLN cc_start: 0.8748 (tt0) cc_final: 0.8480 (tt0) REVERT: C 336 PHE cc_start: 0.7106 (t80) cc_final: 0.6390 (t80) REVERT: C 338 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8244 (m-30) REVERT: C 565 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9031 (mp) REVERT: C 591 MET cc_start: 0.9300 (mmm) cc_final: 0.8915 (mmp) REVERT: E 47 ARG cc_start: 0.8727 (mmt-90) cc_final: 0.8438 (mpt180) REVERT: E 86 ARG cc_start: 0.9057 (mtm-85) cc_final: 0.8709 (mtm-85) REVERT: E 90 ARG cc_start: 0.8831 (mtm-85) cc_final: 0.8527 (mtm-85) REVERT: E 95 VAL cc_start: 0.9114 (OUTLIER) cc_final: 0.8878 (t) REVERT: E 103 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8359 (mp10) REVERT: E 116 LYS cc_start: 0.8997 (mmpt) cc_final: 0.8682 (mmtp) REVERT: E 126 PHE cc_start: 0.8858 (m-80) cc_final: 0.8598 (m-80) REVERT: E 166 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.8111 (mmtp) REVERT: F 6 ARG cc_start: 0.8513 (mtm-85) cc_final: 0.8308 (ttm-80) REVERT: G 3 THR cc_start: 0.9360 (OUTLIER) cc_final: 0.9094 (t) REVERT: G 9 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8252 (mppt) REVERT: G 853 ASN cc_start: 0.8713 (m-40) cc_final: 0.8489 (m110) REVERT: G 888 MET cc_start: 0.8082 (mmm) cc_final: 0.7724 (mmt) REVERT: G 902 ASP cc_start: 0.6758 (p0) cc_final: 0.6442 (p0) REVERT: H 34 PHE cc_start: 0.8269 (t80) cc_final: 0.8042 (t80) REVERT: H 36 GLU cc_start: 0.8974 (tt0) cc_final: 0.8544 (tm-30) REVERT: H 38 ARG cc_start: 0.8713 (mtp180) cc_final: 0.8287 (mtp180) REVERT: H 72 ASP cc_start: 0.7689 (t70) cc_final: 0.7329 (t70) REVERT: H 80 ARG cc_start: 0.8196 (ttp-110) cc_final: 0.7521 (tmt170) REVERT: H 285 ILE cc_start: 0.9208 (mt) cc_final: 0.8969 (mp) REVERT: H 295 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.8254 (m-30) REVERT: J 73 MET cc_start: 0.8913 (mtp) cc_final: 0.8684 (mtp) REVERT: J 146 MET cc_start: 0.9283 (mmt) cc_final: 0.9017 (mmm) REVERT: L 243 MET cc_start: 0.9113 (mmp) cc_final: 0.8858 (mmp) REVERT: L 313 MET cc_start: 0.8976 (ttm) cc_final: 0.8575 (ttp) REVERT: L 365 MET cc_start: 0.8293 (mtt) cc_final: 0.8010 (mtp) REVERT: L 449 LYS cc_start: 0.8339 (pttt) cc_final: 0.7975 (tptp) REVERT: L 476 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8364 (pt0) REVERT: L 495 ILE cc_start: 0.9420 (OUTLIER) cc_final: 0.9117 (mp) REVERT: L 529 ARG cc_start: 0.7959 (mtt180) cc_final: 0.7564 (mtm180) REVERT: L 562 ARG cc_start: 0.8102 (mtp180) cc_final: 0.7728 (mtt90) REVERT: M 16 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8954 (mp) REVERT: M 22 ARG cc_start: 0.8865 (ptm160) cc_final: 0.7055 (mmt180) REVERT: M 136 MET cc_start: 0.9173 (mmm) cc_final: 0.8845 (mmm) REVERT: M 234 LYS cc_start: 0.8817 (tttt) cc_final: 0.8554 (tmtt) REVERT: M 303 TRP cc_start: 0.9506 (OUTLIER) cc_final: 0.7766 (m-10) REVERT: M 408 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.8772 (m-80) REVERT: M 455 GLN cc_start: 0.8702 (pt0) cc_final: 0.8116 (pt0) REVERT: N 30 TRP cc_start: 0.8769 (t-100) cc_final: 0.8436 (t-100) REVERT: N 197 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8156 (mtp) REVERT: N 207 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8250 (t80) REVERT: N 427 ARG cc_start: 0.8235 (mtm110) cc_final: 0.7983 (ttp-110) REVERT: N 443 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7467 (m-30) outliers start: 74 outliers final: 34 residues processed: 520 average time/residue: 0.7594 time to fit residues: 469.4062 Evaluate side-chains 506 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 455 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 565 LEU Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 826 GLN Chi-restraints excluded: chain G residue 833 SER Chi-restraints excluded: chain G residue 868 THR Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 476 GLN Chi-restraints excluded: chain L residue 495 ILE Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 408 PHE Chi-restraints excluded: chain M residue 462 LEU Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 