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/7p7m_13240/05_2023/7p7m_13240_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7m_13240/05_2023/7p7m_13240.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7m_13240/05_2023/7p7m_13240_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7m_13240/05_2023/7p7m_13240_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7m_13240/05_2023/7p7m_13240_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7m_13240/05_2023/7p7m_13240.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7m_13240/05_2023/7p7m_13240.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7m_13240/05_2023/7p7m_13240_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7p7m_13240/05_2023/7p7m_13240_updated.pdb" } resolution = 3.2 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= 0.015 sd= 0.054 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 12 5.49 5 S 267 5.16 5 C 24335 2.51 5 N 6171 2.21 5 O 6572 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E ASP 60": "OD1" <-> "OD2" Residue "E TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 59": "OE1" <-> "OE2" Residue "G GLU 792": "OE1" <-> "OE2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C GLU 179": "OE1" <-> "OE2" Residue "C GLU 193": "OE1" <-> "OE2" Residue "C TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H GLU 36": "OE1" <-> "OE2" Residue "H ASP 111": "OD1" <-> "OD2" Residue "H TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 228": "OE1" <-> "OE2" Residue "H TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 81": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 359": "OE1" <-> "OE2" Residue "L PHE 466": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 484": "OE1" <-> "OE2" Residue "M ASP 487": "OD1" <-> "OD2" Residue "N GLU 96": "OE1" <-> "OE2" Residue "N GLU 133": "OE1" <-> "OE2" Residue "N GLU 154": "OE1" <-> "OE2" Residue "N GLU 267": "OE1" <-> "OE2" Residue "K GLU 36": "OE1" <-> "OE2" Residue "K GLU 72": "OE1" <-> "OE2" Residue "K ASP 93": "OD1" <-> "OD2" Residue "J GLU 55": "OE1" <-> "OE2" Residue "J PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 80": "OE1" <-> "OE2" Residue "J ASP 116": "OD1" <-> "OD2" Residue "J GLU 161": "OE1" <-> "OE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/modules/chem_data/mon_lib" Total number of atoms: 37390 Number of models: 1 Model: "" Number of chains: 25 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: 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: 4728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4728 Classifications: {'peptide': 589} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 551} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 1568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1568 Classifications: {'peptide': 198} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 185} 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: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2444 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 296} Chain breaks: 1 Chain: "A" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 808 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain breaks: 1 Chain: "L" Number of atoms: 4549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4549 Classifications: {'peptide': 596} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 577} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 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: 1218 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1218 Classifications: {'peptide': 160} Link IDs: {'PTRANS': 5, 'TRANS': 154} 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: "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: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'HQH': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "L" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 236 Unusual residues: {'3PE': 5, 'LFA': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Chain: "M" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 90 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "N" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 34 Unusual residues: {'LFA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "J" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 73 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 29 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2721 SG CYS F 354 68.304 59.413 189.201 1.00 29.41 S ATOM 2741 SG CYS F 357 72.018 58.525 193.406 1.00 66.62 S ATOM 3062 SG CYS F 398 65.858 55.799 194.107 