Starting phenix.real_space_refine (version: 1.21rc1) on Sun Jul 16 16:10:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyr_12653/07_2023/7nyr_12653_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyr_12653/07_2023/7nyr_12653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyr_12653/07_2023/7nyr_12653.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyr_12653/07_2023/7nyr_12653.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyr_12653/07_2023/7nyr_12653_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nyr_12653/07_2023/7nyr_12653_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 1 9.91 5 Fe 32 7.16 5 P 1 5.49 5 S 243 5.16 5 C 22719 2.51 5 N 5962 2.21 5 O 6270 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 326": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 424": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 35228 Number of models: 1 Model: "" Number of chains: 18 Chain: "B" Number of atoms: 1222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1222 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 148} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 2, 'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 4725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4725 Classifications: {'peptide': 588} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 551} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 3424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3424 Classifications: {'peptide': 441} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 415} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CSX:plan-1': 1} Unresolved non-hydrogen planarities: 1 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: "I" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1220 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 13, 'TRANS': 144} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "K" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 760 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 1, 'TRANS': 98} Chain: "J" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1242 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 5, 'TRANS': 158} Chain: "A" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 668 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain breaks: 1 Unresolved non-hydrogen bonds: 65 Unresolved non-hydrogen angles: 86 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PHE:plan': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "H" Number of atoms: 1985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1985 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 13, 'TRANS': 256} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 137 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 3, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 86 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PTRANS': 21, 'TRANS': 482} Chain: "L" Number of atoms: 4126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4126 Classifications: {'peptide': 612} Incomplete info: {'truncation_to_alanine': 163} Link IDs: {'PTRANS': 18, 'TRANS': 593} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 592 Unresolved non-hydrogen angles: 777 Unresolved non-hydrogen dihedrals: 506 Unresolved non-hydrogen chiralities: 77 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 3, 'TYR:plan': 4, 'ASN:plan1': 5, 'TRP:plan': 6, 'HIS:plan': 8, 'PHE:plan': 11, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 268 Chain: "N" Number of atoms: 3543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3543 Classifications: {'peptide': 467} Link IDs: {'PTRANS': 19, 'TRANS': 447} Chain breaks: 2 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: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 29 Unusual residues: {' CA': 1, 'FES': 1, 'SF4': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 810 SG CYS B 158 176.319 106.819 74.265 1.00 26.83 S ATOM 181 SG CYS B 64 173.867 100.719 74.407 1.00 47.89 S ATOM 175 SG CYS B 63 170.823 104.024 71.208 1.00 53.71 S ATOM 593 SG CYS B 129 171.254 107.059 75.960 1.00 18.29 S ATOM 6594 SG CYS E 92 223.185 162.563 69.448 1.00 26.86 S ATOM 6628 SG CYS E 97 225.902 162.513 67.542 1.00 21.17 S ATOM 6907 SG CYS E 133 220.259 166.128 67.741 1.00 28.24 S ATOM 6933 SG CYS E 137 221.922 166.701 65.917 1.00 26.53 S ATOM 9934 SG CYS F 357 203.697 156.760 68.879 1.00 44.36 S ATOM 9914 SG CYS F 354 198.836 157.055 69.728 1.00 44.74 S ATOM 10255 SG CYS F 398 201.386 162.796 68.756 1.00 23.05 S ATOM 9890 SG CYS F 351 202.010 160.503 74.285 1.00 15.22 S ATOM 10951 SG CYS G 48 186.193 155.118 68.949 1.00 13.42 S ATOM 11100 SG CYS G 67 186.230 157.903 71.472 1.00 14.30 S ATOM 10849 SG CYS G 34 189.082 155.466 74.510 1.00 28.07 S ATOM 10925 SG CYS G 45 189.738 152.721 72.490 1.00 42.19 S ATOM 11831 SG CYS G 157 194.027 152.540 85.378 1.00 28.19 S ATOM 11783 SG CYS G 151 197.390 148.655 81.608 1.00 24.56 S ATOM 11802 SG CYS G 154 191.342 150.738 80.022 1.00 20.46 S ATOM 12179 SG CYS G 201 191.568 146.570 84.269 1.00 4.08 S ATOM 11408 SG CYS G 106 192.484 137.300 83.778 1.00 11.66 S ATOM 11388 SG CYS G 103 192.941 134.531 78.073 1.00 30.01 S ATOM 11448 SG CYS G 112 189.288 140.217 79.397 1.00 7.96 S ATOM 12428 SG CYS G 231 173.947 152.855 102.383 1.00 5.72 S ATOM 12452 SG CYS G 235 173.951 151.957 96.363 1.00 21.99 S ATOM 12404 SG CYS G 228 174.521 147.630 99.933 1.00 12.19 S ATOM 12689 SG CYS G 263 179.215 151.559 99.495 1.00 32.96 S ATOM 18292 SG CYS I 109 192.679 120.424 80.024 1.00 14.30 S ATOM 17915 SG CYS I 60 192.123 120.636 86.718 1.00 14.04 S ATOM 17955 SG CYS I 66 186.942 120.154 83.100 1.00 9.56 S ATOM 17933 SG CYS I 63 190.189 125.202 82.059 1.00 22.65 S ATOM 17978 SG CYS I 70 179.732 116.768 80.012 1.00 12.73 S ATOM 18245 SG CYS I 102 181.395 114.427 74.967 1.00 13.79 S ATOM 18220 SG CYS I 99 181.995 110.303 80.167 1.00 12.53 S ATOM 18263 SG CYS I 105 185.971 115.032 78.523 1.00 12.24 S Time building chain proxies: 16.63, per 1000 atoms: 0.47 Number of scatterers: 35228 At special positions: 0 Unit cell: (253.339, 211.694, 144.