443 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 229 optimal weight: 1.9990 chunk 225 optimal weight: 0.2980 chunk 428 optimal weight: 0.9990 chunk 65 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 170 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 412 optimal weight: 0.7980 chunk 150 optimal weight: 0.0010 chunk 86 optimal weight: 0.8980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 58 ASN C 186 GLN F 237 GLN J 115 ASN L 163 ASN ** L 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.074684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.061104 restraints weight = 50153.136| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.24 r_work: 0.2918 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9048 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.246 38502 Z= 0.384 Angle : 2.496 50.591 52293 Z= 1.429 Chirality : 0.440 6.414 5820 Planarity : 0.004 0.048 6552 Dihedral : 7.667 105.074 5568 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.86 % Allowed : 13.04 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.12), residues: 4710 helix: 2.00 (0.10), residues: 2652 sheet: -0.18 (0.28), residues: 320 loop : -0.26 (0.15), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 293 TYR 0.024 0.001 TYR M 435 PHE 0.027 0.001 PHE L 341 TRP 0.017 0.001 TRP C 382 HIS 0.004 0.001 HIS G 99 Details of bonding type rmsd/Z covalent geometry : bond 0.01127 / 0.38 (38465) covalent geometry : angle 2.16176 / 1.43 (52197) hydrogen bonds : bond 0.04200 / 2.78 ( 2167) hydrogen bonds : angle 4.36946 / 3.08 ( 6180) metal coordination : bond 0.02686 / 1.87 ( 37) metal coordination : angle 29.21206 / 21.91 ( 96) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 467 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 45 MET cc_start: 0.9025 (ttp) cc_final: 0.8727 (ttp) REVERT: B 89 SER cc_start: 0.8316 (t) cc_final: 0.7965 (p) REVERT: B 126 MET cc_start: 0.9280 (ttt) cc_final: 0.9064 (ttt) REVERT: B 197 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8638 (mtm) REVERT: C 76 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8754 (tpp) REVERT: C 199 GLU cc_start: 0.8074 (mp0) cc_final: 0.7694 (mp0) REVERT: C 324 GLN cc_start: 0.8713 (tt0) cc_final: 0.8439 (tt0) REVERT: C 336 PHE cc_start: 0.7211 (t80) cc_final: 0.6496 (t80) REVERT: C 591 MET cc_start: 0.9307 (mmm) cc_final: 0.8929 (mmm) REVERT: E 47 ARG cc_start: 0.8729 (mmt-90) cc_final: 0.8524 (mpt180) REVERT: E 86 ARG cc_start: 0.9054 (mtm-85) cc_final: 0.8689 (mtm-85) REVERT: E 90 ARG cc_start: 0.8825 (mtm-85) cc_final: 0.8469 (mtt180) REVERT: E 95 VAL cc_start: 0.9090 (OUTLIER) cc_final: 0.8853 (t) REVERT: E 103 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8362 (mp10) REVERT: E 116 LYS cc_start: 0.8992 (mmpt) cc_final: 0.8668 (mmtp) REVERT: E 126 PHE cc_start: 0.8816 (m-80) cc_final: 0.8553 (m-80) REVERT: E 166 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8132 (mmtp) REVERT: F 373 ARG cc_start: 0.8168 (ttp-110) cc_final: 0.7810 (mtm-85) REVERT: G 3 THR cc_start: 0.9354 (OUTLIER) cc_final: 0.9098 (t) REVERT: G 9 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8257 (mppt) REVERT: G 738 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8308 (ptp) REVERT: G 853 ASN cc_start: 0.8720 (m-40) cc_final: 0.8506 (m110) REVERT: G 888 MET cc_start: 0.8078 (mmm) cc_final: 0.7704 (mmt) REVERT: G 902 ASP cc_start: 0.6669 (p0) cc_final: 0.6352 (p0) REVERT: H 34 PHE cc_start: 0.8235 (t80) cc_final: 0.8021 (t80) REVERT: H 36 GLU cc_start: 0.8988 (tt0) cc_final: 0.8567 (tm-30) REVERT: H 38 ARG cc_start: 0.8728 (mtp180) cc_final: 0.8278 (mtp180) REVERT: H 72 ASP cc_start: 0.7650 (t70) cc_final: 0.7335 (t70) REVERT: H 80 ARG cc_start: 0.8215 (ttp-110) cc_final: 0.7530 (tmt170) REVERT: H 285 ILE cc_start: 0.9233 (mt) cc_final: 0.8981 (mp) REVERT: H 295 ASP cc_start: 0.8536 (OUTLIER) cc_final: 0.8284 (m-30) REVERT: J 73 MET cc_start: 0.8877 (mtp) cc_final: 0.8676 (mtp) REVERT: J 146 MET cc_start: 0.9251 (mmt) cc_final: 