Starting phenix.real_space_refine (version: 1.21rc1) on Mon May 15 16:02:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7r_14535/05_2023/7z7r_14535_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7r_14535/05_2023/7z7r_14535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7r_14535/05_2023/7z7r_14535.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7r_14535/05_2023/7z7r_14535.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7r_14535/05_2023/7z7r_14535_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z7r_14535/05_2023/7z7r_14535_updated.pdb" } resolution = 3.36 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= 0.006 sd= 0.020 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 3 5.49 5 S 267 5.16 5 C 24182 2.51 5 N 6222 2.21 5 O 6545 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F GLU 106": "OE1" <-> "OE2" Residue "F TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 312": "OE1" <-> "OE2" Residue "G ASP 141": "OD1" <-> "OD2" Residue "G TYR 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 564": "OD1" <-> "OD2" Residue "G ASP 619": "OD1" <-> "OD2" Residue "G ASP 667": "OD1" <-> "OD2" Residue "G TYR 817": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 862": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 472": "OE1" <-> "OE2" Residue "B PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 152": "OD1" <-> "OD2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "I TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 174": "OD1" <-> "OD2" Residue "H PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 36": "OE1" <-> "OE2" Residue "H TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 63": "OD1" <-> "OD2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "H TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 295": "OD1" <-> "OD2" Residue "A TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 79": "OD1" <-> "OD2" Residue "A ASP 124": "OD1" <-> "OD2" Residue "L PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 82": "OD1" <-> "OD2" Residue "L TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 210": "OD1" <-> "OD2" Residue "L PHE 397": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 68": "OD1" <-> "OD2" Residue "M TYR 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 364": "OE1" <-> "OE2" Residue "M PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 487": "OD1" <-> "OD2" Residue "N TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 72": "OE1" <-> "OE2" Residue "J GLU 55": "OE1" <-> "OE2" Residue "J GLU 80": "OE1" <-> "OE2" Residue "J GLU 84": "OE1" <-> "OE2" Residue "J ASP 120": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 37252 Number of models: 1 Model: "" Number of chains: 21 Chain: "F" Number of atoms: 3407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3407 Classifications: {'peptide': 439} Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 413} 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: 7027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 905, 7027 Classifications: {'peptide': 905} Link IDs: {'PTRANS': 41, 'TRANS': 863} Chain: "C" Number of atoms: 4736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 586, 4736 Classifications: {'peptide': 586} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 548} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1656 Classifications: {'peptide': 208} Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 193} Chain breaks: 2 Chain: "I" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1436 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 166} Chain: "H" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2529 Classifications: {'peptide': 322} Modifications used: {'COO': 1} Incomplete info: {'n_c_alpha_c_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 306} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 894 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 2, 'TRANS': 110} Chain breaks: 1 Chain: "L" Number of atoms: 4627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4627 Classifications: {'peptide': 605} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 586} Chain breaks: 1 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: 3563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3563 Classifications: {'peptide': 470} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 450} Chain breaks: 2 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: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1226 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 5, 'TRANS': 156} 