1.00 84.13 S ATOM 2697 SG CYS F 351 69.711 52.852 190.349 1.00 62.48 S ATOM 4054 SG CYS E 92 79.392 48.996 209.249 1.00 90.80 S ATOM 4088 SG CYS E 97 79.863 49.754 212.667 1.00 81.17 S ATOM 4366 SG CYS E 133 74.149 48.842 209.239 1.00110.33 S ATOM 4392 SG CYS E 137 73.610 49.597 212.541 1.00117.34 S ATOM 5476 SG CYS G 114 78.366 64.998 171.392 1.00 22.23 S ATOM 5416 SG CYS G 105 84.028 67.967 172.844 1.00 38.50 S ATOM 5436 SG CYS G 108 83.943 62.063 170.096 1.00 26.07 S ATOM 5830 SG CYS G 156 71.881 57.611 176.372 1.00 25.53 S ATOM 5811 SG CYS G 153 77.742 55.933 179.006 1.00 38.78 S ATOM 5859 SG CYS G 159 74.316 51.637 175.561 1.00 26.36 S ATOM 6203 SG CYS G 203 76.772 56.692 172.459 1.00 33.79 S ATOM 6428 SG CYS G 230 71.426 49.270 151.292 1.00 48.42 S ATOM 6713 SG CYS G 265 71.310 45.359 156.522 1.00 32.16 S ATOM 6476 SG CYS G 237 66.267 49.363 154.746 1.00 29.99 S ATOM 6452 SG CYS G 233 67.695 43.931 151.365 1.00 60.94 S ATOM 4877 SG CYS G 36 65.724 59.106 179.248 1.00 32.61 S ATOM 4953 SG CYS G 47 67.751 62.179 179.699 1.00 41.12 S ATOM 4979 SG CYS G 50 62.122 64.480 180.096 1.00 40.68 S ATOM 5128 SG CYS G 69 61.334 60.863 179.628 1.00 35.12 S ATOM 17223 SG CYS B 129 90.398 91.720 147.173 1.00 35.97 S ATOM 16720 SG CYS B 64 96.078 94.754 148.831 1.00 50.87 S ATOM 16714 SG CYS B 63 90.921 97.242 151.186 1.00 54.56 S ATOM 17440 SG CYS B 158 92.401 91.175 153.006 1.00 43.38 S ATOM 18818 SG CYS I 109 95.242 74.535 166.721 1.00 39.57 S ATOM 18481 SG CYS I 66 92.882 74.217 160.709 1.00 49.62 S ATOM 18441 SG CYS I 60 96.471 69.340 162.803 1.00 35.38 S ATOM 18459 SG CYS I 63 90.468 70.563 165.525 1.00 31.58 S ATOM 18771 SG CYS I 102 90.750 85.322 159.269 1.00 45.45 S ATOM 18746 SG CYS I 99 95.778 83.637 155.153 1.00 56.07 S ATOM 18789 SG CYS I 105 94.528 80.312 160.571 1.00 56.71 S ATOM 18504 SG CYS I 70 90.254 80.165 155.590 1.00 32.30 S Time building chain proxies: 20.78, per 1000 atoms: 0.56 Number of scatterers: 37390 At special positions: 0 Unit cell: (156.09, 220.22, 242, 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 12 15.00 O 6572 8.00 N 6171 7.00 C 24335 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: 14.18 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E 201 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 133 " pdb="FE1 FES E 201 " - pdb=" SG CYS E 92 " pdb="FE2 FES E 201 " - pdb=" SG CYS E 137 " 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="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="FE3 SF4 F 501 " - pdb=" SG CYS F 398 " pdb="FE1 SF4 F 501 " - pdb=" SG CYS F 354 " 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="FE1 SF4 G1003 " - pdb=" SG CYS G 230 " pdb="FE3 SF4 G1003 " - pdb=" SG CYS G 237 " pdb="FE4 SF4 G1003 " - pdb=" SG CYS G 233 " pdb="FE2 SF4 G1003 " - pdb=" SG CYS G 265 " pdb=" SF4 I 201 " pdb="FE2 SF4 I 201 " - pdb=" SG CYS I 66 " pdb="FE4 SF4 I 201 " - pdb=" SG CYS I 63 " pdb="FE3 SF4 I 201 " - pdb=" SG CYS I 60 " pdb="FE1 SF4 I 201 " - pdb=" SG CYS I 109 " pdb=" SF4 I 202 " pdb="FE3 SF4 I 202 " - pdb=" SG CYS I 105 " pdb="FE4 SF4 I 202 " - pdb=" SG CYS I 70 " pdb="FE2 SF4 I 202 " - pdb=" SG CYS I 99 " pdb="FE1 SF4 I 202 " - pdb=" SG CYS I 102 " Number of angles added : 93 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8624 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 196 helices and 26 sheets defined 54.9% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.99 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 106 Processing helix chain 'F' and resid 109 through 121 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 270 through 275 Processing helix chain 'F' and resid 302 through 304 No H-bonds generated for 'chain 'F' and resid 302 through 304' Processing helix chain 'F' and resid 311 through 315 Processing helix chain 'F' and resid 335 through 348 Processing helix chain 'F' and resid 355 through 372 Proline residue: F 362 - end of helix Processing helix chain 'F' and resid 380 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: 3.628A pdb=" N ALA F 421 " --> pdb=" O GLU F 417 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY F 422 " --> pdb=" O GLU F 418 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 28 removed outlier: 3.956A pdb=" N HIS E 28 " --> pdb=" O HIS E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 47 removed outlier: 4.516A pdb=" N ILE E 37 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU E 38 " --> pdb=" O ALA E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 removed outlier: 4.145A 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: 