0.8976 (mmm) REVERT: L 313 MET cc_start: 0.8943 (ttm) cc_final: 0.8529 (ttp) REVERT: L 365 MET cc_start: 0.8225 (mtt) cc_final: 0.7954 (mtp) REVERT: L 449 LYS cc_start: 0.8300 (pttt) cc_final: 0.7937 (tptp) REVERT: L 476 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8349 (pt0) REVERT: L 495 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9092 (mp) REVERT: L 529 ARG cc_start: 0.7964 (mtt180) cc_final: 0.7699 (mtt90) REVERT: L 562 ARG cc_start: 0.8097 (mtp180) cc_final: 0.7718 (mtt90) REVERT: M 16 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8973 (mp) REVERT: M 22 ARG cc_start: 0.8837 (ptm160) cc_final: 0.7036 (mmt180) REVERT: M 136 MET cc_start: 0.9169 (mmm) cc_final: 0.8828 (mmm) REVERT: M 234 LYS cc_start: 0.8812 (tttt) cc_final: 0.8554 (tmtt) REVERT: M 264 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8829 (mm) REVERT: M 303 TRP cc_start: 0.9502 (OUTLIER) cc_final: 0.7763 (m-10) REVERT: M 408 PHE cc_start: 0.9254 (OUTLIER) cc_final: 0.8769 (m-80) REVERT: M 455 GLN cc_start: 0.8669 (pt0) cc_final: 0.8077 (pt0) REVERT: N 30 TRP cc_start: 0.8769 (t-100) cc_final: 0.8513 (t-100) REVERT: N 197 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.8139 (mtp) REVERT: N 207 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8263 (t80) REVERT: N 427 ARG cc_start: 0.8226 (mtm110) cc_final: 0.7970 (ttp-110) REVERT: N 443 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7474 (m-30) outliers start: 72 outliers final: 38 residues processed: 509 average time/residue: 0.7457 time to fit residues: 451.1313 Evaluate side-chains 513 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 457 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 732 THR Chi-restraints excluded: chain G residue 738 MET Chi-restraints excluded: chain G residue 826 GLN Chi-restraints excluded: chain G residue 833 SER Chi-restraints excluded: chain G residue 868 THR Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain L residue 372 ILE Chi-restraints excluded: chain L residue 476 GLN Chi-restraints excluded: chain L residue 495 ILE Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 145 MET Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain M residue 408 PHE Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 443 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 438 optimal weight: 2.9990 chunk 193 optimal weight: 5.9990 chunk 290 optimal weight: 1.9990 chunk 457 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 359 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 369 optimal weight: 1.9990 chunk 464 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 58 ASN C 186 GLN C 355 HIS F 237 GLN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 653 HIS G 671 HIS J 115 ASN K 82 GLN K 88 GLN ** L 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 446 HIS L 524 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.071844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.058126 restraints weight = 49754.900| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.23 r_work: 0.2851 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9096 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.245 38502 Z= 0.419 Angle : 2.514 52.090 52293 Z= 1.437 Chirality : 0.443 6.471 5820 Planarity : 0.004 0.054 6552 Dihedral : 8.005 99.681 5568 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.48 % Favored : 97.49 % Rotamer: Outliers : 1.88 % Allowed : 13.12 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.12), residues: 4710 helix: 1.77 (0.10), residues: 2653 sheet: -0.34 (0.28), residues: 317 loop : -0.28 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 47 TYR 0.024 0.002 TYR M 197 PHE 0.025 0.002 PHE L 341 TRP 0.013 0.001 TRP N 367 HIS 0.008 0.001 HIS C 315 Details of bonding type rmsd/Z covalent geometry : bond 0.01193 / 0.42 (38465) covalent geometry : angle 2.18154 / 1.43 (52197) hydrogen bonds : bond 0.05256 / 3.50 ( 2167) hydrogen bonds : angle 4.60080 / 3.24 ( 6180) metal coordination : bond 0.03890 / 2.82 ( 37) metal coordination : angle 29.23838 / 21.90 ( 96) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 467 time to evaluate : 1.384 Fit side-chains REVERT: B 45 MET cc_start: 0.9020 (ttp) cc_final: 0.8688 (ttp) REVERT: B 89 SER cc_start: 0.8515 (t) cc_final: 0.8143 (p) REVERT: B 126 MET cc_start: 0.9269 (ttt) cc_final: 0.9026 (ttt) REVERT: B 197 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8651 (mtm) REVERT: C 76 MET cc_start: 0.9125 (OUTLIER) cc_final: 0.8685 (tpp) REVERT: C 199 GLU cc_start: 0.8050 (mp0) cc_final: 0.7654 (mp0) REVERT: C 250 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.7843 (ptp-170) REVERT: C 324 GLN cc_start: 0.8769 (tt0) cc_final: 0.8447 (tt0) REVERT: C 336 PHE cc_start: 0.7237 (t80) cc_final: 0.6546 (t80) REVERT: C 392 LYS cc_start: 0.7787 (tmmt) cc_final: 0.7385 (tptp) REVERT: E 47 ARG cc_start: 0.8758 (mmt-90) cc_final: 0.8481 (mpt180) REVERT: E 86 ARG cc_start: 0.9088 (mtm-85) cc_final: 0.8707 (mtm-85) REVERT: E 90 ARG cc_start: 0.8831 (mtm-85) cc_final: 0.8565 (mtt90) REVERT: E 103 GLN cc_start: 0.8822 (OUTLIER) cc_final: 0.8403 (mp10) REVERT: E 116 LYS cc_start: 0.9000 (mtpt) cc_final: 0.8704 (mmtp) REVERT: E 166 LYS cc_start: 0.8490 (OUTLIER) cc_final: 0.8171 (mmtp) REVERT: F 373 ARG cc_start: 0.8158 (ttp-110) cc_final: 0.7806 (mtm-85) REVERT: G 3 THR cc_start: 0.9356 (OUTLIER) cc_final: 0.9121 (t) REVERT: G 9 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8283 (mppt) REVERT: G 738 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8298 (ptp) REVERT: G 853 ASN cc_start: 0.8752 (m-40) cc_final: 0.8528 (m110) REVERT: G 888 MET cc_start: 0.8175 (mmm) cc_final: 0.7872 (mmt) REVERT: G 902 ASP cc_start: 0.6921 (p0) cc_final: 0.6615 (p0) REVERT: H 27 THR cc_start: 0.9129 (m) cc_final: 0.8915 (p) REVERT: H 36 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8607 (tm-30) REVERT: H 38 ARG cc_start: 0.8738 (mtp180) cc_final: 0.8289 (mtp180) REVERT: H 80 ARG cc_start: 0.8265 (ttp-110) cc_final: 0.7565 (tmt170) REVERT: H 281 MET cc_start: 0.8081 (tpp) cc_final: 0.7855 (mpp) REVERT: H 285 ILE cc_start: 0.9196 (mt) cc_final: 0.8950 (mp) REVERT: H 295 ASP cc_start: 0.8589 (OUTLIER) cc_final: 0.8345 (m-30) REVERT: J 73 MET cc_start: 0.9057 (mtp) cc_final: 0.8833 (mtp) REVERT: J 146 MET cc_start: 0.9257 (mmt) cc_final: 0.8911 (mmt) REVERT: K 44 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8666 (tp) REVERT: L 313 MET cc_start: 0.9026 (ttm) cc_final: 0.8621 (ttp) REVERT: L 365 MET cc_start: 0.8502 (mtt) cc_final: 0.8293 (mtt) REVERT: L 449 LYS cc_start: 0.8566 (pttt) cc_final: 0.8135 (tptp) REVERT: L 495 ILE cc_start: 0.9375 (OUTLIER) cc_final: 0.9063 (mp) REVERT: L 529 ARG cc_start: 0.7922 (mtt180) cc_final: 0.7699 (mtt90) REVERT: L 562 ARG cc_start: 0.8143 (mtp180) cc_final: 0.7747 (mtt90) REVERT: M 16 LEU cc_start: 0.9177 (OUTLIER) cc_final: 0.8969 (mp) REVERT: M 22 ARG cc_start: 0.8904 (ptm160) cc_final: 0.7064 (mmt180) REVERT: M 66 GLU cc_start: 0.8888 (pt0) cc_final: 0.8673 (pt0) REVERT: M 136 MET cc_start: 0.9200 (mmm) cc_final: 0.8791 (mmm) REVERT: M 234 LYS cc_start: 0.8831 (tttt) cc_final: 0.8533 (tmtt) REVERT: M 264 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8903 (mm) REVERT: M 303 TRP cc_start: 0.9521 (OUTLIER) cc_final: 0.7925 (m-10) REVERT: M 455 GLN cc_start: 0.8675 (pt0) cc_final: 0.8079 (pt0) REVERT: N 30 TRP cc_start: 0.8791 (t-100) cc_final: 0.8541 (t-100) REVERT: N 197 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.8187 (mtp) REVERT: N 427 ARG cc_start: 0.8277 (mtm110) cc_final: 0.7996 (ttp-110) REVERT: N 443 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7448 (m-30) outliers start: 73 outliers final: 35 residues processed: 508 average time/residue: 0.7651 time to fit residues: 458.2718 Evaluate side-chains 508 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 456 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 39 MET Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain C residue 76 