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 32 26.01 Ca 1 19.99 S 243 16.00 P 1 15.00 O 6270 8.00 N 5962 7.00 C 22719 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 - 3.50 Amino acid : False - 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: 15.04 Conformation dependent library (CDL) restraints added in 6.1 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1001 " pdb="FE1 FES G1001 " - pdb=" SG CYS G 48 " pdb="FE2 FES G1001 " - pdb=" SG CYS G 45 " pdb="FE1 FES G1001 " - pdb=" SG CYS G 67 " pdb="FE2 FES G1001 " - pdb=" SG CYS G 34 " pdb=" SF4 B 301 " pdb="FE1 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 129 " pdb="FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb="FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 501 " pdb="FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb="FE2 SF4 F 501 " - pdb=" SG CYS F 354 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 357 " pdb=" SF4 G1002 " pdb="FE3 SF4 G1002 " - pdb=" SG CYS G 154 " pdb="FE4 SF4 G1002 " - pdb=" SG CYS G 201 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 151 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 157 " pdb=" SF4 G1003 " pdb="FE3 SF4 G1003 " - pdb=" NE2 HIS G 99 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 112 " pdb="FE1 SF4 G1003 " - pdb=" SG CYS G 106 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 103 " pdb=" SF4 G1004 " pdb="FE4 SF4 G1004 " - pdb=" SG CYS G 263 " pdb="FE1 SF4 G1004 " - pdb=" SG CYS G 231 " pdb="FE2 SF4 G1004 " - pdb=" SG CYS G 235 " pdb="FE3 SF4 G1004 " - pdb=" SG CYS G 228 " pdb=" SF4 I 201 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 109 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 63 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 60 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 66 " pdb=" SF4 I 202 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 102 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 99 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 105 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 70 " Number of angles added : 93 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8440 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 197 helices and 22 sheets defined 52.7% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.71 Creating SS restraints... Processing helix chain 'B' and resid 45 through 52 Processing helix chain 'B' and resid 65 through 75 removed outlier: 3.771A pdb=" N ALA B 74 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 116 Processing helix chain 'B' and resid 128 through 131 No H-bonds generated for 'chain 'B' and resid 128 through 131' Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 162 through 176 Processing helix chain 'B' and resid 200 through 203 No H-bonds generated for 'chain 'B' and resid 200 through 203' Processing helix chain 'B' and resid 205 through 209 Processing helix chain 'D' and resid 20 through 29 Processing helix chain 'D' and resid 53 through 61 Processing helix chain 'D' and resid 128 through 140 removed outlier: 3.990A pdb=" N TRP D 132 " --> pdb=" O ASN D 129 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU D 140 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 182 through 192 removed outlier: 4.232A pdb=" N GLN D 186 " --> pdb=" O THR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 258 removed outlier: 3.807A pdb=" N GLU D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG D 258 " --> pdb=" O LYS D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 270 removed outlier: 3.853A pdb=" N ASP D 269 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ARG D 270 " --> pdb=" O PRO D 266 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 265 through 270' Processing helix chain 'D' and resid 277 through 291 Proline residue: D 282 - end of helix Processing helix chain 'D' and resid 297 through 325 Processing helix chain 'D' and resid 332 through 349 removed outlier: 3.897A pdb=" N GLU D 347 " --> pdb=" O ASP D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 395 Proline residue: D 384 - end of helix Processing helix chain 'D' and resid 399 through 403 Processing helix chain 'D' and resid 412 through 417 Processing helix chain 'D' and resid 423 through 426 No H-bonds generated for 'chain 'D' and resid 423 through 426' Processing helix chain 'D' and resid 434 through 437 No H-bonds generated for 'chain 'D' and resid 434 through 437' Processing helix chain 'D' and resid 443 through 445 No H-bonds generated for 'chain 'D' and resid 443 through 445' Processing helix chain 'D' and resid 459 through 482 Processing helix chain 'D' and resid 501 through 504 No H-bonds generated for 'chain 'D' and resid 501 through 504' Processing helix chain 'D' and resid 508 through 519 Processing helix chain 'D' and resid 560 through 571 removed outlier: 3.988A pdb=" N ILE D 568 " --> pdb=" O HIS D 564 " (cutoff:3.500A) Proline residue: D 569 - end of helix Processing helix chain 'D' and resid 577 through 586 Processing helix chain 'D' and resid 591 through 595 Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.893A pdb=" N HIS E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N HIS E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.495A pdb=" N ILE E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.125A pdb=" N HIS E 56 " --> pdb=" O ASP E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 95 through 100 Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 137 through 139 No H-bonds generated for 'chain 'E' and resid 137 through 139' Processing helix chain 'E' and resid 155 through 165 Proline residue: E 159 - end of helix Processing helix chain 'F' and resid 26 through 31 removed outlier: 3.577A pdb=" N SER F 31 " --> pdb=" O ASP F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 44 Processing helix chain 'F' and resid 47 through 57 Processing helix chain 'F' and resid 69 through 75 Processing helix chain 'F' and resid 100 through 107 removed outlier: 3.659A pdb=" N LEU F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 123 Processing helix chain 'F' and resid 137 through 150 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 178 through 181 Processing helix chain 'F' and resid 183 through 190 Processing helix chain 'F' and resid 209 through 211 No H-bonds generated for 'chain 'F' and resid 209 through 211' Processing helix chain 'F' and resid 219 through 231 removed outlier: 3.903A pdb=" N VAL F 225 " --> pdb=" O THR F 221 " (cutoff:3.500A) Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 270 through 275 Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 311 through 315 Processing helix chain 'F' and resid 335 through 348 Processing helix chain 'F' and resid 355 through 358 No H-bonds generated for 'chain 'F' and resid 355 through 358' Processing helix chain 'F' and resid 360 through 373 Processing helix chain 'F' and resid 380 through 390 Processing helix chain 'F' and resid 400 through 414 Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 416 through 421 Processing helix chain 'G' and resid 19 through 25 Processing helix chain 'G' and resid 82 through 98 removed outlier: 4.767A pdb=" N ASN G 98 " --> pdb=" O TRP G 94 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 105 No H-bonds generated for 'chain 'G' and resid 103 through 105' Processing helix chain 'G' and resid 113 through 121 Processing helix chain 'G' and resid 148 through 150 No H-bonds generated for 'chain 'G' and resid 148 through 150' Processing helix chain 'G' and resid 156 through 161 Processing helix chain 'G' and resid 176 through 178 No H-bonds generated for 'chain 'G' and resid 176 through 178' Processing helix chain 'G' and resid 195 through 200 Processing helix chain 'G' and resid 209 through 213 removed outlier: 3.597A pdb=" N GLU G 213 " --> pdb=" O LYS G 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 209 through 213' Processing helix chain 'G' and resid 218 through 220 No H-bonds generated for 'chain 'G' and resid 218 through 220' Processing helix chain 'G' and resid 264 through 268 Processing helix chain 'G' and resid 271 through 274 Processing helix chain 'G' and resid 295 through 308 Processing helix chain 'G' and resid 322 through 332 Processing helix chain 'G' and resid 343 through 358 Processing helix chain 'G' and resid 368 through 371 Processing helix chain 'G' and resid 387 through 407 removed outlier: 3.608A pdb=" N GLY G 399 " --> pdb=" O GLN G 395 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LYS G 400 " --> pdb=" O ALA G 396 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ALA G 401 " --> pdb=" O VAL G 397 " (cutoff:3.500A) Processing helix chain 'G' and resid 415 through 422 Processing helix chain 'G' and resid 451 through 465 Processing helix chain 'G' and resid 477 through 491 Processing helix chain 'G' and resid 502 through 504 No H-bonds generated for 'chain 'G' and resid 502 through 504' Processing helix chain 'G' and resid 507 through 522 Processing helix chain 'G' and resid 538 through 544 Processing helix chain 'G' and resid 549 through 557 Processing helix chain 'G' and resid 577 through 585 Processing helix chain 'G' and resid 599 through 601 No H-bonds generated for 'chain 'G' and resid 599 through 601' Processing helix chain 'G' and resid 613 through 615 No H-bonds generated for 'chain 'G' and resid 613 through 615' Processing helix chain 'G' and resid 648 through 661 Processing helix chain 'G' and resid 669 through 679 Processing helix chain 'G' and resid 681 through 688 removed outlier: 5.157A pdb=" N GLY G 685 " --> pdb=" O GLU G 682 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE G 686 " --> pdb=" O LEU G 683 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS G 687 " --> pdb=" O ALA G 684 " (cutoff:3.500A) Processing helix chain 'G' and resid 762 through 768 Processing helix chain 'G' and resid 825 through 827 No H-bonds generated for 'chain 'G' and resid 825 through 827' Processing helix chain 'G' and resid 829 through 834 removed outlier: 4.175A pdb=" N SER G 833 " --> pdb=" O VAL G 830 " (cutoff:3.500A) Processing helix chain 'G' and resid 844 through 850 Processing helix chain 'G' and resid 893 through 895 No H-bonds generated for 'chain 'G' and resid 893 through 895' Processing helix chain 'I' and resid 24 through 28 Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 128 through 130 No H-bonds generated for 'chain 'I' and resid 128 through 130' Processing helix chain 'I' and resid 134 through 137 No H-bonds generated for 'chain 'I' and resid 134 through 137' Processing helix chain 'I' and resid 150 through 153 No H-bonds generated for 'chain 'I' and resid 150 through 153' Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 52 Processing helix chain 'K' and resid 59 through 86 removed outlier: 4.163A pdb=" N ILE K 63 " --> pdb=" O GLN K 59 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LEU K 64 " --> pdb=" O VAL K 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 19 Processing helix chain 'J' and resid 25 through 46 Processing helix chain 'J' and resid 49 through 58 removed outlier: 4.205A pdb=" N ALA J 53 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU J 54 " --> pdb=" O PHE J 50 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE J 56 " --> pdb=" O GLY J 52 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ILE J 57 " --> pdb=" O ALA J 53 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL J 58 " --> pdb=" O LEU J 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 82 through 87 Processing helix chain 'J' and resid 90 through 113 removed outlier: 3.697A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix removed outlier: 3.846A pdb=" N LEU J 99 " --> pdb=" O GLY J 95 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET J 103 " --> pdb=" O LEU J 99 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY J 113 " --> pdb=" O TYR J 109 " (cutoff:3.500A) Processing helix chain 'J' and resid 126 through 132 removed outlier: 3.793A pdb=" N ILE J 131 " --> pdb=" O LYS J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 158 Processing helix chain 'A' and resid 16 through 37 Processing helix chain 'A' and resid 70 through 90 removed outlier: 3.763A pdb=" N VAL A 80 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR A 84 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU A 85 " --> pdb=" O GLU A 81 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 120 Processing helix chain 'H' and resid 57 through 67 Processing helix chain 'H' and resid 81 through 100 Proline residue: H 87 - end of helix removed outlier: 3.634A pdb=" N ALA H 90 " --> pdb=" O ALA H 86 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER H 93 " --> pdb=" O ILE H 89 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE H 98 " --> pdb=" O LEU H 94 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 137 removed outlier: 4.600A pdb=" N VAL H 127 " --> pdb=" O ALA H 123 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N TYR H 128 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL H 130 " --> pdb=" O ALA H 126 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 156 Processing helix chain 'H' and resid 159 through 171 removed outlier: 4.070A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 182 Processing helix chain 'H' and resid 193 through 205 Processing helix chain 'H' and resid 232 through 255 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 299 Processing helix chain 'H' and resid 305 through 320 Processing helix chain 'M' and resid 2 through 20 Proline residue: M 10 - end of helix Processing helix chain 'M' and resid 27 through 49 removed outlier: 3.523A pdb=" N ILE M 34 " --> pdb=" O TRP M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 104 Processing helix chain 'M' and resid 114 through 131 Processing helix chain 'M' and resid 136 through 145 Processing helix chain 'M' and resid 149 through 158 Processing helix chain 'M' and resid 164 through 166 No H-bonds generated for 'chain 'M' and resid 164 through 166' Processing helix chain 'M' and resid 170 through 199 removed outlier: 3.821A pdb=" N THR M 178 " --> pdb=" O PHE M 174 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER M 181 " --> pdb=" O TYR M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 207 through 210 No H-bonds generated for 'chain 'M' and resid 207 through 210' Processing helix chain 'M' and resid 220 through 232 removed outlier: 3.868A pdb=" N ALA M 230 " --> pdb=" O GLY M 226 " (cutoff:3.500A) Processing helix chain 'M' and resid 243 through 250 Processing helix chain 'M' and resid 253 through 261 Processing helix chain 'M' and resid 265 through 273 Processing helix chain 'M' and resid 280 through 306 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 312 through 330 removed outlier: 3.986A pdb=" N VAL M 320 " --> pdb=" O ALA M 316 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER M 321 " --> pdb=" O TYR M 317 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY M 324 " --> pdb=" O VAL M 320 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE M 325 " --> pdb=" O SER M 321 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL M 326 " --> pdb=" O HIS M 322 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 366 removed outlier: 3.532A pdb=" N ILE M 343 " --> pdb=" O GLN M 339 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY M 354 " --> pdb=" O LEU M 350 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU M 355 " --> pdb=" O SER M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 384 through 395 Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 443 removed outlier: 4.759A pdb=" N PHE M 427 " --> pdb=" O VAL M 423 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLY M 428 " --> pdb=" O ILE M 424 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU M 429 " --> pdb=" O SER M 425 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL M 430 " --> pdb=" O THR M 426 " (cutoff:3.500A) Processing helix chain 'M' and resid 448 through 450 No H-bonds generated for 'chain 'M' and resid 448 through 450' Processing helix chain 'M' and resid 452 through 455 removed outlier: 3.532A pdb=" N GLN M 455 " --> pdb=" O ILE M 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 452 through 455' Processing helix chain 'M' and resid 462 through 480 removed outlier: 3.719A pdb=" N LEU M 471 " --> pdb=" O MET M 467 " (cutoff:3.500A) Processing helix chain 'M' and resid 483 through 502 removed outlier: 5.119A pdb=" N SER M 491 " --> pdb=" O ASP M 487 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ALA M 492 " --> pdb=" O THR M 488 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 20 removed outlier: 4.231A pdb=" N ILE L 9 " --> pdb=" O LEU L 6 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N LEU L 10 " --> pdb=" O THR L 7 " (cutoff:3.500A) Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 27 through 54 removed outlier: 4.014A pdb=" N VAL L 38 " --> pdb=" O GLY L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 106 removed outlier: 3.677A pdb=" N VAL L 92 " --> pdb=" O MET L 88 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N PHE L 97 " --> pdb=" O THR L 93 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TRP L 105 " --> pdb=" O MET L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 113 through 132 removed outlier: 3.801A pdb=" N ASN L 121 " --> pdb=" O PHE L 117 " (cutoff:3.500A) Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 192 removed outlier: 3.932A pdb=" N ALA L 167 " --> pdb=" O ASN L 163 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N MET L 168 " --> pdb=" O GLY L 164 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS L 169 " --> pdb=" O ALA L 165 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA L 170 " --> pdb=" O ALA L 166 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA L 184 " --> pdb=" O PHE L 180 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 207 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 213 through 229 removed outlier: 4.276A pdb=" N TRP L 217 " --> pdb=" O ASN L 213 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY L 228 " --> pdb=" O GLY L 224 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LYS L 229 " --> pdb=" O GLY L 225 " (cutoff:3.500A) Processing helix chain 'L' and resid 233 through 235 No H-bonds generated for 'chain 'L' and resid 233 through 235' Processing helix chain 'L' and resid 241 through 244 Processing helix chain 'L' and resid 247 through 254 Processing helix chain 'L' and resid 262 through 268 removed outlier: 3.566A pdb=" N ILE L 266 " --> pdb=" O GLY L 262 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 274 Processing helix chain 'L' and resid 277 through 291 removed outlier: 3.712A pdb=" N VAL L 283 " --> pdb=" O VAL L 279 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY L 284 " --> pdb=" O LEU L 280 " (cutoff:3.500A) Processing helix chain 'L' and resid 296 through 300 Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 356 removed outlier: 4.079A pdb=" N PHE L 340 " --> pdb=" O MET L 336 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE L 341 " --> pdb=" O THR L 337 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU L 344 " --> pdb=" O PHE L 340 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER L 349 " --> pdb=" O LEU L 345 " (cutoff:3.500A) Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 396 through 409 Processing helix chain 'L' and resid 412 through 436 removed outlier: 4.348A pdb=" N PHE L 430 " --> pdb=" O SER L 426 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG L 431 " --> pdb=" O LEU L 427 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N MET L 432 " --> pdb=" O TYR L 428 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ILE L 433 " --> pdb=" O THR L 429 " (cutoff:3.500A) Processing helix chain 'L' and resid 451 through 464 Proline residue: L 456 - end of helix Processing helix chain 'L' and resid 466 through 470 removed outlier: 3.548A pdb=" N LEU L 470 " --> pdb=" O PHE L 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 466 through 470' Processing helix chain 'L' and resid 490 through 513 Processing helix chain 'L' and resid 517 through 522 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 541 through 547 Processing helix chain 'L' and resid 550 through 559 Processing helix chain 'L' and resid 564 through 568 Processing helix chain 'L' and resid 571 through 586 Processing helix chain 'L' and resid 591 through 610 Processing helix chain 'N' and resid 5 through 10 Processing helix chain 'N' and resid 12 through 30 removed outlier: 3.590A pdb=" N GLY N 18 " --> pdb=" O LEU N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 57 removed outlier: 4.104A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE N 54 " --> pdb=" O VAL N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 97 removed outlier: 3.539A pdb=" N LEU N 75 " --> pdb=" O GLY N 71 " (cutoff:3.500A) Proline residue: N 93 - end of helix removed outlier: 4.604A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 119 Processing helix chain 'N' and resid 125 through 141 removed outlier: 3.576A pdb=" N PHE N 129 " --> pdb=" O LEU N 125 " (cutoff:3.500A) Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 152 through 178 removed outlier: 3.697A pdb=" N TYR N 178 " --> pdb=" O MET N 174 " (cutoff:3.500A) Processing helix chain 'N' and resid 201 through 215 Processing helix chain 'N' and resid 221 through 233 removed outlier: 3.972A pdb=" N HIS N 224 " --> pdb=" O VAL N 221 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LEU N 225 " --> pdb=" O PRO N 222 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N TRP N 226 " --> pdb=" O PHE N 223 " (cutoff:3.500A) Proline residue: N 228 - end of helix Processing helix chain 'N' and resid 236 through 260 removed outlier: 3.613A pdb=" N PHE N 241 " --> pdb=" O PRO N 237 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY N 252 " --> pdb=" O ILE N 248 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL N 253 " --> pdb=" O ALA N 249 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE N 258 " --> pdb=" O VAL N 254 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 285 removed outlier: 3.887A pdb=" N VAL N 272 " --> pdb=" O ALA N 268 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 315 removed outlier: 3.825A pdb=" N ILE N 303 " --> pdb=" O GLY N 299 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER N 304 " --> pdb=" O TYR N 300 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA N 315 " --> pdb=" O VAL N 311 " (cutoff:3.500A) Processing helix chain 'N' and resid 321 through 347 Processing helix chain 'N' and resid 370 through 382 Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 433 removed outlier: 4.654A pdb=" N TYR N 423 " --> pdb=" O ALA N 419 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N TYR N 424 " --> pdb=" O ILE N 420 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TYR N 425 " --> pdb=" O GLY N 421 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU N 432 " --> pdb=" O VAL N 428 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR N 433 " --> pdb=" O ALA N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 481 Processing sheet with id= A, first strand: chain 'B' and resid 56 through 59 removed outlier: 6.629A pdb=" N LEU B 95 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N PHE B 59 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL B 97 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N VAL B 98 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N ILE B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL B 153 " --> pdb=" O SER B 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'D' and resid 44 through 47 removed outlier: 6.579A pdb=" N ILE D 99 " --> pdb=" O LEU D 70 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LEU D 70 " --> pdb=" O ILE D 99 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 119 through 121 removed outlier: 6.719A pdb=" N THR D 144 " --> pdb=" O VAL D 120 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'D' and resid 212 through 214 removed outlier: 3.901A pdb=" N ARG D 228 " --> pdb=" O ASP D 244 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP D 240 " --> pdb=" O GLN D 232 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ASP D 234 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N ILE D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 527 through 534 Processing sheet with id= F, first strand: chain 'E' and resid 126 through 131 removed outlier: 6.703A pdb=" N HIS E 87 " --> pdb=" O THR E 127 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU E 129 " --> pdb=" O HIS E 87 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N ILE E 89 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N THR E 131 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N TYR E 91 " --> pdb=" O THR E 131 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 86 through 91 removed outlier: 6.752A pdb=" N ARG F 127 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N CYS F 89 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N TYR F 129 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N ALA F 91 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE F 131 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N LEU F 132 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N HIS F 172 " --> pdb=" O LEU F 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'F' and resid 260 through 265 Processing sheet with id= I, first strand: chain 'G' and resid 9 through 13 removed outlier: 6.269A pdb=" N THR G 75 " --> pdb=" O HIS G 5 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N PHE G 76 " --> pdb=" O TYR G 53 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 144 through 146 Processing sheet with id= K, first strand: chain 'G' and resid 171 through 173 Processing sheet with id= L, first strand: chain 'G' and resid 222 through 227 removed outlier: 3.661A pdb=" N ALA G 224 " --> pdb=" O PRO G 239 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG G 248 " --> pdb=" O GLY G 240 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ARG G 242 " --> pdb=" O LEU G 246 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU G 246 " --> pdb=" O ARG G 242 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 282 through 286 Processing sheet with id= N, first strand: chain 'G' and resid 312 through 315 removed outlier: 6.571A pdb=" N ALA G 563 " --> pdb=" O ILE G 313 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE G 315 " --> pdb=" O ALA G 563 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL G 565 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU G 589 " --> pdb=" O VAL G 564 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL G 566 " --> pdb=" O LEU G 589 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N MET G 591 " --> pdb=" O VAL G 566 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LEU G 606 " --> pdb=" O VAL G 592 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ASP G 594 " --> pdb=" O LEU G 606 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LEU G 608 " --> pdb=" O ASP G 594 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'G' and resid 445 through 448 removed outlier: 6.726A pdb=" N VAL G 375 " --> pdb=" O PHE G 430 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N THR G 432 " --> pdb=" O VAL G 375 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL G 377 " --> pdb=" O THR G 432 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLY G 501 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLY G 528 " --> pdb=" O ILE G 498 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N SER G 500 " --> pdb=" O GLY G 528 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR G 530 " --> pdb=" O SER G 500 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 618 through 621 Processing sheet with id= Q, first strand: chain 'G' and resid 811 through 815 removed outlier: 7.278A pdb=" N TYR G 839 " --> pdb=" O PRO G 885 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N LEU G 842 " --> pdb=" O PRO G 870 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLU G 872 " --> pdb=" O LEU G 842 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'G' and resid 865 through 869 removed outlier: 3.772A pdb=" N LEU G 869 " --> pdb=" O VAL G 858 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASP G 902 " --> pdb=" O SER G 861 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 48 through 50 Processing sheet with id= T, first strand: chain 'I' and resid 75 through 81 removed outlier: 3.768A pdb=" N PHE I 91 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ALA I 80 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'L' and resid 60 through 63 Processing sheet with id= V, first strand: chain 'L' and resid 66 through 70 removed outlier: 7.211A pdb=" N ILE L 75 " --> pdb=" O TRP L 67 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N SER L 69 " --> pdb=" O PHE L 73 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N PHE L 73 " --> pdb=" O SER L 69 " (cutoff:3.500A) 1634 hydrogen bonds defined for protein. 4641 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: 13.41 Time building geometry restraints manager: 16.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 15349 1.43 - 1.65: 20281 1.65 - 1.86: 366 1.86 - 2.08: 0 2.08 - 2.29: 92 Bond restraints: 36088 Sorted by residual: bond pdb=" CB CSX E 132 " pdb=" SG CSX E 132 " ideal model delta sigma weight residual 1.831 1.758 0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" CB CSX B 102 " pdb=" SG CSX B 102 " ideal model delta sigma weight residual 1.831 1.758 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" CB CSX F 215 " pdb=" SG CSX F 215 " ideal model delta sigma weight residual 1.831 1.758 0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" N VAL B 192 " pdb=" CA VAL B 192 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.31e+00 bond pdb=" N CSX F 215 " pdb=" CA CSX F 215 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.49e+00 ... (remaining 36083 not shown) Histogram of bond angle deviations from ideal: 73.61 - 85.71: 88 85.71 - 97.81: 2 97.81 - 109.91: 6176 109.91 - 122.01: 36490 122.01 - 134.11: 6359 Bond angle restraints: 49115 Sorted by residual: angle pdb=" CA TYR M 435 " pdb=" CB TYR M 435 " pdb=" CG TYR M 435 " ideal model delta sigma weight residual 113.90 120.52 -6.62 1.80e+00 3.09e-01 1.35e+01 angle pdb=" N GLY L 317 " pdb=" CA GLY L 317 " pdb=" C GLY L 317 " ideal model delta sigma weight residual 113.37 108.46 4.91 1.34e+00 5.57e-01 1.34e+01 angle pdb=" C TYR D 343 " pdb=" N ASP D 344 " pdb=" CA ASP D 344 " ideal model delta sigma weight residual 120.72 115.03 5.69 1.67e+00 3.59e-01 1.16e+01 angle pdb=" C LYS D 341 " pdb=" N ILE D 342 " pdb=" CA ILE D 342 " ideal model delta sigma weight residual 120.42 115.71 4.71 1.42e+00 4.96e-01 1.10e+01 angle pdb=" CA PHE L 341 " pdb=" CB PHE L 341 " pdb=" CG PHE L 341 " ideal model delta sigma weight residual 113.80 117.08 -3.28 1.00e+00 1.00e+00 1.08e+01 ... (remaining 49110 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.08: 20672 34.08 - 68.15: 401 68.15 - 102.23: 29 102.23 - 136.31: 0 136.31 - 170.39: 1 Dihedral angle restraints: 21103 sinusoidal: 7915 harmonic: 13188 Sorted by residual: dihedral pdb=" C10 FMN F 502 " pdb=" C1' FMN F 502 " pdb=" N10 FMN F 502 " pdb=" C2' FMN F 502 " ideal model delta sinusoidal sigma weight residual 257.59 87.21 170.39 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" CA TRP L 535 " pdb=" C TRP L 535 " pdb=" N TYR L 536 " pdb=" CA TYR L 536 " ideal model delta harmonic sigma weight residual 180.00 153.09 26.91 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" CA VAL K 23 " pdb=" C VAL K 23 " pdb=" N ILE K 24 " pdb=" CA ILE K 24 " ideal model delta harmonic sigma weight residual -180.00 -153.93 -26.07 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 21100 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 4320 0.054 - 0.108: 1041 0.108 - 0.162: 176 0.162 - 0.216: 14 0.216 - 0.270: 3 Chirality restraints: 5554 Sorted by residual: chirality pdb=" CA PHE L 341 " pdb=" N PHE L 341 " pdb=" C PHE L 341 " pdb=" CB PHE L 341 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CB VAL L 35 " pdb=" CA VAL L 35 " pdb=" CG1 VAL L 35 " pdb=" CG2 VAL L 35 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CG LEU L 299 " pdb=" CB LEU L 299 " pdb=" CD1 LEU L 299 " pdb=" CD2 LEU L 299 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 5551 not shown) Planarity restraints: 6255 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU G 457 " 0.022 2.00e-02 2.50e+03 4.45e-02 1.98e+01 pdb=" C LEU G 457 " -0.077 2.00e-02 2.50e+03 pdb=" O LEU G 457 " 0.029 2.00e-02 2.50e+03 pdb=" N GLY G 458 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 30 " 0.031 2.00e-02 2.50e+03 2.34e-02 1.36e+01 pdb=" CG TRP M 30 " -0.062 2.00e-02 2.50e+03 pdb=" CD1 TRP M 30 " 0.008 2.00e-02 2.50e+03 pdb=" CD2 TRP M 30 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP M 30 " 0.021 2.00e-02 2.50e+03 pdb=" CE2 TRP M 30 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP M 30 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 30 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 30 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP M 30 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 342 " 0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C ILE D 342 " -0.061 2.00e-02 2.50e+03 pdb=" O ILE D 342 " 0.023 2.00e-02 2.50e+03 pdb=" N TYR D 343 " 0.020 2.00e-02 2.50e+03 ... (remaining 6252 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1303 2.71 - 3.26: 35995 3.26 - 3.80: 57718 3.80 - 4.35: 74383 4.35 - 4.90: 123013 Nonbonded interactions: 292412 Sorted by model distance: nonbonded pdb=" OE2 GLU G 624 " pdb=" NH2 ARG G 784 " model vdw 2.160 2.520 nonbonded pdb=" OE2 GLU D 347 " pdb=" NH1 ARG D 353 " model vdw 2.197 2.520 nonbonded pdb=" CE2 PHE J 156 " pdb=" OE2 GLU N 104 " model vdw 2.200 3.340 nonbonded pdb=" OG SER D 100 " pdb=" OD1 ASP D 102 " model vdw 2.217 2.440 nonbonded pdb=" OD1 ASP N 265 " pdb=" NE2 GLN N 317 " model vdw 2.218 2.520 ... (remaining 292407 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 10.430 Check model and map are aligned: 0.570 Set scattering table: 0.350 Process input model: 91.590 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.150 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 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 : 0.005 0.073 36088 Z= 0.346 Angle : 0.871 8.504 49115 Z= 0.462 Chirality : 0.047 0.270 5554 Planarity : 0.007 0.087 6255 Dihedral : 14.050 170.385 12663 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.11), residues: 4573 helix: -0.98 (0.09), residues: 2471 sheet: -0.47 (0.29), residues: 307 loop : -1.34 (0.14), residues: 1795 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1212 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1183 time to evaluate : 3.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 7 residues processed: 1204 average time/residue: 0.4720 time to fit residues: 913.6539 Evaluate side-chains 977 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 970 time to evaluate : 3.730 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4201 time to fit residues: 10.0910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 385 optimal weight: 40.0000 chunk 345 optimal weight: 20.0000 chunk 191 optimal weight: 4.9990 chunk 118 optimal weight: 0.2980 chunk 233 optimal weight: 0.6980 chunk 184 optimal weight: 2.9990 chunk 357 optimal weight: 50.0000 chunk 138 optimal weight: 1.9990 chunk 217 optimal weight: 0.7980 chunk 266 optimal weight: 6.9990 chunk 414 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 ASN D 397 ASN D 527 ASN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 304 HIS ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN G 454 GLN G 537 ASN G 899 HIS ** H 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.111 36088 Z= 0.305 Angle : 0.680 9.224 49115 Z= 0.347 Chirality : 0.045 0.233 5554 Planarity : 0.005 0.075 6255 Dihedral : 5.598 173.048 4983 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.12), residues: 4573 helix: 0.02 (0.10), residues: 2492 sheet: -0.23 (0.30), residues: 280 loop : -1.12 (0.14), residues: 1801 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1085 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 995 time to evaluate : 3.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 61 residues processed: 1032 average time/residue: 0.5041 time to fit residues: 847.4656 Evaluate side-chains 1005 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 944 time to evaluate : 3.888 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.3581 time to fit residues: 45.6079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 230 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 chunk 344 optimal weight: 0.0970 chunk 281 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 414 optimal weight: 7.9990 chunk 448 optimal weight: 5.9990 chunk 369 optimal weight: 9.9990 chunk 411 optimal weight: 0.8980 chunk 141 optimal weight: 0.5980 chunk 332 optimal weight: 10.0000 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 97 HIS D 527 ASN ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN G 111 ASN ** G 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 ASN G 726 GLN K 40 ASN ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 179 GLN ** M 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 308 GLN ** M 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.059 36088 Z= 0.210 Angle : 0.646 12.901 49115 Z= 0.320 Chirality : 0.042 0.234 5554 Planarity : 0.004 0.085 6255 Dihedral : 5.350 171.218 4983 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.12), residues: 4573 helix: 0.43 (0.10), residues: 2494 sheet: -0.20 (0.30), residues: 288 loop : -0.97 (0.14), residues: 1791 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1030 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 975 time to evaluate : 3.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 27 residues processed: 1003 average time/residue: 0.5052 time to fit residues: 825.4788 Evaluate side-chains 959 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 932 time to evaluate : 3.953 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.3591 time to fit residues: 23.3639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 409 optimal weight: 20.0000 chunk 311 optimal weight: 9.9990 chunk 215 optimal weight: 0.0670 chunk 45 optimal weight: 2.9990 chunk 197 optimal weight: 1.9990 chunk 278 optimal weight: 0.9980 chunk 416 optimal weight: 8.9990 chunk 440 optimal weight: 30.0000 chunk 217 optimal weight: 0.0270 chunk 394 optimal weight: 20.0000 chunk 118 optimal weight: 1.9990 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 527 ASN ** E 136 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 ASN G 760 ASN ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 232 GLN ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.080 36088 Z= 0.249 Angle : 0.649 13.670 49115 Z= 0.322 Chirality : 0.043 0.232 5554 Planarity : 0.004 0.074 6255 Dihedral : 5.319 171.486 4983 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 2.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.12), residues: 4573 helix: 0.64 (0.11), residues: 2479 sheet: -0.07 (0.30), residues: 284 loop : -0.95 (0.14), residues: 1810 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1068 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 983 time to evaluate : 4.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 45 residues processed: 1020 average time/residue: 0.4899 time to fit residues: 808.4828 Evaluate side-chains 979 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 934 time to evaluate : 3.684 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.3499 time to fit residues: 34.1747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 367 optimal weight: 4.9990 chunk 250 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 328 optimal weight: 20.0000 chunk 181 optimal weight: 0.5980 chunk 376 optimal weight: 7.9990 chunk 304 optimal weight: 40.0000 chunk 0 optimal weight: 8.9990 chunk 225 optimal weight: 1.9990 chunk 395 optimal weight: 0.0870 chunk 111 optimal weight: 6.9990 overall best weight: 1.9364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 ASN ** G 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 22 HIS ** J 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 ASN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.132 36088 Z= 0.379 Angle : 0.722 14.108 49115 Z= 0.357 Chirality : 0.047 0.372 5554 Planarity : 0.005 0.076 6255 Dihedral : 5.464 172.270 4983 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.12), residues: 4573 helix: 0.61 (0.11), residues: 2471 sheet: -0.25 (0.30), residues: 296 loop : -1.04 (0.14), residues: 1806 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 983 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 907 time to evaluate : 3.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 47 residues processed: 944 average time/residue: 0.4869 time to fit residues: 739.2488 Evaluate side-chains 919 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 872 time to evaluate : 3.897 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 0 residues processed: 47 average time/residue: 0.3626 time to fit residues: 36.4199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 148 optimal weight: 0.6980 chunk 396 optimal weight: 0.4980 chunk 87 optimal weight: 0.3980 chunk 258 optimal weight: 4.9990 chunk 108 optimal weight: 0.2980 chunk 441 optimal weight: 0.9980 chunk 366 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 231 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 ASN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 668 GLN J 24 ASN ** H 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 483 GLN L 135 ASN ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.3919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 36088 Z= 0.198 Angle : 0.662 12.617 49115 Z= 0.325 Chirality : 0.043 0.265 5554 Planarity : 0.004 0.077 6255 Dihedral : 5.262 171.256 4983 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.12), residues: 4573 helix: 0.77 (0.11), residues: 2470 sheet: 0.07 (0.30), residues: 289 loop : -0.88 (0.14), residues: 1814 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 941 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 893 time to evaluate : 3.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 25 residues processed: 916 average time/residue: 0.4963 time to fit residues: 731.0097 Evaluate side-chains 886 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 861 time to evaluate : 3.584 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.3265 time to fit residues: 20.8046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 425 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 251 optimal weight: 9.9990 chunk 322 optimal weight: 0.0470 chunk 249 optimal weight: 5.9990 chunk 371 optimal weight: 5.9990 chunk 246 optimal weight: 7.9990 chunk 439 optimal weight: 0.9990 chunk 275 optimal weight: 0.4980 chunk 267 optimal weight: 0.9990 chunk 202 optimal weight: 0.2980 overall best weight: 0.5682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 ASN D 224 HIS ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 ASN G 668 GLN ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 179 GLN ** M 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.4082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 36088 Z= 0.202 Angle : 0.670 13.451 49115 Z= 0.329 Chirality : 0.043 0.367 5554 Planarity : 0.004 0.078 6255 Dihedral : 5.154 170.829 4983 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.13), residues: 4573 helix: 0.84 (0.11), residues: 2464 sheet: 0.03 (0.31), residues: 296 loop : -0.81 (0.15), residues: 1813 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 888 time to evaluate : 4.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 19 residues processed: 907 average time/residue: 0.5202 time to fit residues: 762.1806 Evaluate side-chains 880 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 861 time to evaluate : 3.844 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3417 time to fit residues: 17.6471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 271 optimal weight: 30.0000 chunk 175 optimal weight: 3.9990 chunk 262 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 279 optimal weight: 0.8980 chunk 299 optimal weight: 6.9990 chunk 217 optimal weight: 4.9990 chunk 40 optimal weight: 0.2980 chunk 345 optimal weight: 20.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 511 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 ASN ** G 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.068 36088 Z= 0.234 Angle : 0.682 14.486 49115 Z= 0.337 Chirality : 0.044 0.298 5554 Planarity : 0.004 0.079 6255 Dihedral : 5.151 171.099 4983 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 1.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.13), residues: 4573 helix: 0.93 (0.11), residues: 2451 sheet: 0.05 (0.31), residues: 290 loop : -0.84 (0.15), residues: 1832 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 900 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 862 time to evaluate : 3.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 22 residues processed: 876 average time/residue: 0.5038 time to fit residues: 710.1179 Evaluate side-chains 862 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 840 time to evaluate : 3.695 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.3452 time to fit residues: 18.9477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 399 optimal weight: 10.0000 chunk 421 optimal weight: 10.0000 chunk 384 optimal weight: 0.4980 chunk 409 optimal weight: 2.9990 chunk 420 optimal weight: 0.0170 chunk 246 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 321 optimal weight: 7.9990 chunk 125 optimal weight: 0.9990 chunk 370 optimal weight: 5.9990 chunk 387 optimal weight: 0.1980 overall best weight: 0.5420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 439 ASN G 537 ASN ** H 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6884 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 36088 Z= 0.199 Angle : 0.692 15.134 49115 Z= 0.341 Chirality : 0.044 0.337 5554 Planarity : 0.004 0.076 6255 Dihedral : 5.103 170.806 4983 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.13), residues: 4573 helix: 0.90 (0.11), residues: 2465 sheet: 0.14 (0.31), residues: 296 loop : -0.80 (0.15), residues: 1812 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 876 time to evaluate : 3.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 884 average time/residue: 0.4966 time to fit residues: 707.8826 Evaluate side-chains 867 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 855 time to evaluate : 3.585 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3228 time to fit residues: 12.7834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 408 optimal weight: 5.9990 chunk 268 optimal weight: 0.0010 chunk 433 optimal weight: 8.9990 chunk 264 optimal weight: 6.9990 chunk 205 optimal weight: 0.4980 chunk 301 optimal weight: 7.9990 chunk 454 optimal weight: 0.9990 chunk 418 optimal weight: 20.0000 chunk 361 optimal weight: 50.0000 chunk 37 optimal weight: 6.9990 chunk 279 optimal weight: 6.9990 overall best weight: 2.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 52 ASN ** F 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 ASN ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 439 ASN G 101 HIS ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 605 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 907 GLN ** H 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 241 HIS ** M 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.167 36088 Z= 0.537 Angle : 0.832 16.297 49115 Z= 0.413 Chirality : 0.053 0.372 5554 Planarity : 0.005 0.075 6255 Dihedral : 5.602 172.273 4983 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer Outliers : 0.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.12), residues: 4573 helix: 0.59 (0.11), residues: 2454 sheet: -0.44 (0.31), residues: 295 loop : -1.16 (0.14), residues: 1824 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9146 Ramachandran restraints generated. 4573 Oldfield, 0 Emsley, 4573 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 869 time to evaluate : 3.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 18 residues processed: 875 average time/residue: 0.5198 time to fit residues: 728.8738 Evaluate side-chains 872 residues out of total 3766 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 854 time to evaluate : 3.911 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3509 time to fit residues: 17.2033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 221 optimal weight: 2.9990 chunk 287 optimal weight: 0.0770 chunk 385 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 333 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 362 optimal weight: 0.0670 chunk 151 optimal weight: 0.5980 chunk 372 optimal weight: 9.9990 chunk 45 optimal weight: 0.6980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 527 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 434 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 537 ASN H 138 ASN ** H 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 ASN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 338 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.256188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.201326 restraints weight = 46149.839| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 3.21 r_work: 0.3659 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 36088 Z= 0.208 Angle : 0.738 14.236 49115 Z= 0.362 Chirality : 0.044 0.288 5554 Planarity : 0.004 0.073 6255 Dihedral : 5.262 171.385 4983 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 0.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.13), residues: 4573 helix: 0.80 (0.11), residues: 2448 sheet: 0.02 (0.32), residues: 288 loop : -0.99 (0.14), residues: 1837 =============================================================================== Job complete usr+sys time: 11933.87 seconds wall clock time: 212 minutes 58.76 seconds (12778.76 seconds total)