3.562A pdb=" N GLU E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) removed outlier: 4.152A 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 97 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 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 297 through 310 Processing helix chain 'G' and resid 324 through 334 Processing helix chain 'G' and resid 345 through 360 Processing helix chain 'G' and resid 370 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: 4.273A pdb=" N LYS G 402 " --> pdb=" O ALA G 398 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ALA G 403 " --> pdb=" O VAL G 399 " (cutoff:3.500A) removed outlier: 3.771A 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 440 through 443 removed outlier: 4.417A 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 494 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 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 604 removed outlier: 3.842A pdb=" N GLU G 604 " --> pdb=" O ALA G 601 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 601 through 604' Processing helix chain 'G' and resid 638 through 641 No H-bonds generated for 'chain 'G' and resid 638 through 641' 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 688 No H-bonds generated for 'chain 'G' and resid 686 through 688' Processing helix chain 'G' and resid 764 through 770 removed outlier: 3.586A pdb=" N TRP G 767 " --> pdb=" O PRO G 764 " (cutoff:3.500A) Processing helix chain 'G' and resid 825 through 829 Processing helix chain 'G' and resid 832 through 836 removed outlier: 3.654A 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 65 removed outlier: 5.019A pdb=" N LEU C 58 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 145 removed outlier: 3.716A pdb=" N ASN C 135 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N TRP C 136 " --> pdb=" O ASN C 133 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU C 144 " --> pdb=" O THR C 141 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N PHE C 145 " --> pdb=" O TRP C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 197 removed outlier: 3.621A pdb=" N LEU C 197 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 256 through 260 Processing helix chain 'C' and resid 269 through 275 removed outlier: 3.832A pdb=" N ILE C 275 " --> pdb=" O TYR C 271 " (cutoff:3.500A) 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 422 Processing helix chain 'C' and resid 427 through 432 removed outlier: 4.191A 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 598 No H-bonds generated for 'chain 'C' and resid 595 through 598' Processing helix chain 'B' and resid 38 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 107 through 115 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: 3.519A pdb=" N LYS B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 208 removed outlier: 4.595A pdb=" N GLY B 206 " --> pdb=" O GLU B 202 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N GLU B 207 " --> pdb=" O ARG B 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 25 removed outlier: 3.936A pdb=" N PHE I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 69 Processing helix chain 'I' and resid 104 through 107 No H-bonds generated for 'chain 'I' and resid 104 through 107' 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 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: 4.464A pdb=" N LEU H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE H 100 " --> pdb=" O LEU H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 136 removed outlier: 3.741A pdb=" N VAL H 127 " --> pdb=" O GLY H 124 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU H 131 " --> pdb=" O TYR H 128 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE H 132 " --> pdb=" O ALA H 129 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP H 135 " --> pdb=" O PHE H 132 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER H 136 " --> pdb=" O ALA H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 157 Processing helix chain 'H' and resid 160 through 171 removed outlier: 4.230A pdb=" N GLY H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N VAL H 167 " --> pdb=" O SER H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 181 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 303 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: 3.717A pdb=" N THR A 90 " --> pdb=" O PHE A 86 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE A 92 " --> pdb=" O TRP A 88 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ARG A 93 " --> pdb=" O SER