MET Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain E residue 166 LYS Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 252 PHE Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 334 GLU Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 738 MET Chi-restraints excluded: chain G residue 826 GLN Chi-restraints excluded: chain G residue 833 SER Chi-restraints excluded: chain G residue 868 THR Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain I residue 77 LEU Chi-restraints excluded: chain I residue 83 LYS Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain L residue 150 SER Chi-restraints excluded: chain L residue 495 ILE Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain L residue 585 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 401 VAL Chi-restraints excluded: chain N residue 443 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 428 optimal weight: 2.9990 chunk 310 optimal weight: 3.9990 chunk 189 optimal weight: 0.8980 chunk 88 optimal weight: 0.9980 chunk 330 optimal weight: 0.9990 chunk 216 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 29 optimal weight: 0.0030 chunk 152 optimal weight: 0.9990 chunk 294 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 58 ASN C 186 GLN C 224 HIS E 100 ASN F 237 GLN J 115 ASN K 27 ASN L 62 GLN ** L 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.073826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.060198 restraints weight = 50086.603| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.24 r_work: 0.2899 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9062 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.248 38502 Z= 0.386 Angle : 2.502 50.597 52293 Z= 1.431 Chirality : 0.440 6.447 5820 Planarity : 0.004 0.046 6552 Dihedral : 7.767 103.133 5568 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.25 % Favored : 97.73 % Rotamer: Outliers : 1.44 % Allowed : 14.02 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.12), residues: 4710 helix: 1.92 (0.10), residues: 2657 sheet: -0.27 (0.27), residues: 325 loop : -0.23 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 293 TYR 0.023 0.001 TYR M 197 PHE 0.027 0.001 PHE L 341 TRP 0.018 0.001 TRP C 382 HIS 0.004 0.001 HIS G 99 Details of bonding type rmsd/Z covalent geometry : bond 0.01130 / 0.39 (38465) covalent geometry : angle 2.16665 / 1.43 (52197) hydrogen bonds : bond 0.04417 / 2.93 ( 2167) hydrogen bonds : angle 4.43377 / 3.13 ( 6180) metal coordination : bond 0.02682 / 1.85 ( 37) metal coordination : angle 29.27482 / 21.98 ( 96) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 468 time to evaluate : 1.278 Fit side-chains REVERT: B 45 MET cc_start: 0.9011 (ttp) cc_final: 0.8697 (ttp) REVERT: B 89 SER cc_start: 0.8430 (t) cc_final: 0.8050 (p) REVERT: B 117 MET cc_start: 0.9213 (mtp) cc_final: 0.8895 (mtp) REVERT: B 126 MET cc_start: 0.9265 (ttt) cc_final: 0.9040 (ttt) REVERT: B 197 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8627 (mtm) REVERT: C 74 HIS cc_start: 0.9304 (OUTLIER) cc_final: 0.8987 (t-90) REVERT: C 199 GLU cc_start: 0.8045 (mp0) cc_final: 0.7638 (mp0) REVERT: C 324 GLN cc_start: 0.8703 (tt0) cc_final: 0.8392 (tt0) REVERT: C 336 PHE cc_start: 0.7181 (t80) cc_final: 0.6563 (t80) REVERT: C 392 LYS cc_start: 0.7855 (tmmt) cc_final: 0.7437 (tptp) REVERT: E 47 ARG cc_start: 0.8736 (mmt-90) cc_final: 0.8463 (mpt180) REVERT: E 86 ARG cc_start: 0.9081 (mtm-85) cc_final: 0.8862 (mtm-85) REVERT: E 90 ARG cc_start: 0.8886 (mtm-85) cc_final: 0.8653 (mtm-85) REVERT: E 95 VAL cc_start: 0.9124 (OUTLIER) cc_final: 0.8898 (t) REVERT: E 103 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8382 (mp10) REVERT: E 116 LYS cc_start: 0.8995 (mtpt) cc_final: 0.8662 (mmtp) REVERT: F 373 ARG cc_start: 0.8161 (ttp-110) cc_final: 0.7820 (mtm-85) REVERT: G 9 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8236 (mppt) REVERT: G 738 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8303 (ptp) REVERT: G 853 ASN cc_start: 0.8735 (m-40) cc_final: 0.8515 (m110) REVERT: G 888 MET cc_start: 0.8129 (mmm) cc_final: 0.7838 (mmt) REVERT: G 902 ASP cc_start: 0.6646 (p0) cc_final: 0.6360 (p0) REVERT: H 27 THR cc_start: 0.9064 (m) cc_final: 0.8850 (p) REVERT: H 36 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8493 (tt0) REVERT: H 38 ARG cc_start: 0.8714 (mtp180) cc_final: 0.8254 (mtp180) REVERT: H 72 ASP cc_start: 0.7694 (t70) cc_final: 0.7355 (t70) REVERT: H 80 ARG cc_start: 0.8247 (ttp-110) cc_final: 0.7576 (tmt170) REVERT: H 281 MET cc_start: 0.8026 (tpp) cc_final: 0.7746 (mpp) REVERT: H 285 ILE cc_start: 0.9208 (mt) cc_final: 0.8947 (mp) REVERT: H 295 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8298 (m-30) REVERT: J 73 MET cc_start: 0.8924 (mtp) cc_final: 0.8690 (mtp) REVERT: J 146 MET cc_start: 0.9263 (mmt) cc_final: 0.9016 (mmm) REVERT: L 243 MET cc_start: 0.9316 (mmp) cc_final: 0.8841 (mmt) REVERT: L 313 MET cc_start: 0.8969 (ttm) cc_final: 0.8585 (ttp) REVERT: L 449 LYS cc_start: 0.8361 (pttt) cc_final: 0.8021 (tptp) REVERT: L 495 ILE cc_start: 0.9401 (OUTLIER) cc_final: 0.9088 (mp) REVERT: L 529 ARG cc_start: 0.7892 (mtt180) cc_final: 0.7671 (mtt90) REVERT: L 562 ARG cc_start: 0.8053 (mtp180) cc_final: 0.7666 (mtt90) REVERT: M 16 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8945 (mp) REVERT: M 22 ARG cc_start: 0.8882 (ptm160) cc_final: 0.7027 (mmt180) REVERT: M 136 MET cc_start: 0.9174 (mmm) cc_final: 0.8897 (mmm) REVERT: M 234 LYS cc_start: 0.8798 (tttt) cc_final: 0.8549 (tmtt) REVERT: M 264 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8849 (mm) REVERT: M 303 TRP cc_start: 0.9510 (OUTLIER) cc_final: 0.7806 (m-10) REVERT: M 455 GLN cc_start: 0.8693 (pt0) cc_final: 0.8082 (pt0) REVERT: N 30 TRP cc_start: 0.8763 (t-100) cc_final: 0.8430 (t-100) REVERT: N 197 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8219 (mtp) REVERT: N 207 PHE cc_start: 0.9111 (OUTLIER) cc_final: 0.8143 (t80) REVERT: N 427 ARG cc_start: 0.8266 (mtm110) cc_final: 0.8034 (ttp-110) outliers start: 56 outliers final: 30 residues processed: 504 average time/residue: 0.7704 time to fit residues: 459.7089 Evaluate side-chains 497 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 453 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain C residue 74 HIS Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 382 TRP Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 738 MET Chi-restraints excluded: chain G residue 826 GLN Chi-restraints excluded: chain G residue 833 SER Chi-restraints excluded: chain G residue 868 THR Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain I residue 83 LYS Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain L residue 495 ILE Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 207 PHE Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 401 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 110 optimal weight: 0.6980 chunk 467 optimal weight: 1.9990 chunk 345 optimal weight: 2.9990 chunk 245 optimal weight: 4.9990 chunk 383 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 244 optimal weight: 0.9980 chunk 303 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 355 optimal weight: 1.9990 chunk 148 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 186 GLN C 224 HIS F 237 GLN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 115 ASN K 27 ASN K 88 GLN ** L 446 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.073445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.059783 restraints weight = 49868.151| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.24 r_work: 0.2889 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9069 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.245 38502 Z= 0.390 Angle : 2.503 50.619 52293 Z= 1.432 Chirality : 0.441 6.462 5820 Planarity : 0.004 0.044 6552 Dihedral : 7.716 101.418 5566 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.29 % Favored : 97.69 % Rotamer: Outliers : 1.31 % Allowed : 14.41 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.12), residues: 