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: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} 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: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'LFA': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 67.987 59.921 187.891 1.00 31.95 S ATOM 2741 SG CYS F 357 71.589 59.357 192.301 1.00 60.22 S ATOM 3062 SG CYS F 398 65.737 56.077 192.749 1.00 54.73 S ATOM 2697 SG CYS F 351 70.042 53.562 189.061 1.00 33.90 S ATOM 4054 SG CYS E 92 78.260 50.402 208.658 1.00 68.10 S ATOM 4088 SG CYS E 97 78.596 51.276 212.045 1.00 53.60 S ATOM 4366 SG CYS E 133 73.123 50.045 208.413 1.00 66.31 S ATOM 4392 SG CYS E 137 72.397 50.867 211.788 1.00 82.18 S ATOM 5476 SG CYS G 114 79.265 66.162 170.859 1.00 47.02 S ATOM 5416 SG CYS G 105 84.790 69.216 172.664 1.00 62.92 S ATOM 5436 SG CYS G 108 84.967 63.747 169.259 1.00 34.29 S ATOM 5830 SG CYS G 156 72.950 58.389 175.307 1.00 31.54 S ATOM 5811 SG CYS G 153 78.784 57.210 178.236 1.00 62.34 S ATOM 5859 SG CYS G 159 75.828 52.582 174.705 1.00 51.39 S ATOM 6207 SG CYS G 203 78.108 57.729 171.666 1.00 56.45 S ATOM 6432 SG CYS G 230 74.622 50.009 150.219 1.00 41.15 S ATOM 6717 SG CYS G 265 74.397 46.181 155.529 1.00 52.92 S ATOM 6480 SG CYS G 237 69.265 49.918 153.465 1.00 41.66 S ATOM 6456 SG CYS G 233 71.190 44.501 150.248 1.00 80.99 S ATOM 4877 SG CYS G 36 66.230 59.527 177.722 1.00 38.20 S ATOM 4953 SG CYS G 47 68.126 62.737 178.351 1.00 33.05 S ATOM 4979 SG CYS G 50 62.390 64.725 178.536 1.00 54.60 S ATOM 5128 SG CYS G 69 61.837 61.073 177.973 1.00 40.35 S ATOM 17324 SG CYS B 129 90.788 93.665 147.268 1.00 38.24 S ATOM 16821 SG CYS B 64 96.158 97.070 149.031 1.00 38.82 S ATOM 16815 SG CYS B 63 90.678 99.315 151.088 1.00 60.66 S ATOM 17541 SG CYS B 158 92.531 93.546 153.277 1.00 62.62 S ATOM 18872 SG CYS I 102 90.831 87.304 159.132 1.00 36.25 S ATOM 18847 SG CYS I 99 96.308 85.919 155.536 1.00 48.08 S ATOM 18890 SG CYS I 105 94.860 82.616 160.903 1.00 91.54 S ATOM 18605 SG CYS I 70 91.035 82.012 155.634 1.00 38.72 S ATOM 18919 SG CYS I 109 95.474 76.820 166.808 1.00 69.31 S ATOM 18582 SG CYS I 66 93.537 76.213 160.685 1.00 69.56 S ATOM 18542 SG CYS I 60 97.331 71.585 163.174 1.00 39.17 S ATOM 18560 SG CYS I 63 91.102 72.480 165.405 1.00 46.86 S Time building chain proxies: 22.23, per 1000 atoms: 0.60 Number of scatterers: 37252 At special positions: 0 Unit cell: (157.3, 220.22, 239.58, 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 267 16.00 P 3 15.00 O 6545 8.00 N 6222 7.00 C 24182 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: 15.92 Conformation dependent library (CDL) restraints added in 6.1 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 47 " pdb="FE2 FES G1004 " - pdb=" SG CYS G 69 " pdb="FE1 FES G1004 " - pdb=" SG CYS G 36 " pdb=" SF4 B 301 " pdb="FE4 SF4 B 301 " - pdb=" SG CYS B 158 " pdb="FE1 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="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="FE4 SF4 G1002 " - pdb=" SG CYS G 203 " pdb="FE1 SF4 G1002 " - pdb=" SG CYS G 156 " pdb="FE2 SF4 G1002 " - pdb=" SG CYS G 153 " 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="FE4 SF4 I 202 " - pdb=" SG CYS I 63 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 60 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 109 " Number of angles added : 93 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8680 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 191 helices and 27 sheets defined 53.9% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.83 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 56 Processing helix chain 'F' and resid 69 through 75 removed outlier: 3.531A pdb=" N LEU F 75 " --> pdb=" O LEU F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 107 removed outlier: 3.842A pdb=" N GLN F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 122 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 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 Proline residue: F 226 - end of helix Processing helix chain 'F' and resid 234 through 237 No H-bonds generated for 'chain 'F' and resid 234 through 237' Processing helix chain 'F' and resid 311 through 317 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 381 through 391 Processing helix chain 'F' and resid 400 through 414 Proline residue: F 407 - end of helix Processing helix chain 'F' and resid 416 through 422 removed outlier: 4.190A pdb=" N GLY F 422 " --> pdb=" O GLU F 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 26 Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.567A pdb=" N ILE