A 89 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N GLU A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N TRP A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N VAL A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 21 removed outlier: 4.561A pdb=" N ALA L 5 " --> pdb=" O ASN L 2 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR L 7 " --> pdb=" O LEU L 4 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LEU L 10 " --> pdb=" O THR L 7 " (cutoff:3.500A) Proline residue: L 11 - end of helix removed outlier: 3.513A pdb=" N LEU L 18 " --> pdb=" O PHE L 15 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER L 21 " --> pdb=" O LEU L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 54 Processing helix chain 'L' and resid 83 through 106 removed outlier: 4.033A pdb=" N TRP L 105 " --> pdb=" O MET L 101 " (cutoff:3.500A) 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 209 Proline residue: L 205 - end of helix removed outlier: 3.762A pdb=" N ALA L 209 " --> pdb=" O PRO L 205 " (cutoff:3.500A) Processing helix chain 'L' and resid 213 through 229 Processing helix chain 'L' and resid 237 through 244 removed outlier: 4.382A pdb=" N ASP L 241 " --> pdb=" O THR L 237 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N MET L 243 " --> pdb=" O LEU L 239 " (cutoff:3.500A) removed outlier: 5.865A 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 261 through 268 Processing helix chain 'L' and resid 270 through 274 Processing helix chain 'L' and resid 277 through 300 removed outlier: 4.158A 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 356 Processing helix chain 'L' and resid 373 through 386 Processing helix chain 'L' and resid 394 through 408 Processing helix chain 'L' and resid 412 through 436 Processing helix chain 'L' and resid 455 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 518 through 523 Processing helix chain 'L' and resid 526 through 536 Processing helix chain 'L' and resid 538 through 548 removed outlier: 6.062A pdb=" N ASP L 542 " --> pdb=" O TRP L 539 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N VAL L 548 " --> pdb=" O TYR L 545 " (cutoff:3.500A) Processing helix chain 'L' and resid 550 through 562 removed outlier: 5.004A pdb=" N ARG L 562 " --> pdb=" O TRP L 558 " (cutoff:3.500A) Processing helix chain 'L' and resid 564 through 586 Proline residue: L 572 - end of helix removed outlier: 3.850A pdb=" N LEU L 585 " --> pdb=" O LYS L 581 " (cutoff:3.500A) removed outlier: 4.641A 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 2 through 23 Proline residue: M 10 - end of helix removed outlier: 3.899A pdb=" N GLU M 21 " --> pdb=" O CYS M 17 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N ARG M 22 " --> pdb=" O TRP M 18 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N PHE M 23 " --> pdb=" O GLN M 19 " (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 105 Processing helix chain 'M' and resid 113 through 132 Processing helix chain 'M' and resid 136 through 157 removed outlier: 4.582A pdb=" N LEU M 147 " --> pdb=" O TRP M 143 " (cutoff:3.500A) removed outlier: 4.296A 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 219 through 233 Processing helix chain 'M' and resid 242 through 249 Processing helix chain 'M' and resid 256 through 260 Processing helix chain 'M' and resid 266 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 306 Proline residue: M 288 - end of helix Processing helix chain 'M' and resid 311 through 332 removed outlier: 3.695A pdb=" N TYR M 331 " --> pdb=" O LEU M 327 " (cutoff:3.500A) removed outlier: 4.035A 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 396 removed outlier: 3.687A 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 removed outlier: 4.043A pdb=" N GLY M 428 " --> pdb=" O ILE M 424 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU M 429 " --> pdb=" O SER M 425 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N VAL M 430 " --> pdb=" O THR M 426 " (cutoff:3.500A) 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 502 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: 4.300A pdb=" N TRP N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N PHE N 54 " --> pdb=" O VAL N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 71 through 97 Proline residue: N 93 - end of helix removed outlier: 4.428A 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 227 through 233 Processing helix chain 'N' and resid 236 through 260 removed outlier: 4.426A pdb=" N SER N 246 " --> pdb=" O LEU N 242 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N