4710 helix: 1.91 (0.10), residues: 2665 sheet: -0.29 (0.27), residues: 330 loop : -0.22 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 293 TYR 0.025 0.002 TYR M 197 PHE 0.026 0.001 PHE L 341 TRP 0.015 0.001 TRP C 382 HIS 0.005 0.001 HIS C 224 Details of bonding type rmsd/Z covalent geometry : bond 0.01137 / 0.39 (38465) covalent geometry : angle 2.16918 / 1.43 (52197) hydrogen bonds : bond 0.04544 / 3.01 ( 2167) hydrogen bonds : angle 4.44233 / 3.14 ( 6180) metal coordination : bond 0.03252 / 2.19 ( 37) metal coordination : angle 29.23629 / 21.92 ( 96) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 457 time to evaluate : 1.352 Fit side-chains REVERT: B 89 SER cc_start: 0.8479 (t) cc_final: 0.8101 (p) REVERT: B 117 MET cc_start: 0.9228 (mtp) cc_final: 0.8899 (mtp) REVERT: B 126 MET cc_start: 0.9277 (ttt) cc_final: 0.9059 (ttt) REVERT: B 197 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8634 (mtm) REVERT: C 199 GLU cc_start: 0.8036 (mp0) cc_final: 0.7617 (mp0) REVERT: C 250 ARG cc_start: 0.8778 (OUTLIER) cc_final: 0.7506 (ptp-170) REVERT: C 324 GLN cc_start: 0.8700 (tt0) cc_final: 0.8392 (tt0) REVERT: C 336 PHE cc_start: 0.7193 (t80) cc_final: 0.6581 (t80) REVERT: C 392 LYS cc_start: 0.7827 (tmmt) cc_final: 0.7411 (tptp) REVERT: E 47 ARG cc_start: 0.8735 (mmt-90) cc_final: 0.8460 (mpt180) REVERT: E 86 ARG cc_start: 0.9076 (mtm-85) cc_final: 0.8828 (mtm-85) REVERT: E 90 ARG cc_start: 0.8888 (mtm-85) cc_final: 0.8573 (mtt90) REVERT: E 95 VAL cc_start: 0.9126 (OUTLIER) cc_final: 0.8890 (t) REVERT: E 103 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8371 (mp10) REVERT: E 116 LYS cc_start: 0.8997 (mtpt) cc_final: 0.8663 (mmtp) REVERT: F 373 ARG cc_start: 0.8153 (ttp-110) cc_final: 0.7817 (mtm-85) REVERT: G 3 THR cc_start: 0.9353 (OUTLIER) cc_final: 0.9115 (t) REVERT: G 9 LYS cc_start: 0.8825 (OUTLIER) cc_final: 0.8256 (mppt) REVERT: G 738 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8307 (ptp) REVERT: G 853 ASN cc_start: 0.8735 (m-40) cc_final: 0.8513 (m110) REVERT: G 888 MET cc_start: 0.8142 (mmm) cc_final: 0.7852 (mmt) REVERT: G 902 ASP cc_start: 0.6821 (p0) cc_final: 0.6513 (p0) REVERT: H 27 THR cc_start: 0.9070 (m) cc_final: 0.8852 (p) REVERT: H 36 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8638 (tm-30) REVERT: H 38 ARG cc_start: 0.8654 (mtp180) cc_final: 0.8316 (mtp180) REVERT: H 60 LEU cc_start: 0.8510 (mm) cc_final: 0.8307 (mp) REVERT: H 72 ASP cc_start: 0.7687 (t70) cc_final: 0.7365 (t70) REVERT: H 80 ARG cc_start: 0.8271 (ttp-110) cc_final: 0.7605 (tmt170) REVERT: H 157 GLU cc_start: 0.8703 (tt0) cc_final: 0.8478 (tt0) REVERT: H 281 MET cc_start: 0.8010 (tpp) cc_final: 0.7744 (mpp) REVERT: H 285 ILE cc_start: 0.9205 (mt) cc_final: 0.8948 (mp) REVERT: H 295 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8314 (m-30) REVERT: J 73 MET cc_start: 0.8949 (mtp) cc_final: 0.8720 (mtp) REVERT: J 146 MET cc_start: 0.9268 (mmt) cc_final: 0.9016 (mmm) REVERT: L 243 MET cc_start: 0.9319 (mmp) cc_final: 0.8908 (mmt) REVERT: L 313 MET cc_start: 0.8974 (ttm) cc_final: 0.8579 (ttp) REVERT: L 449 LYS cc_start: 0.8341 (pttt) cc_final: 0.8002 (tptp) REVERT: L 495 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9085 (mp) REVERT: L 529 ARG cc_start: 0.7885 (mtt180) cc_final: 0.7659 (mtt90) REVERT: L 562 ARG cc_start: 0.8088 (mtp180) cc_final: 0.7696 (mtt90) REVERT: M 16 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8962 (mp) REVERT: M 22 ARG cc_start: 0.8884 (ptm160) cc_final: 0.7030 (mmt180) REVERT: M 136 MET cc_start: 0.9185 (mmm) cc_final: 0.8909 (mmm) REVERT: M 234 LYS cc_start: 0.8812 (tttt) cc_final: 0.8573 (tmtt) REVERT: M 264 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8890 (mm) REVERT: M 303 TRP cc_start: 0.9521 (OUTLIER) cc_final: 0.7930 (m-10) REVERT: M 455 GLN cc_start: 0.8692 (pt0) cc_final: 0.8083 (pt0) REVERT: N 30 TRP cc_start: 0.8767 (t-100) cc_final: 0.8435 (t-100) REVERT: N 197 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8192 (mtp) REVERT: N 427 ARG cc_start: 0.8237 (mtm110) cc_final: 0.7983 (ttp-110) outliers start: 51 outliers final: 29 residues processed: 490 average time/residue: 0.7988 time to fit residues: 463.2594 Evaluate side-chains 496 residues out of total 3879 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 453 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain B residue 26 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 175 SER Chi-restraints excluded: chain B residue 197 MET Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 338 ASP Chi-restraints excluded: chain C residue 382 TRP Chi-restraints excluded: chain C residue 403 ARG Chi-restraints excluded: chain C residue 590 VAL Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 103 GLN Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 354 CYS Chi-restraints excluded: chain G residue 3 THR Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 111 ASN Chi-restraints excluded: chain G residue 157 CYS Chi-restraints excluded: chain G residue 617 ASP Chi-restraints excluded: chain G residue 738 MET Chi-restraints excluded: chain G residue 826 GLN Chi-restraints excluded: chain G residue 833 SER Chi-restraints excluded: chain G residue 868 THR Chi-restraints excluded: chain H residue 36 GLU Chi-restraints excluded: chain H residue 295 ASP Chi-restraints excluded: chain I residue 83 LYS Chi-restraints excluded: chain I residue 177 SER Chi-restraints excluded: chain K residue 46 PHE Chi-restraints excluded: chain L residue 495 ILE Chi-restraints excluded: chain L residue 542 ASP Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 100 LEU Chi-restraints excluded: chain M residue 235 MET Chi-restraints excluded: chain M residue 264 LEU Chi-restraints excluded: chain M residue 303 TRP Chi-restraints excluded: chain N residue 25 MET Chi-restraints excluded: chain N residue 197 MET Chi-restraints excluded: chain N residue 318 THR Chi-restraints excluded: chain N residue 401 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 469 random chunks: chunk 384 optimal weight: 0.0170 chunk 387 optimal weight: 0.7980 chunk 225 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 268 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 348 optimal weight: 4.9990 chunk 331 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 358 optimal weight: 0.1980 overall best weight: 0.7620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 58 ASN C 74 HIS C 186 GLN C 224 HIS F 237 GLN J 115 ASN K 27 ASN ** L 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 446 HIS M 308 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.073749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.060126 restraints weight = 49738.185| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.24 r_work: 0.2897 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9064 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.245 38502 Z= 0.388 Angle : 2.501 50.598 52293 Z= 1.431 Chirality : 0.441 6.522 5820 Planarity : 0.004 0.045 6552 Dihedral : 7.670 101.194 5566 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.06 % Favored : 97.92 % Rotamer: Outliers : 1.39 % Allowed : 14.36 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.39 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.12), residues: 4710 helix: 1.93 (0.10), residues: 2664 sheet: -0.27 (0.27), residues: 330 loop : -0.20 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 293 TYR 0.024 0.001 TYR M 197 PHE 0.027 0.001 PHE L 341 TRP 0.016 0.001 TRP C 382 HIS 0.005 0.001 HIS C 224 Details of bonding type rmsd/Z covalent geometry : bond 0.01132 / 0.39 (38465) covalent geometry : angle 2.16750 / 1.43 (52197) hydrogen bonds : bond 0.04437 / 2.94 ( 2167) hydrogen bonds : angle 4.42155 / 3.12 ( 6180) metal coordination : bond 0.03067 / 2.02 ( 37) metal coordination : angle 29.18453 / 21.82 ( 96) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15211.31 seconds wall clock time: 258 minutes 48.43 seconds (15528.43 seconds total)