E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU E 38 " --> pdb=" O ALA E 35 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ARG E 47 " --> pdb=" O GLN E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.184A 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 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 164 removed outlier: 4.291A pdb=" N ARG E 164 " --> pdb=" O GLU E 160 " (cutoff:3.500A) 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 removed outlier: 3.721A pdb=" N ILE G 202 " --> pdb=" O LEU G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 215 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 272 through 274 No H-bonds generated for 'chain 'G' and resid 272 through 274' 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 368 through 373 removed outlier: 4.243A pdb=" N GLU G 372 " --> pdb=" O LEU G 368 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N SER G 373 " --> pdb=" O ARG G 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 368 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: 4.294A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN G 410 " --> pdb=" O MET G 406 " (cutoff:3.500A) Processing helix chain 'G' and resid 417 through 423 Processing helix chain 'G' and resid 453 through 467 Processing helix chain 'G' and resid 479 through 493 Processing helix chain 'G' and resid 504 through 506 No H-bonds generated for 'chain 'G' and resid 504 through 506' Processing helix chain 'G' and resid 509 through 525 removed outlier: 3.597A pdb=" N ARG G 525 " --> pdb=" O ALA G 521 " (cutoff:3.500A) Processing helix chain 'G' and resid 540 through 546 Processing helix chain 'G' and resid 551 through 559 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 650 through 662 Processing helix chain 'G' and resid 671 through 681 Processing helix chain 'G' and resid 686 through 690 removed outlier: 3.849A pdb=" N LYS G 689 " --> pdb=" O ALA G 686 " (cutoff:3.500A) Processing helix chain 'G' and resid 764 through 767 removed outlier: 3.741A pdb=" N TRP G 767 " --> pdb=" O PRO G 764 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 764 through 767' Processing helix chain 'G' and resid 827 through 829 No H-bonds generated for 'chain 'G' and resid 827 through 829' Processing helix chain 'G' and resid 833 through 836 No H-bonds generated for 'chain 'G' and resid 833 through 836' 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 57 through 65 Processing helix chain 'C' and resid 132 through 145 removed outlier: 3.509A pdb=" N TYR C 137 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TRP C 142 " --> pdb=" O ARG C 139 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU C 144 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE C 145 " --> pdb=" O TRP C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 196 Processing helix chain 'C' and resid 201 through 204 No H-bonds generated for 'chain 'C' and resid 201 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 281 through 295 Proline residue: C 286 - end of helix Processing helix chain 'C' and resid 301 through 330 Processing helix chain 'C' and resid 334 through 353 Processing helix chain 'C' and resid 376 through 397 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 432 removed outlier: 4.449A pdb=" N THR C 432 " --> pdb=" O GLY C 428 " (cutoff:3.500A) 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 522 Processing helix chain 'C' and resid 564 through 576 Proline residue: C 573 - end of helix Processing helix chain 'C' and resid 581 through 589 Processing helix chain 'C' and resid 595 through 599 Processing helix chain 'B' and resid 37 through 51 Processing helix chain 'B' and resid 63 through 71 Processing helix chain 'B' and resid 78 through 81 Processing helix chain 'B' and resid 104 through 116 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 178 removed outlier: 3.561A pdb=" N LYS B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 208 removed outlier: 4.435A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLU B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 24 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 150 through 153 No H-bonds generated for 'chain 'I' and resid 150 through 153' Processing helix chain 'H' and resid 6 through 43 Processing helix chain 'H' and resid 54 through 56 No H-bonds generated for 'chain 'H' and resid 54 through 56' 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: 4.515A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 136 removed outlier: 3.879A pdb=" N SER H 136 " --> pdb=" O ALA H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 