LYS N 247 " --> pdb=" O ALA N 243 " (cutoff:3.500A) Processing helix chain 'N' and resid 262 through 265 Processing helix chain 'N' and resid 267 through 288 removed outlier: 4.333A pdb=" N ALA N 288 " --> pdb=" O GLY N 284 " (cutoff:3.500A) Processing helix chain 'N' and resid 294 through 316 removed outlier: 4.019A pdb=" N ALA N 315 " --> pdb=" O VAL N 311 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU N 316 " --> pdb=" O ALA N 312 " (cutoff:3.500A) 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 383 Processing helix chain 'N' and resid 390 through 404 Processing helix chain 'N' and resid 408 through 433 removed outlier: 4.076A pdb=" N TYR N 433 " --> pdb=" O ALA N 429 " (cutoff:3.500A) Processing helix chain 'N' and resid 448 through 469 Processing helix chain 'N' and resid 472 through 480 Processing helix chain 'K' and resid 4 through 23 Processing helix chain 'K' and resid 28 through 53 Processing helix chain 'K' and resid 57 through 87 Processing helix chain 'J' and resid 2 through 19 Processing helix chain 'J' and resid 25 through 46 Processing helix chain 'J' and resid 49 through 57 Processing helix chain 'J' and resid 63 through 74 Processing helix chain 'J' and resid 90 through 113 removed outlier: 5.814A pdb=" N GLY J 95 " --> pdb=" O GLN J 91 " (cutoff:3.500A) Proline residue: J 96 - end of helix removed outlier: 3.752A pdb=" N GLY J 113 " --> pdb=" O TYR J 109 " (cutoff:3.500A) 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: 6.563A pdb=" N ARG F 127 " --> pdb=" O LEU F 87 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N CYS F 89 " --> pdb=" O ARG F 127 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N TYR F 129 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA F 91 " --> pdb=" O TYR F 129 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N PHE F 131 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLU F 168 " --> pdb=" O GLY F 128 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ILE F 130 " --> pdb=" O GLU F 168 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N PHE F 170 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LEU F 132 " --> pdb=" O PHE F 170 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N HIS F 172 " --> pdb=" O LEU F 132 " (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 143 through 145 Processing sheet with id= F, first strand: chain 'G' and resid 11 through 14 removed outlier: 6.469A pdb=" N THR G 77 " --> pdb=" O HIS G 7 " (cutoff:3.500A) removed outlier: 4.428A 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: 6.286A pdb=" N ARG G 244 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N LEU G 248 " --> pdb=" O ARG G 244 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'G' and resid 285 through 288 Processing sheet with id= K, first strand: chain 'G' and resid 314 through 317 removed outlier: 6.862A pdb=" N ALA G 565 " --> pdb=" O ILE G 315 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ILE G 317 " --> pdb=" O ALA G 565 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL G 567 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU G 591 " --> pdb=" O VAL G 566 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N VAL G 568 " --> pdb=" O LEU G 591 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N MET G 593 " --> pdb=" O VAL G 568 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU G 608 " --> pdb=" O VAL G 594 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ASP G 596 " --> pdb=" O LEU G 608 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N LEU G 610 " --> pdb=" O ASP G 596 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'G' and resid 530 through 534 removed outlier: 6.403A pdb=" N ALA G 376 " --> pdb=" O LEU G 499 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ILE G 501 " --> pdb=" O ALA G 376 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N LEU G 378 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N GLY G 503 " --> pdb=" O LEU G 378 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N LEU G 380 " --> pdb=" O GLY G 503 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL G 379 " --> pdb=" O PRO G 430 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N PHE G 432 " --> pdb=" O VAL G 379 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TRP G 447 " --> pdb=" O VAL G 433 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASN G 435 " --> pdb=" O TRP G 447 " (cutoff:3.500A) removed outlier: 5.535A 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 813 through 816 Processing sheet with id= O, first strand: chain 'G' and resid 841 through 844 removed outlier: 8.006A pdb=" N ILE G 842 " --> pdb=" O THR G 870 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU G 844 " --> pdb=" O PRO G 872 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLU G 874 " --> pdb=" O LEU G 844 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER G 861 " --> pdb=" O LYS G 906 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS G 906 " --> pdb=" O SER G 861 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ASP G 904 " --> pdb=" O SER G 863 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 38 through 41 removed outlier: 4.175A pdb=" N VAL C 49 " --> pdb=" O GLN C 41 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA C 116 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ILE C 103 " --> pdb=" O LEU C 74 " (cutoff:3.500A) removed outlier: 5.506A 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: 6.441A 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 219 removed outlier: 3.632A pdb=" N ASP C 244 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ASP C 238 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 5.494A 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: 3.721A pdb=" N GLY C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'B' and resid 3 through 6 Processing sheet with id= U, first strand: chain 'B' and resid 95 through 99 removed outlier: 6.368A pdb=" N TRP B 122 " --> pdb=" O MET B 96 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL B 98 " --> pdb=" O TRP B 122 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 124 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 6.975A 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 81 removed outlier: 3.541A pdb=" N GLN I 78 " --> pdb=" O PHE I 91 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE I 91 " --> pdb=" O GLN I 78 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ALA I 80 " --> pdb=" O PRO I 89 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'L' and resid 68 through 70 Processing sheet with id= Y, first strand: chain 'L' and resid 60 through 66 removed outlier: 7.113A pdb=" N PHE L 77 " --> pdb=" O LEU L 64 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'M' and resid 65 through 72 removed outlier: 6.764A pdb=" N ILE M 77 " --> pdb=" O TRP M 71 " (cutoff:3.500A) 1855 hydrogen bonds defined for protein. 5298 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: 15.58 Time building geometry restraints manager: 15.43 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: 15914 1.42 - 1.64: 21903 1.64 - 1.86: 409 1.86 - 2.09: 0 2.09 - 2.31: 92 Bond restraints: 38318 Sorted by residual: bond pdb=" C24 HQH H 701 " pdb=" C25 HQH H 701 " ideal model delta sigma weight residual 1.539 1.366 0.173 2.00e-02 2.50e+03 7.49e+01 bond pdb=" C12 HQH H 701 " pdb=" C19 HQH H 701 " ideal model delta sigma weight residual 1.534 1.362 0.172 2.00e-02 2.50e+03 7.42e+01 bond pdb=" C24 HQH H 701 " pdb=" N5 HQH H 701 " ideal model delta sigma weight residual 1.498 1.371 0.127 2.00e-02 2.50e+03 4.01e+01 bond pdb=" C12 HQH H 701 " pdb=" N5 HQH H 701 " ideal model delta sigma weight residual 1.494 1.371 0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" C11 HQH H 701 " pdb=" C18 HQH H 701 " ideal model delta sigma weight residual 1.558 1.466 0.092 2.00e-02 2.50e+03 2.10e+01 ... (remaining 38313 not shown) Histogram of bond angle deviations from ideal: 69.36 - 82.86: 88 82.86 - 96.35: 0 96.35 - 109.84: 4979 109.84 - 123.33: 45488 123.33 - 136.83: 1428 Bond angle restraints: 51983 Sorted by residual: angle pdb=" C14 HQH H 701 " pdb=" C9 HQH H 701 " pdb=" C7 HQH H 701 " ideal model delta sigma weight residual 68.20 118.40 -50.20 3.00e+00 1.11e-01 2.80e+02 angle pdb=" C18 HQH H 701 " pdb=" C11 HQH H 701 " pdb=" C22 HQH H 701 " ideal model delta sigma weight residual 74.50 118.63 -44.13 3.00e+00 1.11e-01 2.16e+02 angle pdb=" C13 HQH H 701 " pdb=" C20 HQH H 701 " pdb=" C17 HQH H 701 " ideal model delta sigma weight residual 85.93 126.12 -40.19 3.00e+00 1.11e-01 1.80e+02 angle pdb=" C16 HQH H 701 " pdb=" C9 HQH H 701 " pdb=" C7 HQH H 701 " ideal model delta sigma weight residual 85.85 119.62 -33.77 3.00e+00 1.11e-01 1.27e+02 angle pdb=" C14 HQH H 701 " pdb=" C9 HQH H 701 " pdb=" C16 HQH H 701 " ideal model delta sigma weight residual 152.69 121.94 30.75 3.00e+00 1.11e-01 1.05e+02 ... (remaining 51978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.91: 21867 33.91 - 67.83: 528 67.83 - 101.74: 27 101.74 - 135.65: 0 135.65 - 169.57: 1 Dihedral angle restraints: 22423 sinusoidal: 8940 harmonic: 13483 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 180.00 131.51 48.49 0 5.00e+00 4.00e-02 9.40e+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 88.02 169.57 1 2.00e+01 2.50e-03 4.76e+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 180.00 146.34 33.66 0 5.00e+00 4.00e-02 4.53e+01 ... (remaining 22420 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.245: 5774 4.245 - 8.491: 0 8.491 - 12.736: 0 12.736 - 16.981: 0 16.981 - 21.226: 28 Chirality restraints: 5802 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 -10.67 21.23 2.00e-01 2.50e+01 1.13e+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 -10.62 21.17 2.00e-01 2.50e+01 1.12e+04 chirality pdb="FE4 SF4 I 201 " pdb=" S1 SF4 I 201 " pdb=" S2 SF4 I 201 " pdb=" S3 SF4 I 201 " both_signs ideal model delta sigma weight residual False 10.55 -10.61 21.16 2.00e-01 2.50e+01 1.12e+04 ... (remaining 5799 not shown) Planarity restraints: 6502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 HQH H 701 " -0.016 2.00e-02 2.50e+03 2.50e-02 1.72e+01 pdb=" C13 HQH H 701 " 0.057 2.00e-02 2.50e+03 pdb=" C19 HQH H 701 " -0.013 2.00e-02 2.50e+03 pdb=" C23 HQH H 701 " -0.007 2.00e-02 2.50e+03 pdb=" C24 HQH H 701 " -0.018 2.00e-02 2.50e+03 pdb=" C25 HQH H 701 " -0.003 2.00e-02 2.50e+03 pdb=" C28 HQH H 701 " -0.010 2.00e-02 2.50e+03 pdb=" N5 HQH H 701 " -0.031 2.00e-02 2.50e+03 pdb=" O2 HQH H 701 " -0.000 2.00e-02 2.50e+03 pdb=" O3 HQH H 701 " 0.042 2.00e-02 2.50e+03 pdb=" O4 HQH H 701 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU G 792 " 0.019 2.00e-02 2.50e+03 3.85e-02 1.48e+01 pdb=" CD GLU G 792 " -0.067 2.00e-02 2.50e+03 pdb=" OE1 GLU G 792 " 0.024 2.00e-02 2.50e+03 pdb=" OE2 GLU G 792 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR N 64 " 0.051 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO N 65 " -0.132 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 ... (remaining 6499 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 3878 2.75 - 3.29: 36552 3.29 - 3.83: 67516 3.83 - 4.36: 80550 4.36 - 4.90: 137631 Nonbonded interactions: 326127 Sorted by model distance: nonbonded pdb=" O ILE N 386 " pdb=" OG1 THR N 389 " model vdw 2.214 2.440 nonbonded pdb=" OH TYR H 128 " pdb=" O ALA J 60 " model vdw 2.221 2.440 nonbonded pdb=" OH TYR A 69 " pdb=" O SER K 74 " model vdw 2.242 2.440 nonbonded pdb=" O THR M 422 " pdb=" OG1 THR M 426 " model vdw 2.253 2.440 nonbonded pdb=" OH TYR L 594 " pdb=" OD2 ASP N 229 " model vdw 2.273 2.440 ... (remaining 326122 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: 0.010 Normalize map: mean=0, sd=1: 0.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 4.320 Check model and map are aligned: 0.490 Set scattering table: 0.280 Process input model: 101.950 Find NCS groups from input model: 1.480 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: 0.020 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 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 0.173 38318 Z= 0.307 Angle : 0.875 50.197 51983 Z= 0.411 Chirality : 1.468 21.226 5802 Planarity : 0.006 0.077 6502 Dihedral : 14.330 169.568 13799 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.35 % Favored : 97.63 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.94 % Cis-general : 0.00 % Twisted Proline : 0.46 % 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: -0.55 (0.11), residues: 4680 helix: 0.34 (0.09), residues: 2665 sheet: -1.09 (0.26), residues: 333 loop : -1.24 (0.14), residues: 1682 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9360 Ramachandran restraints generated. 4680 Oldfield, 0 Emsley, 4680 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 375 time to evaluate : 4.368 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 382 average time/residue: 0.4782 time to fit residues: 307.5198 Evaluate side-chains 355 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 348 time to evaluate : 4.282 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3591 time to fit residues: 10.1446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 467 random chunks: chunk 394 optimal weight: 9.9990 chunk 353 optimal weight: 20.0000 chunk 196 optimal weight: 6.9990 chunk 120 optimal weight: 0.4980 chunk 238 optimal weight: 5.9990 chunk 189 optimal weight: 9.9990 chunk 366 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 222 optimal weight: 20.0000 chunk 272 optimal weight: 2.9990 chunk 424 optimal weight: 5.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- 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: