Starting phenix.real_space_refine (version: dev) on Tue Dec 20 04:26:30 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7e_13236/12_2022/7p7e_13236_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7e_13236/12_2022/7p7e_13236.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7e_13236/12_2022/7p7e_13236.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7e_13236/12_2022/7p7e_13236.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7e_13236/12_2022/7p7e_13236_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7e_13236/12_2022/7p7e_13236_updated.pdb" } resolution = 2.7 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= 0.005 sd= 0.022 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "F GLU 80": "OE1" <-> "OE2" Residue "F GLU 302": "OE1" <-> "OE2" Residue "F GLU 344": "OE1" <-> "OE2" Residue "F GLU 420": "OE1" <-> "OE2" Residue "E GLU 163": "OE1" <-> "OE2" Residue "G GLU 454": "OE1" <-> "OE2" Residue "G GLU 792": "OE1" <-> "OE2" Residue "G PHE 862": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 382": "OE1" <-> "OE2" Residue "C GLU 453": "OE1" <-> "OE2" Residue "H GLU 157": "OE1" <-> "OE2" Residue "H GLU 228": "OE1" <-> "OE2" Residue "A GLU 102": "OE1" <-> "OE2" Residue "M GLU 144": "OE1" <-> "OE2" Residue "M GLU 407": "OE1" <-> "OE2" Residue "N GLU 133": "OE1" <-> "OE2" Residue "J GLU 84": "OE1" <-> "OE2" Residue "J TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 37326 Number of models: 1 Model: "" Number of chains: 36 Chain: "F" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3432 Classifications: {'peptide': 442} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 416} Chain: "E" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 146} Chain: "G" Number of atoms: 7022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7022 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "C" Number of atoms: 4571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4571 Classifications: {'peptide': 565} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 530} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1320 Classifications: {'peptide': 166} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 154} Chain breaks: 3 Chain: "I" Number of atoms: 1149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1149 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 12, 'TRANS': 132} Chain: "H" Number of atoms: 2330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2330 Classifications: {'peptide': 298} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 283} Chain breaks: 2 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 790 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 99} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "L" Number of atoms: 4508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4508 Classifications: {'peptide': 592} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 573} Chain breaks: 3 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "M" Number of atoms: 3953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 3953 Classifications: {'peptide': 504} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 482} Chain: "N" Number of atoms: 3638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3638 Classifications: {'peptide': 480} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 459} Chain breaks: 1 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: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1203 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 5, 'TRANS': 152} Chain breaks: 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: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 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: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'3PE': 1, 'LFA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 182 Unusual residues: {'3PE': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "M" Number of atoms: 153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 153 Unusual residues: {'3PE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 40 Unusual residues: {'LFA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 83 Classifications: {'water': 83} Link IDs: {None: 82} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "G" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 367 Classifications: {'water': 367} Link IDs: {None: 366} Chain: "C" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "I" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "L" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "M" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 47 Classifications: {'water': 47} Link IDs: {None: 46} Chain: "N" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "K" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "J" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2746 SG CYS F 354 81.895 55.434 191.821 1.00 9.21 S ATOM 2766 SG CYS F 357 85.579 55.023 196.013 1.00 12.11 S ATOM 3087 SG CYS F 398 80.201 51.064 196.582 1.00 18.40 S ATOM 2722 SG CYS F 351 84.613 49.245 192.558 1.00 9.65 S ATOM 4079 SG CYS E 92 94.729 46.915 211.595 1.00 36.85 S ATOM 4113 SG CYS E 97 95.069 47.410 215.097 1.00 33.34 S ATOM 4391 SG CYS E 133 89.585 45.769 211.558 1.00 27.78 S ATOM 4417 SG CYS E 137 88.962 46.257 214.880 1.00 38.87 S ATOM 5501 SG CYS G 114 90.606 63.602 174.094 1.00 14.25 S ATOM 5441 SG CYS G 105 95.542 67.842 175.545 1.00 13.84 S ATOM 5461 SG CYS G 108 96.710 62.038 172.974 1.00 15.90 S ATOM 5855 SG CYS G 156 85.954 54.975 178.884 1.00 16.70 S ATOM 5836 SG CYS G 153 92.043 54.233 181.492 1.00 19.12 S ATOM 5884 SG CYS G 159 89.408 49.600 177.824 1.00 10.89 S ATOM 6228 SG CYS G 203 90.850 55.166 174.958 1.00 10.87 S ATOM 6453 SG CYS G 230 86.941 47.614 153.562 1.00 15.17 S ATOM 6738 SG CYS G 265 87.571 43.521 158.654 1.00 18.20 S ATOM 6501 SG CYS G 237 81.895 46.610 157.020 1.00 7.20 S ATOM 6477 SG CYS G 233 84.361 41.649 153.456 1.00 14.58 S ATOM 4902 SG CYS G 36 79.630 55.021 182.081 1.00 17.75 S ATOM 4978 SG CYS G 47 80.948 58.536 182.548 1.00 16.12 S ATOM 5004 SG CYS G 50 75.047 59.600 182.936 1.00 11.76 S ATOM 5153 SG CYS G 69 74.827 56.037 182.328 1.00 12.48 S ATOM 16854 SG CYS B 129 96.888 93.226 151.405 1.00 25.43 S ATOM 16490 SG CYS B 64 101.672 97.519 152.939 1.00 54.49 S ATOM 16484 SG CYS B 63 95.828 98.368 155.424 1.00 46.87 S ATOM 17071 SG CYS B 158 99.276 92.994 157.071 1.00 40.22 S ATOM 18104 SG CYS I 102 98.570 86.666 162.812 1.00 13.24 S ATOM 18079 SG CYS I 99 103.919 86.037 158.805 1.00 15.22 S ATOM 18122 SG CYS I 105 103.162 82.340 164.036 1.00 21.87 S ATOM 17837 SG CYS I 70 98.985 81.609 159.071 1.00 9.60 S ATOM 18151 SG CYS I 109 105.056 76.628 169.907 1.00 15.42 S ATOM 17814 SG CYS I 66 102.751 76.060 163.902 1.00 16.32 S ATOM 17774 SG CYS I 60 107.435 72.053 165.673 1.00 11.86 S ATOM 17792 SG CYS I 63 101.317 71.826 168.571 1.00 8.61 S Time building chain proxies: 19.67, per 1000 atoms: 0.53 Number of scatterers: 37326 At special positions: 0 Unit cell: (157.5, 215.5, 246, 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 264 16.00 P 10 15.00 O 7243 8.00 N 6010 7.00 C 23766 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: 15.86 Conformation dependent library (CDL) restraints added in 5.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb=" FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb=" FE2 FES E 201 " - pdb=" SG CYS E 137 " pdb=" FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb=" FE1 FES E 201 " - pdb=" SG CYS E 97 " pdb=" FES G1004 " pdb=" FE2 FES G1004 " - pdb=" SG CYS G 50 " pdb=" FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb=" FE1 FES G1004 " - pdb=" SG CYS G 47 " pdb=" FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb=" SF4 B 301 " pdb=" FE1 SF4 B 301 " - pdb=" SG CYS B 129 " pdb=" FE3 SF4 B 301 " - pdb=" SG CYS B 63 " pdb=" FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb=" FE2 SF4 B 301 " - pdb=" SG CYS B 64 " pdb=" SF4 F 501 " pdb=" FE2 SF4 F 501 " - pdb=" SG CYS F 357 " pdb=" FE1 SF4 F 501 " - pdb=" SG CYS F 354 " pdb=" FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb=" FE4 SF4 F 501 " - pdb=" SG CYS F 351 " pdb=" SF4 G1001 " pdb=" FE3 SF4 G1001 " - pdb=" NE2 HIS G 101 " pdb=" FE4 SF4 G1001 " - pdb=" SG CYS G 108 " pdb=" FE1 SF4 G1001 " - pdb=" SG CYS G 114 " pdb=" FE2 SF4 G1001 " - pdb=" SG CYS G 105 " pdb=" SF4 G1002 " pdb=" FE3 SF4 G1002 " - pdb=" SG CYS G 159 " pdb=" FE2 SF4 G1002 " - pdb=" SG CYS G 153 " pdb=" FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb=" FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb=" SF4 G1003 " pdb=" FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb=" FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb=" FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb=" FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb=" SF4 I 201 " pdb=" FE3 SF4 I 201 " - pdb=" SG CYS I 105 " pdb=" FE4 SF4 I 201 " - pdb=" SG CYS I 70 " pdb=" FE2 SF4 I 201 " - pdb=" SG CYS I 99 " pdb=" FE1 SF4 I 201 " - pdb=" SG CYS I 102 " pdb=" SF4 I 202 " pdb=" FE2 SF4 I 202 " - pdb=" SG CYS I 66 " pdb=" FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb=" FE4 SF4 I 202 " - pdb=" SG CYS I 63 " pdb=" FE1 SF4 I 202 " - pdb=" SG CYS I 109 " Number of angles added : 93 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8430 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 194 helices and 23 sheets defined 54.9% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.96 Creating SS restraints... Processing helix chain 'F' and resid 26 through 31 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 Processing helix chain 'F' and resid 109 through 123 Processing helix chain 'F' and resid 137 through 152 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 179 through 181 No H-bonds generated for 'chain 'F' and resid 179 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 Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 233 through 237 Processing helix chain 'F' and resid 270 through 276 Processing helix chain 'F' and resid 302 through 306 removed outlier: 4.258A pdb=" N ASP F 306 " --> pdb=" O ALA F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 311 through 316 Processing helix chain 'F' and resid 335 through 348 Processing helix chain 'F' and resid 355 through 372 Proline residue: F 362 - end of helix 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 'E' and resid 16 through 28 removed outlier: 3.916A pdb=" N HIS E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.683A pdb=" N ILE E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG E 47 " --> pdb=" O GLN E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 Processing helix chain 'E' and resid 66 through 75 Processing helix chain 'E' and resid 95 through 99 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 158 through 162 Processing helix chain 'G' and resid 21 through 27 Processing helix chain 'G' and resid 84 through 99 Processing helix chain 'G' and resid 105 through 107 No H-bonds generated for 'chain 'G' and resid 105 through 107' Processing helix chain 'G' and resid 115 through 123 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 158 through 165 Processing helix chain 'G' and resid 196 through 202 Processing helix chain 'G' and resid 211 through 216 removed outlier: 4.058A pdb=" N ARG G 216 " --> pdb=" O THR G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 222 No H-bonds generated for 'chain 'G' and resid 220 through 222' Processing helix chain 'G' and resid 266 through 270 Processing helix chain 'G' and resid 273 through 276 Processing helix chain 'G' and resid 297 through 309 Processing helix chain 'G' and resid 324 through 334 Processing helix chain 'G' and resid 345 through 360 Processing helix chain 'G' and resid 369 through 373 Processing helix chain 'G' and resid 384 through 387 No H-bonds generated for 'chain 'G' and resid 384 through 387' Processing helix chain 'G' and resid 389 through 410 removed outlier: 4.510A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 423 Processing helix chain 'G' and resid 440 through 443 removed outlier: 4.317A pdb=" N ASP G 443 " --> pdb=" O ARG G 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 440 through 443' Processing helix chain 'G' and resid 453 through 467 Processing helix chain 'G' and resid 479 through 493 Processing helix chain 'G' and resid 509 through 524 Processing helix chain 'G' and resid 540 through 546 Processing helix chain 'G' and resid 551 through 560 Processing helix chain 'G' and resid 579 through 588 Processing helix chain 'G' and resid 601 through 603 No H-bonds generated for 'chain 'G' and resid 601 through 603' Processing helix chain 'G' and resid 615 through 617 No H-bonds generated for 'chain 'G' and resid 615 through 617' Processing helix chain 'G' and resid 650 through 662 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 683 through 689 removed outlier: 4.762A pdb=" N GLY G 687 " --> pdb=" O GLU G 684 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS G 689 " --> pdb=" O ALA G 686 " (cutoff:3.500A) Processing helix chain 'G' and resid 764 through 770 Processing helix chain 'G' and resid 825 through 828 No H-bonds generated for 'chain 'G' and resid 825 through 828' Processing helix chain 'G' and resid 831 through 836 removed outlier: 3.997A pdb=" N SER G 835 " --> pdb=" O VAL G 832 " (cutoff:3.500A) Processing helix chain 'G' and resid 846 through 852 Processing helix chain 'G' and resid 895 through 897 No H-bonds generated for 'chain 'G' and resid 895 through 897' Processing helix chain 'C' and resid 24 through 33 Processing helix chain 'C' and resid 54 through 66 removed outlier: 5.095A pdb=" N LEU C 58 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 145 removed outlier: 3.605A pdb=" N ASN C 135 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N TRP C 136 " --> pdb=" O ASN C 133 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU C 144 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N PHE C 145 " --> pdb=" O TRP C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 193 Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 256 through 260 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 280 through 295 removed outlier: 3.550A pdb=" N MET C 285 " --> pdb=" O VAL C 282 " (cutoff:3.500A) Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 326 Processing helix chain 'C' and resid 342 through 354 Processing helix chain 'C' and resid 376 through 398 Proline residue: C 388 - end of helix Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 427 through 431 Processing helix chain 'C' and resid 438 through 441 No H-bonds generated for 'chain 'C' and resid 438 through 441' Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 463 through 486 Processing helix chain 'C' and resid 505 through 510 Processing helix chain 'C' and resid 512 through 523 Processing helix chain 'C' and resid 564 through 570 Processing helix chain 'C' and resid 581 through 590 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 41 through 52 Processing helix chain 'B' and resid 65 through 68 No H-bonds generated for 'chain 'B' and resid 65 through 68' Processing helix chain 'B' and resid 104 through 115 Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 127 through 132 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 177 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 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 127 through 130 Processing helix chain 'I' and resid 134 through 136 No H-bonds generated for 'chain 'I' and resid 134 through 136' Processing helix chain 'I' and resid 150 through 152 No H-bonds generated for 'chain 'I' and resid 150 through 152' Processing helix chain 'H' and resid 6 through 36 Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 80 through 100 Proline residue: H 87 - end of helix removed outlier: 5.020A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 136 removed outlier: 3.795A pdb=" N VAL H 127 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU H 131 " --> pdb=" O TYR H 128 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE H 132 " --> pdb=" O ALA H 129 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER H 136 " --> pdb=" O ALA H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 4.879A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 183 Processing helix chain 'H' and resid 188 through 191 No H-bonds generated for 'chain 'H' and resid 188 through 191' Processing helix chain 'H' and resid 193 through 206 Processing helix chain 'H' and resid 232 through 256 Processing helix chain 'H' and resid 267 through 288 Processing helix chain 'H' and resid 294 through 322 Proline residue: H 307 - end of helix Processing helix chain 'A' and resid 7 through 36 Processing helix chain 'A' and resid 67 through 91 removed outlier: 3.697A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N SER A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 119 Processing helix chain 'L' and resid 4 through 21 Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 27 through 54 Processing helix chain 'L' and resid 83 through 106 Processing helix chain 'L' and resid 113 through 132 Processing helix chain 'L' and resid 136 through 154 Processing helix chain 'L' and resid 161 through 192 Processing helix chain 'L' and resid 197 through 207 Proline residue: L 205 - end of helix Processing helix chain 'L' and resid 213 through 230 Processing helix chain 'L' and resid 237 through 241 Processing helix chain 'L' and resid 247 through 255 Processing helix chain 'L' and resid 258 through 268 removed outlier: 4.047A pdb=" N GLY L 262 " --> pdb=" O VAL L 259 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL L 263 " --> pdb=" O THR L 260 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG L 268 " --> pdb=" O LEU L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 274 Processing helix chain 'L' and resid 277 through 300 removed outlier: 3.758A pdb=" N LEU L 299 " --> pdb=" O GLY L 295 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N VAL L 300 " --> pdb=" O PHE L 296 " (cutoff:3.500A) Processing helix chain 'L' and resid 304 through 324 Processing helix chain 'L' and resid 328 through 355 Processing helix chain 'L' and resid 373 through 387 Processing helix chain 'L' and resid 394 through 408 Processing helix chain 'L' and resid 413 through 437 Processing helix chain 'L' and resid 455 through 462 Processing helix chain 'L' and resid 466 through 469 No H-bonds generated for 'chain 'L' and resid 466 through 469' Processing helix chain 'L' and resid 490 through 511 Processing helix chain 'L' and resid 518 through 524 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 538 through 559 removed outlier: 6.006A pdb=" N ASP L 542 " --> pdb=" O TRP L 539 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TRP L 543 " --> pdb=" O GLY L 540 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU L 544 " --> pdb=" O PHE L 541 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL L 548 " --> pdb=" O TYR L 545 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N VAL L 550 " --> pdb=" O LYS L 547 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LYS L 551 " --> pdb=" O VAL L 548 " (cutoff:3.500A) Proline residue: L 552 - end of helix Processing helix chain 'L' and resid 564 through 586 Proline residue: L 572 - end of helix removed outlier: 3.766A pdb=" N LEU L 585 " --> pdb=" O LYS L 581 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER L 586 " --> pdb=" O GLY L 582 " (cutoff:3.500A) Processing helix chain 'L' and resid 591 through 611 Processing helix chain 'M' and resid 3 through 23 Proline residue: M 10 - end of helix removed outlier: 3.883A pdb=" N GLU M 21 " --> pdb=" O CYS M 17 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N ARG M 22 " --> pdb=" O TRP M 18 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N PHE M 23 " --> pdb=" O GLN M 19 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 48 Processing helix chain 'M' and resid 52 through 54 No H-bonds generated for 'chain 'M' and resid 52 through 54' Processing helix chain 'M' and resid 85 through 104 Processing helix chain 'M' and resid 113 through 132 Processing helix chain 'M' and resid 136 through 155 removed outlier: 3.955A pdb=" N MET M 146 " --> pdb=" O PHE M 142 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N VAL M 148 " --> pdb=" O GLU M 144 " (cutoff:3.500A) Proline residue: M 149 - end of helix Processing helix chain 'M' and resid 164 through 200 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 217 through 234 removed outlier: 3.813A pdb=" N LYS M 234 " --> pdb=" O ALA M 230 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 249 removed outlier: 4.354A pdb=" N ASP M 246 " --> pdb=" O GLY M 242 " (cutoff:3.500A) Processing helix chain 'M' and resid 257 through 261 Processing helix chain 'M' and resid 266 through 278 removed outlier: 4.523A pdb=" N LEU M 276 " --> pdb=" O LEU M 272 " (cutoff:3.500A) Proline residue: M 277 - end of helix Processing helix chain 'M' and resid 280 through 307 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 332 removed outlier: 3.778A pdb=" N TYR M 331 " --> pdb=" O LEU M 327 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR M 332 " --> pdb=" O ILE M 328 " (cutoff:3.500A) Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 371 through 373 No H-bonds generated for 'chain 'M' and resid 371 through 373' Processing helix chain 'M' and resid 377 through 379 No H-bonds generated for 'chain 'M' and resid 377 through 379' 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 444 Processing helix chain 'M' and resid 452 through 454 No H-bonds generated for 'chain 'M' and resid 452 through 454' Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 502 removed outlier: 4.931A pdb=" N SER M 491 " --> pdb=" O ASP M 487 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N ALA M 492 " --> pdb=" O THR M 488 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 10 Processing helix chain 'N' and resid 12 through 30 Processing helix chain 'N' and resid 34 through 57 Processing helix chain 'N' and resid 71 through 96 Proline residue: N 93 - end of helix Processing helix chain 'N' and resid 103 through 120 Processing helix chain 'N' and resid 125 through 143 Proline residue: N 138 - end of helix Processing helix chain 'N' and resid 150 through 181 Processing helix chain 'N' and resid 186 through 188 No H-bonds generated for 'chain 'N' and resid 186 through 188' Processing helix chain 'N' and resid 201 through 217 Processing helix chain 'N' and resid 226 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.415A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 removed outlier: 4.071A pdb=" N ASP N 265 " --> pdb=" O PRO N 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 262 through 265' Processing helix chain 'N' and resid 267 through 287 Processing helix chain 'N' and resid 294 through 314 Processing helix chain 'N' and resid 322 through 347 Processing helix chain 'N' and resid 365 through 367 No H-bonds generated for 'chain 'N' and resid 365 through 367' Processing helix chain 'N' and resid 370 through 384 Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 432 Processing helix chain 'N' and resid 449 through 469 Processing helix chain 'N' and resid 472 through 479 Processing helix chain 'K' and resid 4 through 24 Processing helix chain 'K' and resid 28 through 52 Processing helix chain 'K' and resid 57 through 87 Processing helix chain 'J' and resid 2 through 21 removed outlier: 3.699A pdb=" N THR J 21 " --> pdb=" O LEU J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 46 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 86 through 88 No H-bonds generated for 'chain 'J' and resid 86 through 88' Processing helix chain 'J' and resid 90 through 111 removed outlier: 5.895A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix Processing helix chain 'J' and resid 126 through 133 Processing helix chain 'J' and resid 138 through 159 Processing sheet with id= A, first strand: chain 'F' and resid 214 through 218 removed outlier: 6.698A pdb=" N TYR F 86 " --> pdb=" O CYS F 215 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ASN F 217 " --> pdb=" O TYR F 86 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N LEU F 88 " --> pdb=" O ASN F 217 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ARG F 127 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N CYS F 89 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N TYR F 129 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ALA F 91 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N PHE F 131 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU F 132 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N HIS F 172 " --> pdb=" O LEU F 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'F' and resid 260 through 265 removed outlier: 3.559A pdb=" N PHE F 252 " --> pdb=" O GLY F 260 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'E' and resid 87 through 92 Processing sheet with id= D, first strand: chain 'E' and resid 143 through 145 Processing sheet with id= E, first strand: chain 'G' and resid 11 through 14 removed outlier: 6.517A pdb=" N THR G 77 " --> pdb=" O HIS G 7 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N PHE G 78 " --> pdb=" O TYR G 55 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= G, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= H, first strand: chain 'G' and resid 224 through 229 removed outlier: 6.517A pdb=" N ARG G 244 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N LEU G 248 " --> pdb=" O ARG G 244 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'G' and resid 284 through 288 Processing sheet with id= J, first strand: chain 'G' and resid 314 through 317 removed outlier: 6.503A pdb=" N ALA G 565 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE G 317 " --> pdb=" O ALA G 565 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N VAL G 567 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU G 591 " --> pdb=" O VAL G 566 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL G 568 " --> pdb=" O LEU G 591 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N MET G 593 " --> pdb=" O VAL G 568 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU G 608 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ASP G 596 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N LEU G 610 " --> pdb=" O ASP G 596 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'G' and resid 530 through 534 removed outlier: 6.419A pdb=" N ALA G 376 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N ILE G 501 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU G 378 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N GLY G 503 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N LEU G 380 " --> pdb=" O GLY G 503 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL G 379 " --> pdb=" O PRO G 430 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N PHE G 432 " --> pdb=" O VAL G 379 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N TRP G 447 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ASN G 435 " --> pdb=" O TRP G 447 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N TYR G 449 " --> pdb=" O ASN G 435 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 620 through 623 Processing sheet with id= M, first strand: chain 'G' and resid 813 through 816 removed outlier: 7.983A pdb=" N ILE G 842 " --> pdb=" O THR G 870 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N LEU G 844 " --> pdb=" O PRO G 872 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLU G 874 " --> pdb=" O LEU G 844 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.221A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE C 103 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N LEU C 74 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 123 through 125 removed outlier: 6.435A pdb=" N THR C 148 " --> pdb=" O VAL C 124 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 216 through 220 removed outlier: 3.762A pdb=" N LEU C 220 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP C 244 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASP C 238 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N ILE C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 531 through 539 removed outlier: 3.646A pdb=" N GLY C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 56 through 60 removed outlier: 6.628A pdb=" N LEU B 95 " --> pdb=" O TYR B 57 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N PHE B 59 " --> pdb=" O LEU B 95 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL B 97 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TRP B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL B 98 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ILE B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL B 153 " --> pdb=" O SER B 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= R 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: 3.942A pdb=" N PHE I 91 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ALA I 80 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'L' and resid 68 through 70 Processing sheet with id= V, first strand: chain 'L' and resid 60 through 66 removed outlier: 6.916A pdb=" N PHE L 77 " --> pdb=" O LEU L 64 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'M' and resid 65 through 72 removed outlier: 6.828A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) 1820 hydrogen bonds defined for protein. 5151 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: 13.46 Time building geometry restraints manager: 17.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 15501 1.42 - 1.64: 21394 1.64 - 1.86: 402 1.86 - 2.09: 0 2.09 - 2.31: 92 Bond restraints: 37389 Sorted by residual: bond pdb=" O13 3PE H 401 " pdb=" P 3PE H 401 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.80e+00 bond pdb=" O13 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.80e+00 bond pdb=" O13 3PE L 804 " pdb=" P 3PE L 804 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.64e+00 bond pdb=" O13 3PE L 802 " pdb=" P 3PE L 802 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.62e+00 bond pdb=" O13 3PE A 202 " pdb=" P 3PE A 202 " ideal model delta sigma weight residual 1.654 1.595 0.059 2.00e-02 2.50e+03 8.62e+00 ... (remaining 37384 not shown) Histogram of bond angle deviations from ideal: 69.11 - 82.34: 88 82.34 - 95.58: 0 95.58 - 108.81: 2337 108.81 - 122.04: 41521 122.04 - 135.27: 6760 Bond angle restraints: 50706 Sorted by residual: angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 97.07 12.74 2.21e+00 2.05e-01 3.33e+01 angle pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta sigma weight residual 121.80 134.02 -12.22 2.44e+00 1.68e-01 2.51e+01 angle pdb=" CB LYS E 116 " pdb=" CG LYS E 116 " pdb=" CD LYS E 116 " ideal model delta sigma weight residual 111.30 122.71 -11.41 2.30e+00 1.89e-01 2.46e+01 angle pdb=" CA ILE N 135 " pdb=" CB ILE N 135 " pdb=" CG1 ILE N 135 " ideal model delta sigma weight residual 110.40 118.69 -8.29 1.70e+00 3.46e-01 2.38e+01 angle pdb=" C TRP G 668 " pdb=" N THR G 669 " pdb=" CA THR G 669 " ideal model delta sigma weight residual 121.54 130.13 -8.59 1.91e+00 2.74e-01 2.02e+01 ... (remaining 50701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.01: 21179 34.01 - 68.01: 694 68.01 - 102.02: 39 102.02 - 136.03: 0 136.03 - 170.03: 1 Dihedral angle restraints: 21913 sinusoidal: 8741 harmonic: 13172 Sorted by residual: dihedral pdb=" CA VAL N 63 " pdb=" C VAL N 63 " pdb=" N THR N 64 " pdb=" CA THR N 64 " ideal model delta harmonic sigma weight residual 180.00 137.38 42.62 0 5.00e+00 4.00e-02 7.26e+01 dihedral pdb=" CA THR N 64 " pdb=" C THR N 64 " pdb=" N PRO N 65 " pdb=" CA PRO N 65 " ideal model delta harmonic sigma weight residual 180.00 145.35 34.65 0 5.00e+00 4.00e-02 4.80e+01 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 87.56 170.03 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 21910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.241: 5642 4.241 - 8.483: 0 8.483 - 12.724: 0 12.724 - 16.966: 0 16.966 - 21.207: 28 Chirality restraints: 5670 Sorted by residual: chirality pdb=" FE4 SF4 I 202 " pdb=" S1 SF4 I 202 " pdb=" S2 SF4 I 202 " pdb=" S3 SF4 I 202 " both_signs ideal model delta sigma weight residual False 10.55 -10.65 21.21 2.00e-01 2.50e+01 1.12e+04 chirality pdb=" FE1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " pdb=" S4 SF4 I 201 " both_signs ideal model delta sigma weight residual False -10.55 10.64 -21.19 2.00e-01 2.50e+01 1.12e+04 chirality pdb=" FE4 SF4 G1002 " pdb=" S1 SF4 G1002 " pdb=" S2 SF4 G1002 " pdb=" S3 SF4 G1002 " both_signs ideal model delta sigma weight residual False 10.55 -10.64 21.19 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5667 not shown) Planarity restraints: 6329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR N 64 " 0.051 5.00e-02 4.00e+02 7.67e-02 9.42e+00 pdb=" N PRO N 65 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO N 65 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO N 65 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL N 63 " -0.015 2.00e-02 2.50e+03 2.95e-02 8.71e+00 pdb=" C VAL N 63 " 0.051 2.00e-02 2.50e+03 pdb=" O VAL N 63 " -0.019 2.00e-02 2.50e+03 pdb=" N THR N 64 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 48 " 0.015 2.00e-02 2.50e+03 1.79e-02 8.03e+00 pdb=" CG TRP B 48 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP B 48 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 48 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B 48 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 48 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B 48 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 48 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 48 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 48 " -0.001 2.00e-02 2.50e+03 ... (remaining 6326 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1732 2.72 - 3.26: 36846 3.26 - 3.81: 69474 3.81 - 4.35: 88811 4.35 - 4.90: 142342 Nonbonded interactions: 339205 Sorted by model distance: nonbonded pdb=" O GLY L 421 " pdb=" OG1 THR L 425 " model vdw 2.170 2.440 nonbonded pdb=" O HOH G1123 " pdb=" O HOH G1305 " model vdw 2.237 2.440 nonbonded pdb=" OE1 GLN E 103 " pdb=" O HOH E 301 " model vdw 2.248 2.440 nonbonded pdb=" O HOH G1107 " pdb=" O HOH G1379 " model vdw 2.249 2.440 nonbonded pdb=" OG1 THR I 82 " pdb=" OD1 ASP I 84 " model vdw 2.249 2.440 ... (remaining 339200 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 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 10 5.49 5 S 264 5.16 5 C 23766 2.51 5 N 6010 2.21 5 O 7243 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.010 Normalize map: mean=0, sd=1: 5.450 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: 0.040 Extract box with map and model: 18.290 Check model and map are aligned: 0.530 Convert atoms to be neutral: 0.330 Process input model: 99.250 Find NCS groups from input model: 1.410 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8874 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 0.078 37389 Z= 0.307 Angle : 0.779 13.648 50706 Z= 0.400 Chirality : 1.486 21.207 5670 Planarity : 0.006 0.077 6329 Dihedral : 15.964 170.034 13483 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.68 % Favored : 97.28 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.07 % 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: -0.20 (0.12), residues: 4558 helix: 0.39 (0.09), residues: 2634 sheet: -0.45 (0.29), residues: 306 loop : -0.76 (0.14), residues: 1618 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 520 time to evaluate : 4.418 Fit side-chains outliers start: 73 outliers final: 47 residues processed: 580 average time/residue: 1.4587 time to fit residues: 1035.0740 Evaluate side-chains 526 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 479 time to evaluate : 4.243 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 45 residues processed: 2 average time/residue: 0.3639 time to fit residues: 7.0562 ------------------------------------------------------------------------------- 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: 1.9990 chunk 345 optimal weight: 5.9990 chunk 191 optimal weight: 0.6980 chunk 118 optimal weight: 5.9990 chunk 233 optimal weight: 5.9990 chunk 184 optimal weight: 7.9990 chunk 357 optimal weight: 10.0000 chunk 138 optimal weight: 0.6980 chunk 217 optimal weight: 10.0000 chunk 266 optimal weight: 5.9990 chunk 414 optimal weight: 9.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN F 434 ASN E 78 GLN E 82 GLN G 88 GLN G 218 ASN G 299 GLN G 583 ASN G 709 HIS G 765 GLN ** G 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 901 HIS B 173 GLN B 198 GLN B 213 ASN H 181 ASN ** H 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 ASN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 435 HIS K 5 GLN K 82 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.0979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.249 37389 Z= 0.751 Angle : 2.201 50.445 50706 Z= 1.448 Chirality : 0.454 6.619 5670 Planarity : 0.005 0.070 6329 Dihedral : 6.977 169.978 5339 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.46 % Favored : 97.50 % Rotamer Outliers : 3.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % 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: 0.67 (0.12), residues: 4558 helix: 1.16 (0.10), residues: 2609 sheet: -0.31 (0.29), residues: 305 loop : -0.47 (0.15), residues: 1644 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 643 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 497 time to evaluate : 4.222 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 146 outliers final: 66 residues processed: 581 average time/residue: 1.4183 time to fit residues: 1013.3888 Evaluate side-chains 539 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 473 time to evaluate : 4.484 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 48 residues processed: 18 average time/residue: 0.8418 time to fit residues: 25.9676 ------------------------------------------------------------------------------- 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: 9.9990 chunk 128 optimal weight: 9.9990 chunk 344 optimal weight: 9.9990 chunk 281 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 414 optimal weight: 10.0000 chunk 448 optimal weight: 9.9990 chunk 369 optimal weight: 8.9990 chunk 411 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 332 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 224 ASN F 237 GLN F 434 ASN E 98 HIS G 513 GLN G 583 ASN G 709 HIS ** G 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 359 HIS B 173 GLN B 198 GLN B 213 ASN ** H 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 226 HIS H 312 ASN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 46 ASN N 435 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8922 moved from start: 0.1462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.241 37389 Z= 0.785 Angle : 2.216 50.512 50706 Z= 1.454 Chirality : 0.454 6.628 5670 Planarity : 0.005 0.062 6329 Dihedral : 7.572 170.678 5339 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.72 % Favored : 97.24 % Rotamer Outliers : 4.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.07 % 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: 0.74 (0.12), residues: 4558 helix: 1.15 (0.10), residues: 2623 sheet: -0.30 (0.30), residues: 305 loop : -0.32 (0.15), residues: 1630 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 500 time to evaluate : 4.209 Fit side-chains revert: symmetry clash outliers start: 152 outliers final: 81 residues processed: 591 average time/residue: 1.4731 time to fit residues: 1072.7130 Evaluate side-chains 566 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 485 time to evaluate : 4.619 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 57 residues processed: 24 average time/residue: 0.8410 time to fit residues: 33.3251 ------------------------------------------------------------------------------- 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: 7.9990 chunk 311 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 197 optimal weight: 3.9990 chunk 278 optimal weight: 9.9990 chunk 416 optimal weight: 7.9990 chunk 440 optimal weight: 3.9990 chunk 217 optimal weight: 7.9990 chunk 394 optimal weight: 7.9990 chunk 118 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 196 ASN F 237 GLN F 386 GLN G 583 ASN G 709 HIS ** G 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN B 173 GLN B 198 GLN ** H 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 ASN L 58 GLN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 33 ASN N 123 ASN N 435 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.241 37389 Z= 0.807 Angle : 2.223 50.522 50706 Z= 1.457 Chirality : 0.455 6.648 5670 Planarity : 0.005 0.061 6329 Dihedral : 8.051 171.001 5339 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.63 % Favored : 97.30 % Rotamer Outliers : 4.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.67 (0.12), residues: 4558 helix: 1.09 (0.10), residues: 2614 sheet: -0.32 (0.30), residues: 305 loop : -0.33 (0.15), residues: 1639 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 499 time to evaluate : 5.652 Fit side-chains revert: symmetry clash outliers start: 173 outliers final: 82 residues processed: 604 average time/residue: 1.4943 time to fit residues: 1107.6365 Evaluate side-chains 569 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 487 time to evaluate : 4.299 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 59 residues processed: 23 average time/residue: 0.7432 time to fit residues: 30.0346 ------------------------------------------------------------------------------- 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: 2.9990 chunk 250 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 328 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 376 optimal weight: 5.9990 chunk 304 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 225 optimal weight: 9.9990 chunk 395 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN F 386 GLN G 583 ASN G 709 HIS ** G 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN B 198 GLN H 181 ASN ** H 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 33 ASN N 435 HIS J 22 HIS ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.243 37389 Z= 0.756 Angle : 2.203 50.553 50706 Z= 1.450 Chirality : 0.448 6.495 5670 Planarity : 0.004 0.057 6329 Dihedral : 7.667 170.139 5339 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.39 % Favored : 97.56 % Rotamer Outliers : 3.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.05 % 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: 0.98 (0.12), residues: 4558 helix: 1.39 (0.10), residues: 2614 sheet: -0.26 (0.30), residues: 305 loop : -0.26 (0.15), residues: 1639 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 507 time to evaluate : 4.320 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 140 outliers final: 69 residues processed: 601 average time/residue: 1.4848 time to fit residues: 1108.0845 Evaluate side-chains 557 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 488 time to evaluate : 4.145 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 57 residues processed: 12 average time/residue: 0.8991 time to fit residues: 20.3643 ------------------------------------------------------------------------------- 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: 10.0000 chunk 396 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 258 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 chunk 441 optimal weight: 9.9990 chunk 366 optimal weight: 9.9990 chunk 204 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 145 optimal weight: 9.9990 chunk 231 optimal weight: 5.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN F 386 GLN G 218 ASN G 583 ASN G 709 HIS ** G 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN B 173 GLN B 198 GLN H 181 ASN ** H 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 435 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8927 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.240 37389 Z= 0.794 Angle : 2.219 50.563 50706 Z= 1.456 Chirality : 0.453 6.610 5670 Planarity : 0.005 0.060 6329 Dihedral : 8.046 170.623 5339 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.57 % Favored : 97.39 % Rotamer Outliers : 3.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: 0.82 (0.12), residues: 4558 helix: 1.23 (0.10), residues: 2614 sheet: -0.29 (0.30), residues: 305 loop : -0.27 (0.15), residues: 1639 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 497 time to evaluate : 5.127 Fit side-chains revert: symmetry clash outliers start: 147 outliers final: 83 residues processed: 585 average time/residue: 1.4995 time to fit residues: 1075.9129 Evaluate side-chains 568 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 485 time to evaluate : 4.239 Switching outliers to nearest non-outliers outliers start: 83 outliers final: 61 residues processed: 22 average time/residue: 0.8921 time to fit residues: 33.1482 ------------------------------------------------------------------------------- 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: 10.0000 chunk 49 optimal weight: 5.9990 chunk 251 optimal weight: 10.0000 chunk 322 optimal weight: 5.9990 chunk 249 optimal weight: 5.9990 chunk 371 optimal weight: 8.9990 chunk 246 optimal weight: 0.7980 chunk 439 optimal weight: 0.9990 chunk 275 optimal weight: 5.9990 chunk 267 optimal weight: 0.0270 chunk 202 optimal weight: 5.9990 overall best weight: 2.7644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN G 218 ASN G 583 ASN G 709 HIS ** G 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN B 198 GLN H 181 ASN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 435 HIS ** J 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.241 37389 Z= 0.757 Angle : 2.206 50.578 50706 Z= 1.451 Chirality : 0.449 6.501 5670 Planarity : 0.004 0.057 6329 Dihedral : 7.828 170.177 5339 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.39 % Favored : 97.56 % Rotamer Outliers : 3.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.05 % 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: 1.00 (0.12), residues: 4558 helix: 1.40 (0.10), residues: 2611 sheet: -0.27 (0.30), residues: 305 loop : -0.25 (0.15), residues: 1642 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 498 time to evaluate : 4.234 Fit side-chains outliers start: 129 outliers final: 75 residues processed: 586 average time/residue: 1.4978 time to fit residues: 1080.2938 Evaluate side-chains 563 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 488 time to evaluate : 4.305 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 62 residues processed: 13 average time/residue: 0.7279 time to fit residues: 19.4553 ------------------------------------------------------------------------------- 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: 5.9990 chunk 175 optimal weight: 2.9990 chunk 262 optimal weight: 0.7980 chunk 132 optimal weight: 0.4980 chunk 86 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 279 optimal weight: 0.8980 chunk 299 optimal weight: 0.9990 chunk 217 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 345 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN G 583 ASN G 709 HIS ** G 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN B 198 GLN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 ASN N 435 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.249 37389 Z= 0.749 Angle : 2.198 50.664 50706 Z= 1.449 Chirality : 0.445 6.420 5670 Planarity : 0.004 0.062 6329 Dihedral : 7.282 168.512 5339 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.39 % Favored : 97.59 % Rotamer Outliers : 2.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % 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: 1.27 (0.12), residues: 4558 helix: 1.66 (0.10), residues: 2601 sheet: -0.18 (0.29), residues: 305 loop : -0.20 (0.15), residues: 1652 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 624 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 523 time to evaluate : 4.350 Fit side-chains outliers start: 101 outliers final: 67 residues processed: 600 average time/residue: 1.4583 time to fit residues: 1077.2687 Evaluate side-chains 564 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 497 time to evaluate : 4.448 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 59 residues processed: 9 average time/residue: 0.6487 time to fit residues: 14.5764 ------------------------------------------------------------------------------- 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: 3.9990 chunk 421 optimal weight: 2.9990 chunk 384 optimal weight: 6.9990 chunk 409 optimal weight: 8.9990 chunk 420 optimal weight: 1.9990 chunk 246 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 321 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 370 optimal weight: 8.9990 chunk 387 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN F 434 ASN G 583 ASN G 709 HIS ** G 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 315 GLN N 435 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8891 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 0.241 37389 Z= 0.761 Angle : 2.207 50.566 50706 Z= 1.451 Chirality : 0.449 6.533 5670 Planarity : 0.004 0.058 6329 Dihedral : 7.466 169.402 5339 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.50 % Favored : 97.48 % Rotamer Outliers : 2.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % 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: 1.21 (0.12), residues: 4558 helix: 1.56 (0.10), residues: 2608 sheet: -0.10 (0.30), residues: 303 loop : -0.15 (0.15), residues: 1647 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 495 time to evaluate : 4.426 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 71 residues processed: 567 average time/residue: 1.4584 time to fit residues: 1037.4305 Evaluate side-chains 559 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 488 time to evaluate : 4.257 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 61 residues processed: 11 average time/residue: 0.7928 time to fit residues: 18.1454 ------------------------------------------------------------------------------- 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: 1.9990 chunk 268 optimal weight: 2.9990 chunk 433 optimal weight: 10.0000 chunk 264 optimal weight: 5.9990 chunk 205 optimal weight: 8.9990 chunk 301 optimal weight: 0.9980 chunk 454 optimal weight: 0.8980 chunk 418 optimal weight: 0.7980 chunk 361 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 279 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN G 583 ASN G 709 HIS ** G 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 ASN B 173 GLN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 435 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 0.246 37389 Z= 0.750 Angle : 2.204 50.587 50706 Z= 1.451 Chirality : 0.446 6.422 5670 Planarity : 0.004 0.061 6329 Dihedral : 7.184 168.871 5339 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.35 % Favored : 97.63 % Rotamer Outliers : 2.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.02 % 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: 1.33 (0.12), residues: 4558 helix: 1.68 (0.10), residues: 2604 sheet: -0.07 (0.30), residues: 303 loop : -0.13 (0.15), residues: 1651 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9116 Ramachandran restraints generated. 4558 Oldfield, 0 Emsley, 4558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 501 time to evaluate : 4.653 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 81 outliers final: 64 residues processed: 570 average time/residue: 1.4731 time to fit residues: 1035.0391 Evaluate side-chains 561 residues out of total 3771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 497 time to evaluate : 4.738 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 60 residues processed: 4 average time/residue: 0.5377 time to fit residues: 9.2932 ------------------------------------------------------------------------------- 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: 8.9990 chunk 287 optimal weight: 9.9990 chunk 385 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 333 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 chunk 362 optimal weight: 8.9990 chunk 151 optimal weight: 8.9990 chunk 372 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 237 GLN F 386 GLN F 434 ASN G 583 ASN G 709 HIS ** G 845 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN ** H 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 58 GLN ** L 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 ASN N 435 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.091863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.072684 restraints weight = 42643.084| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.16 r_work: 0.2860 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 0.240 37389 Z= 0.817 Angle : 2.234 50.512 50706 Z= 1.461 Chirality : 0.455 6.659 5670 Planarity : 0.005 0.061 6329 Dihedral : 7.966 171.013 5339 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.85 % Favored : 97.10 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 0.00 % Twisted Proline : 0.47 % Twisted General : 0.05 % 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: 0.92 (0.12), residues: 4558 helix: 1.28 (0.10), residues: 2604 sheet: -0.21 (0.30), residues: 309 loop : -0.17 (0.15), residues: 1645 =============================================================================== Job complete usr+sys time: 19439.74 seconds wall clock time: 341 minutes 20.14 seconds (20480.14 seconds total)