171 removed outlier: 5.044A pdb=" N PHE H 159 " --> pdb=" O SER H 155 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU H 162 " --> pdb=" O VAL H 158 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.558A 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 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 214 through 217 No H-bonds generated for 'chain 'H' and resid 214 through 217' 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 302 Processing helix chain 'H' and resid 305 through 323 Processing helix chain 'A' and resid 7 through 36 Processing helix chain 'A' and resid 67 through 119 removed outlier: 3.887A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N SER A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE A 92 " --> pdb=" O TRP A 88 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ARG A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N GLU A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLY A 96 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N TRP A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N VAL A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 21 removed outlier: 4.260A pdb=" N ALA L 5 " --> pdb=" O ASN L 2 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LEU L 10 " --> pdb=" O THR L 7 " (cutoff:3.500A) Proline residue: L 11 - end of helix removed outlier: 3.526A pdb=" N VAL L 16 " --> pdb=" O ILE L 13 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU L 17 " --> pdb=" O GLY L 14 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU L 18 " --> pdb=" O PHE L 15 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE L 20 " --> pdb=" O LEU L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 55 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 229 Processing helix chain 'L' and resid 238 through 244 removed outlier: 4.656A pdb=" N ALA L 244 " --> pdb=" O ALA L 240 " (cutoff:3.500A) Processing helix chain 'L' and resid 247 through 255 Processing helix chain 'L' and resid 259 through 268 removed outlier: 4.624A pdb=" N VAL L 263 " --> pdb=" O VAL L 259 " (cutoff:3.500A) Processing helix chain 'L' and resid 270 through 274 Processing helix chain 'L' and resid 277 through 298 Processing helix chain 'L' and resid 304 through 325 removed outlier: 3.516A pdb=" N VAL L 325 " --> pdb=" O LEU L 321 " (cutoff:3.500A) Processing helix chain 'L' and resid 328 through 355 Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 394 through 409 removed outlier: 3.600A pdb=" N ASN L 409 " --> pdb=" O GLY L 405 " (cutoff:3.500A) Processing helix chain 'L' and resid 413 through 437 Processing helix chain 'L' and resid 454 through 463 Processing helix chain 'L' and resid 466 through 470 Processing helix chain 'L' and resid 487 through 512 Processing helix chain 'L' and resid 519 through 523 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 538 through 549 removed outlier: 6.193A pdb=" N ASP L 542 " --> pdb=" O TRP L 539 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TRP L 543 " --> pdb=" O GLY L 540 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL L 548 " --> pdb=" O TYR L 545 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE L 549 " --> pdb=" O ASP L 546 " (cutoff:3.500A) Processing helix chain 'L' and resid 551 through 560 Processing helix chain 'L' and resid 564 through 586 Proline residue: L 572 - end of helix removed outlier: 3.812A pdb=" N LEU L 585 " --> pdb=" O LYS L 581 " (cutoff:3.500A) removed outlier: 4.492A 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 22 Proline residue: M 10 - end of helix removed outlier: 4.206A pdb=" N GLU M 21 " --> pdb=" O CYS M 17 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ARG M 22 " --> pdb=" O TRP M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 50 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 156 removed outlier: 4.856A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.374A 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 199 Processing helix chain 'M' and resid 207 through 211 removed outlier: 3.527A pdb=" N LEU M 211 " --> pdb=" O TYR M 207 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 207 through 211' Processing helix chain 'M' and resid 219 through 233 Processing helix chain 'M' and resid 242 through 249 Processing helix chain 'M' and resid 256 through 261 Processing helix chain 'M' and resid 267 through 273 Processing helix chain 'M' and resid 275 through 278 No H-bonds generated for 'chain 'M' and resid 275 through 278' Processing helix chain 'M' and resid 280 through 307 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 330 Processing helix chain 'M' and resid 335 through 366 Processing helix chain 'M' and resid 384 through 396 removed outlier: 3.542A pdb=" N LEU M 396 " --> pdb=" O ALA M 392 " (cutoff:3.500A) Processing helix chain 'M' and resid 402 through 417 Processing helix chain 'M' and resid 419 through 444 Processing helix chain 'M' and resid 462 through 480 Processing helix chain 'M' and resid 483 through 488 Processing helix chain 'M' and resid 490 through 503 removed outlier: 4.188A pdb=" N SER M 503 " --> pdb=" O TRP M 499 " (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 58 removed outlier: 3.663A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 97 Proline residue: N 93 - end of helix removed outlier: 4.332A pdb=" N GLY N 97 " --> pdb=" O PRO N 93 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 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: 4.120A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 290 removed outlier: 4.428A pdb=" N ALA N 288 " --> pdb=" O GLY N 284 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU N 289 " --> pdb=" O ASN N 285 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N SER N 290 " --> pdb=" O LEU N 286 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 314 Processing helix chain 'N' and resid 322 through 348 Processing helix chain 'N' and resid 370 through 384 removed outlier: 3.661A pdb=" N ALA N 384 " --> pdb=" O MET N 380 " (cutoff:3.500A) Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 432 Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 480 Processing helix chain 'K' and resid 4 through 23 Processing helix chain 'K' and resid 28 through 53 removed outlier: 3.551A pdb=" N TRP K 53 " --> pdb=" O ALA K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 87 Processing helix chain 'J' and resid 2 through 20 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 112 removed outlier: 5.435A 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 158 Processing sheet with id= A, first strand: chain 'F' and resid 213 through 218 removed outlier: 6.724A pdb=" N ARG F 127 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N CYS F 89 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N TYR F 129 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'F' and resid 247 through 250 Processing sheet with id= C, first strand: chain 'F' and resid 251 through 253 Processing sheet with id= D, first strand: chain 'E' and resid 87 through 92 Processing sheet with id= E, first strand: chain 'E' and resid 142 through 145 Processing sheet with id= F, first strand: chain 'G' and resid 11 through 14 removed outlier: 6.788A pdb=" N THR G 77 " --> pdb=" O HIS G 7 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE G 78 " --> pdb=" O TYR G 55 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 146 through 148 Processing sheet with id= H, first strand: chain 'G' and resid 173 through 175 Processing sheet with id= I, first strand: chain 'G' and resid 224 through 229 removed outlier: 6.470A pdb=" N ARG G 244 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LEU G 248 " --> pdb=" O ARG G 244 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 284 through 288 Processing sheet with id= K, first strand: chain 'G' and resid 314 through 317 removed outlier: 6.648A pdb=" N ALA G 565 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ILE G 317 " --> pdb=" O ALA G 565 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL G 567 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU G 608 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ASP G 596 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N LEU G 610 " --> pdb=" O ASP G 596 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 530 through 534 removed outlier: 6.312A pdb=" N ALA G 376 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ILE G 501 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU G 378 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.654A pdb=" N GLY G 503 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N LEU G 380 " --> pdb=" O GLY G 503 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL G 379 " --> pdb=" O PRO G 430 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N PHE G 432 " --> pdb=" O VAL G 379 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TRP G 447 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N ASN G 435 " --> pdb=" O TRP G 447 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N TYR G 449 " --> pdb=" O ASN G 435 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 620 through 623 Processing sheet with id= N, first strand: chain 'G' and resid 901 through 903 Processing sheet with id= O, first strand: chain 'G' and resid 841 through 844 removed outlier: 8.190A pdb=" N ILE G 842 " --> pdb=" O THR G 870 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU G 844 " --> pdb=" O PRO G 872 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLU G 874 " --> pdb=" O LEU G 844 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.347A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE C 103 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N LEU C 74 " --> pdb=" O ILE C 103 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 123 through 125 removed outlier: 6.581A pdb=" N THR C 148 " --> pdb=" O VAL C 124 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'C' and resid 215 through 220 removed outlier: 3.785A pdb=" N VAL C 234 " --> pdb=" O VAL C 246 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL C 246 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP C 244 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ASP C 238 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ILE C 242 " --> pdb=" O ASP C 238 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 532 through 539 removed outlier: 3.583A pdb=" N GLY C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 20 through 25 removed outlier: 3.862A pdb=" N LYS B 21 " --> pdb=" O ARG B 7 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG B 7 " --> pdb=" O LYS B 21 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.310A pdb=" N TRP B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N VAL B 98 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL B 153 " --> pdb=" O SER B 125 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'I' and resid 48 through 50 Processing sheet with id= W, first strand: chain 'I' and resid 75 through 77 Processing sheet with id= X, first strand: chain 'I' and resid 79 through 81 Processing sheet with id= Y, first strand: chain 'L' and resid 60 through 63 Processing sheet with id= Z, first strand: chain 'L' and resid 66 through 70 removed outlier: 6.861A pdb=" N ILE L 75 " --> pdb=" O TRP L 67 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER L 69 " --> pdb=" O PHE L 73 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N PHE L 73 " --> pdb=" O SER L 69 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 65 through 72 removed outlier: 6.700A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) 1848 hydrogen bonds defined for protein. 5328 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: 17.23 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: 15983 1.42 - 1.64: 21712 1.64 - 1.86: 410 1.86 - 2.09: 0 2.09 - 2.31: 92 Bond restraints: 38197 Sorted by residual: bond pdb=" CG PRO M 61 " pdb=" CD PRO M 61 " ideal model delta sigma weight residual 1.512 1.386 0.126 2.70e-02 1.37e+03 2.19e+01 bond pdb=" CB PRO M 61 " pdb=" CG PRO M 61 " ideal model delta sigma weight residual 1.506 1.653 -0.147 3.90e-02 6.57e+02 1.42e+01 bond pdb=" O13 3PE C 701 " pdb=" P 3PE C 701 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.53e+00 bond pdb=" O13 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.654 1.596 0.058 2.00e-02 2.50e+03 8.29e+00 bond pdb=" O11 3PE L 801 " pdb=" P 3PE L 801 " ideal model delta sigma weight residual 1.644 1.594 0.050 2.00e-02 2.50e+03 6.19e+00 ... (remaining 38192 not shown) Histogram of bond angle deviations from ideal: 69.51 - 83.04: 88 83.04 - 96.57: 3 96.57 - 110.10: 6739 110.10 - 123.63: 43879 123.63 - 137.15: 1192 Bond angle restraints: 51901 Sorted by residual: angle pdb=" N PRO M 61 " pdb=" CD PRO M 61 " pdb=" CG PRO M 61 " ideal model delta sigma weight residual 103.80 93.50 10.30 1.20e+00 6.94e-01 7.37e+01 angle pdb=" CA PRO M 61 " pdb=" N PRO M 61 " pdb=" CD PRO M 61 " ideal model delta sigma weight residual 111.50 101.53 9.97 1.40e+00 5.10e-01 5.08e+01 angle pdb=" CB MET C 387 " pdb=" CG MET C 387 " pdb=" SD MET C 387 " ideal model delta sigma weight residual 112.70 130.17 -17.47 3.00e+00 1.11e-01 3.39e+01 angle pdb=" N THR N 64 " pdb=" CA THR N 64 " pdb=" C THR N 64 " ideal model delta sigma weight residual 109.81 97.35 12.46 2.21e+00 2.05e-01 3.18e+01 angle pdb=" CB MET H 281 " pdb=" CG MET H 281 " pdb=" SD MET H 281 " ideal model delta sigma weight residual 112.70 129.52 -16.82 3.00e+00 1.11e-01 3.14e+01 ... (remaining 51896 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.84: 21495 33.84 - 67.68: 800 67.68 - 101.52: 54 101.52 - 135.36: 0 135.36 - 169.20: 1 Dihedral angle restraints: 22350 sinusoidal: 8781 harmonic: 13569 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 180.00 133.23 46.77 0 5.00e+00 4.00e-02 8.75e+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 88.39 169.20 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" CA TRP G 668 " pdb=" C TRP G 668 " pdb=" N THR G 669 " pdb=" CA THR G 669 " ideal model delta harmonic sigma weight residual 180.00 146.13 33.87 0 5.00e+00 4.00e-02 4.59e+01 ... (remaining 22347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.247: 5796 4.247 - 8.495: 0 8.495 - 12.742: 0 12.742 - 16.990: 0 16.990 - 21.237: 28 Chirality restraints: 5824 Sorted by residual: chirality pdb="FE2 SF4 B 301 " pdb=" S1 SF4 B 301 " pdb=" S3 SF4 B 301 " pdb=" S4 SF4 B 301 " both_signs ideal model delta sigma weight residual False 10.55 -10.68 21.24 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE3 SF4 G1001 " pdb=" S1 SF4 G1001 " pdb=" S2 SF4 G1001 " pdb=" S4 SF4 G1001 " both_signs ideal model delta sigma weight residual False -10.55 10.61 -21.16 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 -10.60 21.16 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5821 not shown) Planarity restraints: 6532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL N 63 " -0.017 2.00e-02 2.50e+03 3.28e-02 1.08e+01 pdb=" C VAL N 63 " 0.057 2.00e-02 2.50e+03 pdb=" O VAL N 63 " -0.022 2.00e-02 2.50e+03 pdb=" N THR N 64 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER G 763 " -0.051 5.00e-02 4.00e+02 7.85e-02 9.85e+00 pdb=" N PRO G 764 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO G 764 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO G 764 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR N 64 " 0.052 5.00e-02 4.00e+02 7.80e-02 9.74e+00 pdb=" N PRO N 65 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO N 65 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO N 65 " 0.044 5.00e-02 4.00e+02 ... (remaining 6529 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 6380 2.77 - 3.30: 35814 3.30 - 3.83: 67669 3.83 - 4.37: 78630 4.37 - 4.90: 134946 Nonbonded interactions: 323439 Sorted by model distance: nonbonded pdb=" O ALA L 256 " pdb=" OG1 THR L 260 " model vdw 2.232 2.440 nonbonded pdb=" O GLU C 276 " pdb=" ND2 ASN C 283 " model vdw 2.255 2.520 nonbonded pdb=" O ILE M 421 " pdb=" OG SER M 425 " model vdw 2.266 2.440 nonbonded pdb=" O TRP M 499 " pdb=" OG SER M 503 " model vdw 2.266 2.440 nonbonded pdb=" O ILE N 386 " pdb=" OG1 THR N 389 " model vdw 2.267 2.440 ... (remaining 323434 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: 0.310 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: 0.060 Extract box with map and model: 4.780 Check model and map are aligned: 0.550 Set scattering table: 0.300 Process input model: 102.550 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.140 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:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 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 : 0.004 0.147 38197 Z= 0.276 Angle : 0.846 17.469 51901 Z= 0.423 Chirality : 1.466 21.237 5824 Planarity : 0.006 0.078 6532 Dihedral : 16.836 169.201 13670 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.72 % Favored : 97.26 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.31 % Cis-general : 0.00 % Twisted Proline : 0.46 % Twisted General : 0.04 % 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: -0.57 (0.11), residues: 4710 helix: 0.10 (0.09), residues: 2641 sheet: -0.40 (0.29), residues: 329 loop : -0.96 (0.14), residues: 1740 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9420 Ramachandran restraints generated. 4710 Oldfield, 0 Emsley, 4710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 495 time to evaluate : 5.303 Fit side-chains outliers start: 16 outliers final: 6 residues processed: 505 average time/residue: 0.4667 time to fit residues: 400.4350 Evaluate side-chains 445 residues out of total 3886 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 439 time to evaluate : 3.363 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.3593 time to fit residues: 9.1362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 470 random chunks: chunk 396 optimal weight: 20.0000 chunk 356 optimal weight: 7.9990 chunk 197 optimal weight: 2.9990 chunk 121 optimal weight: 0.0980 chunk 240 optimal weight: 0.0670 chunk 190 optimal weight: 10.0000 chunk 368 optimal weight: 9.9990 chunk 142 optimal weight: 20.0000 chunk 224 optimal weight: 20.0000 chunk 274 optimal weight: 0.0070 chunk 426 optimal weight: 20.0000 overall best weight: 2.2340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: