Starting phenix.real_space_refine (version: dev) on Wed Feb 22 03:32:09 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utd_26767/02_2023/7utd_26767_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utd_26767/02_2023/7utd_26767.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utd_26767/02_2023/7utd_26767_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utd_26767/02_2023/7utd_26767_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utd_26767/02_2023/7utd_26767_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utd_26767/02_2023/7utd_26767.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utd_26767/02_2023/7utd_26767.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utd_26767/02_2023/7utd_26767_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utd_26767/02_2023/7utd_26767_updated.pdb" } resolution = 2.19 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= 0.003 sd= 0.068 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 Process input model Symmetric amino acids flipped Residue "A GLU 320": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 421": "OE1" <-> "OE2" Residue "B ASP 297": "OD1" <-> "OD2" Residue "C GLU 320": "OE1" <-> "OE2" Residue "C GLU 322": "OE1" <-> "OE2" Residue "E GLU 320": "OE1" <-> "OE2" Residue "E GLU 322": "OE1" <-> "OE2" Residue "E TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 421": "OE1" <-> "OE2" Residue "F ASP 297": "OD1" <-> "OD2" Residue "G GLU 320": "OE1" <-> "OE2" Residue "G GLU 322": "OE1" <-> "OE2" Residue "I GLU 320": "OE1" <-> "OE2" Residue "I GLU 322": "OE1" <-> "OE2" Residue "I TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 421": "OE1" <-> "OE2" Residue "J ASP 297": "OD1" <-> "OD2" Residue "K GLU 320": "OE1" <-> "OE2" Residue "K GLU 322": "OE1" <-> "OE2" Residue "K TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 421": "OE1" <-> "OE2" Residue "L ASP 297": "OD1" <-> "OD2" Residue "M GLU 320": "OE1" <-> "OE2" Residue "M GLU 322": "OE1" <-> "OE2" Residue "O GLU 320": "OE1" <-> "OE2" Residue "O GLU 322": "OE1" <-> "OE2" Residue "Q ARG 26": "NH1" <-> "NH2" Residue "Q GLU 75": "OE1" <-> "OE2" Residue "R ARG 26": "NH1" <-> "NH2" Residue "R GLU 75": "OE1" <-> "OE2" Residue "S ARG 26": "NH1" <-> "NH2" Residue "S GLU 75": "OE1" <-> "OE2" Residue "T ARG 26": "NH1" <-> "NH2" Residue "T GLU 75": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 54200 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4037 Classifications: {'peptide': 513} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 480} Chain: "B" Number of atoms: 2459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2459 Classifications: {'peptide': 322} Link IDs: {'PCIS': 5, 'PTRANS': 18, 'TRANS': 298} Chain: "C" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4037 Classifications: {'peptide': 513} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 480} Chain: "D" Number of atoms: 2459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2459 Classifications: {'peptide': 322} Link IDs: {'PCIS': 5, 'PTRANS': 18, 'TRANS': 298} Chain: "E" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4037 Classifications: {'peptide': 513} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 480} Chain: "F" Number of atoms: 2459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2459 Classifications: {'peptide': 322} Link IDs: {'PCIS': 5, 'PTRANS': 18, 'TRANS': 298} Chain: "G" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4037 Classifications: {'peptide': 513} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 480} Chain: "H" Number of atoms: 2459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2459 Classifications: {'peptide': 322} Link IDs: {'PCIS': 5, 'PTRANS': 18, 'TRANS': 298} Chain: "I" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4037 Classifications: {'peptide': 513} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 480} Chain: "J" Number of atoms: 2459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2459 Classifications: {'peptide': 322} Link IDs: {'PCIS': 5, 'PTRANS': 18, 'TRANS': 298} Chain: "K" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4037 Classifications: {'peptide': 513} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 480} Chain: "L" Number of atoms: 2459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2459 Classifications: {'peptide': 322} Link IDs: {'PCIS': 5, 'PTRANS': 18, 'TRANS': 298} Chain: "M" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4037 Classifications: {'peptide': 513} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 480} Chain: "N" Number of atoms: 2459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2459 Classifications: {'peptide': 322} Link IDs: {'PCIS': 5, 'PTRANS': 18, 'TRANS': 298} Chain: "O" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4037 Classifications: {'peptide': 513} Modifications used: {'COO': 1, 'PEPT-D': 1} Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 480} Chain: "P" Number of atoms: 2459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2459 Classifications: {'peptide': 322} Link IDs: {'PCIS': 5, 'PTRANS': 18, 'TRANS': 298} Chain: "Q" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 442 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "R" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 442 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "S" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 442 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "T" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 442 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Ad-hoc single atom residues: {'3NI': 1} Unusual residues: {' MG': 1, 'FCO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'F3S': 3, 'MQ9': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'MQ9:plan-3': 1, 'MQ9:plan-2': 1, 'MQ9:plan-10': 1, 'MQ9:plan-6': 1, 'MQ9:plan-5': 1, 'MQ9:plan-4': 1} Unresolved non-hydrogen planarities: 30 Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Ad-hoc single atom residues: {'3NI': 1} Unusual residues: {' MG': 1, 'FCO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'F3S': 3, 'MQ9': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'MQ9:plan-3': 1, 'MQ9:plan-2': 1, 'MQ9:plan-10': 1, 'MQ9:plan-6': 1, 'MQ9:plan-5': 1, 'MQ9:plan-4': 1} Unresolved non-hydrogen planarities: 30 Chain: "E" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Ad-hoc single atom residues: {'3NI': 1} Unusual residues: {' MG': 1, 'FCO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "F" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'F3S': 3, 'MQ9': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'MQ9:plan-3': 1, 'MQ9:plan-2': 1, 'MQ9:plan-10': 1, 'MQ9:plan-6': 1, 'MQ9:plan-5': 1, 'MQ9:plan-4': 1} Unresolved non-hydrogen planarities: 30 Chain: "G" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Ad-hoc single atom residues: {'3NI': 1} Unusual residues: {' MG': 1, 'FCO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "H" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'F3S': 3, 'MQ9': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'MQ9:plan-3': 1, 'MQ9:plan-2': 1, 'MQ9:plan-10': 1, 'MQ9:plan-6': 1, 'MQ9:plan-5': 1, 'MQ9:plan-4': 1} Unresolved non-hydrogen planarities: 30 Chain: "I" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Ad-hoc single atom residues: {'3NI': 1} Unusual residues: {' MG': 1, 'FCO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "J" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'F3S': 3, 'MQ9': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'MQ9:plan-3': 1, 'MQ9:plan-2': 1, 'MQ9:plan-10': 1, 'MQ9:plan-6': 1, 'MQ9:plan-5': 1, 'MQ9:plan-4': 1} Unresolved non-hydrogen planarities: 30 Chain: "K" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Ad-hoc single atom residues: {'3NI': 1} Unusual residues: {' MG': 1, 'FCO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "L" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'F3S': 3, 'MQ9': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'MQ9:plan-3': 1, 'MQ9:plan-2': 1, 'MQ9:plan-10': 1, 'MQ9:plan-6': 1, 'MQ9:plan-5': 1, 'MQ9:plan-4': 1} Unresolved non-hydrogen planarities: 30 Chain: "M" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Ad-hoc single atom residues: {'3NI': 1} Unusual residues: {' MG': 1, 'FCO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "N" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'F3S': 3, 'MQ9': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'MQ9:plan-3': 1, 'MQ9:plan-2': 1, 'MQ9:plan-10': 1, 'MQ9:plan-6': 1, 'MQ9:plan-5': 1, 'MQ9:plan-4': 1} Unresolved non-hydrogen planarities: 30 Chain: "O" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Ad-hoc single atom residues: {'3NI': 1} Unusual residues: {' MG': 1, 'FCO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "P" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'F3S': 3, 'MQ9': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'MQ9:plan-3': 1, 'MQ9:plan-2': 1, 'MQ9:plan-10': 1, 'MQ9:plan-6': 1, 'MQ9:plan-5': 1, 'MQ9:plan-4': 1} Unresolved non-hydrogen planarities: 30 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 450 SG CYS A 62 112.110 149.929 83.727 1.00 7.30 S ATOM 468 SG CYS A 65 115.504 149.488 83.550 1.00 7.48 S ATOM 3991 SG CYS A 510 112.332 151.898 86.242 1.00 10.99 S ATOM 4012 SG CYS A 513 114.699 149.077 86.447 1.00 9.30 S ATOM 468 SG CYS A 65 115.504 149.488 83.550 1.00 7.48 S ATOM 4012 SG CYS A 513 114.699 149.077 86.447 1.00 9.30 S ATOM 4880 SG CYS B 113 102.922 141.922 83.809 1.00 6.06 S ATOM 4116 SG CYS B 12 107.714 145.863 81.956 1.00 6.64 S ATOM 5229 SG CYS B 161 105.876 140.521 79.400 1.00 4.36 S ATOM 6033 SG CYS B 263 104.504 138.702 73.867 1.00 4.94 S ATOM 6015 SG CYS B 260 105.801 133.912 69.785 1.00 4.04 S ATOM 5869 SG CYS B 242 104.255 139.867 67.916 1.00 3.80 S ATOM 5557 SG CYS B 203 109.392 133.680 61.376 1.00 3.50 S ATOM 5742 SG CYS B 226 110.465 127.137 62.357 1.00 5.33 S ATOM 5803 SG CYS B 233 109.017 130.791 67.010 1.00 4.65 S ATOM 6946 SG CYS C 62 105.291 159.313 36.029 1.00 7.28 S ATOM 6964 SG CYS C 65 101.899 159.668 36.167 1.00 7.46 S ATOM 10487 SG CYS C 510 105.687 161.981 34.312 1.00 11.00 S ATOM 10508 SG CYS C 513 102.707 160.075 33.270 1.00 9.29 S ATOM 6964 SG CYS C 65 101.899 159.668 36.167 1.00 7.46 S ATOM 10508 SG CYS C 513 102.707 160.075 33.270 1.00 9.29 S ATOM 10612 SG CYS D 12 108.469 153.906 36.094 1.00 6.63 S ATOM 11725 SG CYS D 161 108.811 147.736 36.608 1.00 4.36 S ATOM 11376 SG CYS D 113 112.211 149.769 32.807 1.00 6.08 S ATOM 12365 SG CYS D 242 109.712 142.849 47.109 1.00 3.75 S ATOM 12529 SG CYS D 263 109.439 143.869 41.131 1.00 4.90 S ATOM 12511 SG CYS D 260 106.820 138.463 43.406 1.00 4.07 S ATOM 12053 SG CYS D 203 102.918 136.295 51.385 1.00 3.48 S ATOM 12238 SG CYS D 226 100.299 130.956 48.295 1.00 5.35 S ATOM 12299 SG CYS D 233 102.811 135.489 45.096 1.00 4.72 S ATOM 13442 SG CYS E 62 48.511 112.110 83.727 1.00 7.30 S ATOM 13460 SG CYS E 65 48.952 115.504 83.550 1.00 7.48 S ATOM 16983 SG CYS E 510 46.542 112.332 86.242 1.00 10.99 S ATOM 17004 SG CYS E 513 49.363 114.699 86.447 1.00 9.30 S ATOM 13460 SG CYS E 65 48.952 115.504 83.550 1.00 7.48 S ATOM 17004 SG CYS E 513 49.363 114.699 86.447 1.00 9.30 S ATOM 17872 SG CYS F 113 56.518 102.922 83.809 1.00 6.06 S ATOM 17108 SG CYS F 12 52.577 107.714 81.956 1.00 6.64 S ATOM 18221 SG CYS F 161 57.919 105.876 79.400 1.00 4.36 S ATOM 19025 SG CYS F 263 59.738 104.504 73.867 1.00 4.94 S ATOM 19007 SG CYS F 260 64.528 105.801 69.785 1.00 4.04 S ATOM 18861 SG CYS F 242 58.573 104.255 67.916 1.00 3.80 S ATOM 18549 SG CYS F 203 64.760 109.392 61.376 1.00 3.50 S ATOM 18734 SG CYS F 226 71.303 110.465 62.357 1.00 5.33 S ATOM 18795 SG CYS F 233 67.649 109.017 67.010 1.00 4.65 S ATOM 19938 SG CYS G 62 39.127 105.291 36.029 1.00 7.28 S ATOM 19956 SG CYS G 65 38.772 101.899 36.167 1.00 7.46 S ATOM 23479 SG CYS G 510 36.459 105.687 34.312 1.00 11.00 S ATOM 23500 SG CYS G 513 38.365 102.707 33.270 1.00 9.29 S ATOM 19956 SG CYS G 65 38.772 101.899 36.167 1.00 7.46 S ATOM 23500 SG CYS G 513 38.365 102.707 33.270 1.00 9.29 S ATOM 23604 SG CYS H 12 44.534 108.469 36.094 1.00 6.63 S ATOM 24717 SG CYS H 161 50.704 108.811 36.608 1.00 4.36 S ATOM 24368 SG CYS H 113 48.671 112.211 32.807 1.00 6.08 S ATOM 25357 SG CYS H 242 55.591 109.712 47.109 1.00 3.75 S ATOM 25521 SG CYS H 263 54.571 109.439 41.131 1.00 4.90 S ATOM 25503 SG CYS H 260 59.977 106.820 43.406 1.00 4.07 S ATOM 25045 SG CYS H 203 62.145 102.918 51.385 1.00 3.48 S ATOM 25230 SG CYS H 226 67.484 100.299 48.295 1.00 5.35 S ATOM 25291 SG CYS H 233 62.951 102.811 45.096 1.00 4.72 S ATOM 26434 SG CYS I 62 149.928 86.331 83.727 1.00 7.30 S ATOM 26452 SG CYS I 65 149.487 82.937 83.550 1.00 7.48 S ATOM 29975 SG CYS I 510 151.897 86.109 86.242 1.00 10.99 S ATOM 29996 SG CYS I 513 149.076 83.742 86.447 1.00 9.30 S ATOM 26452 SG CYS I 65 149.487 82.937 83.550 1.00 7.48 S ATOM 29996 SG CYS I 513 149.076 83.742 86.447 1.00 9.30 S ATOM 30864 SG CYS J 113 141.921 95.519 83.809 1.00 6.06 S ATOM 30100 SG CYS J 12 145.862 90.727 81.956 1.00 6.64 S ATOM 31213 SG CYS J 161 140.520 92.565 79.400 1.00 4.36 S ATOM 32017 SG CYS J 263 138.701 93.937 73.867 1.00 4.94 S ATOM 31999 SG CYS J 260 133.911 92.640 69.785 1.00 4.04 S ATOM 31853 SG CYS J 242 139.866 94.186 67.916 1.00 3.80 S ATOM 31541 SG CYS J 203 133.679 89.049 61.376 1.00 3.50 S ATOM 31726 SG CYS J 226 127.136 87.976 62.357 1.00 5.33 S ATOM 31787 SG CYS J 233 130.790 89.424 67.010 1.00 4.65 S ATOM 32930 SG CYS K 62 86.330 48.511 83.727 1.00 7.30 S ATOM 32948 SG CYS K 65 82.936 48.952 83.550 1.00 7.48 S ATOM 36471 SG CYS K 510 86.108 46.542 86.242 1.00 10.99 S ATOM 36492 SG CYS K 513 83.741 49.363 86.447 1.00 9.30 S ATOM 32948 SG CYS K 65 82.936 48.952 83.550 1.00 7.48 S ATOM 36492 SG CYS K 513 83.741 49.363 86.447 1.00 9.30 S ATOM 37360 SG CYS L 113 95.518 56.518 83.809 1.00 6.06 S ATOM 36596 SG CYS L 12 90.726 52.577 81.956 1.00 6.64 S ATOM 37709 SG CYS L 161 92.564 57.919 79.400 1.00 4.36 S ATOM 38513 SG CYS L 263 93.936 59.738 73.867 1.00 4.94 S ATOM 38495 SG CYS L 260 92.639 64.528 69.785 1.00 4.04 S ATOM 38349 SG CYS L 242 94.185 58.573 67.916 1.00 3.80 S ATOM 38037 SG CYS L 203 89.048 64.760 61.376 1.00 3.50 S ATOM 38222 SG CYS L 226 87.975 71.303 62.357 1.00 5.33 S ATOM 38283 SG CYS L 233 89.423 67.649 67.010 1.00 4.65 S ATOM 39426 SG CYS M 62 93.149 39.127 36.029 1.00 7.28 S ATOM 39444 SG CYS M 65 96.541 38.772 36.167 1.00 7.46 S ATOM 42967 SG CYS M 510 92.753 36.459 34.312 1.00 11.00 S ATOM 42988 SG CYS M 513 95.733 38.365 33.270 1.00 9.29 S ATOM 39444 SG CYS M 65 96.541 38.772 36.167 1.00 7.46 S ATOM 42988 SG CYS M 513 95.733 38.365 33.270 1.00 9.29 S ATOM 43092 SG CYS N 12 89.971 44.534 36.094 1.00 6.63 S ATOM 44205 SG CYS N 161 89.629 50.704 36.608 1.00 4.36 S ATOM 43856 SG CYS N 113 86.229 48.671 32.807 1.00 6.08 S ATOM 44845 SG CYS N 242 88.728 55.591 47.109 1.00 3.75 S ATOM 45009 SG CYS N 263 89.001 54.571 41.131 1.00 4.90 S ATOM 44991 SG CYS N 260 91.620 59.977 43.406 1.00 4.07 S ATOM 44533 SG CYS N 203 95.522 62.145 51.385 1.00 3.48 S ATOM 44718 SG CYS N 226 98.141 67.484 48.295 1.00 5.35 S ATOM 44779 SG CYS N 233 95.629 62.951 45.096 1.00 4.72 S ATOM 45922 SG CYS O 62 159.312 93.150 36.029 1.00 7.28 S ATOM 45940 SG CYS O 65 159.667 96.542 36.167 1.00 7.46 S ATOM 49463 SG CYS O 510 161.980 92.754 34.312 1.00 11.00 S ATOM 49484 SG CYS O 513 160.074 95.734 33.270 1.00 9.29 S ATOM 45940 SG CYS O 65 159.667 96.542 36.167 1.00 7.46 S ATOM 49484 SG CYS O 513 160.074 95.734 33.270 1.00 9.29 S ATOM 49588 SG CYS P 12 153.905 89.972 36.094 1.00 6.63 S ATOM 50701 SG CYS P 161 147.735 89.630 36.608 1.00 4.36 S ATOM 50352 SG CYS P 113 149.768 86.230 32.807 1.00 6.08 S ATOM 51341 SG CYS P 242 142.848 88.729 47.109 1.00 3.75 S ATOM 51505 SG CYS P 263 143.868 89.002 41.131 1.00 4.90 S ATOM 51487 SG CYS P 260 138.462 91.621 43.406 1.00 4.07 S ATOM 51029 SG CYS P 203 136.294 95.523 51.385 1.00 3.48 S ATOM 51214 SG CYS P 226 130.955 98.142 48.295 1.00 5.35 S ATOM 51275 SG CYS P 233 135.488 95.630 45.096 1.00 4.72 S Time building chain proxies: 23.03, per 1000 atoms: 0.42 Number of scatterers: 54200 At special positions: 0 Unit cell: (199.26, 199.26, 120.54, 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) Ni 8 28.00 Fe 80 26.01 S 408 16.00 Mg 8 11.99 O 10084 8.00 N 9160 7.00 C 34452 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.63 Conformation dependent library (CDL) restraints added in 6.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B 402 " pdb="FE1 F3S B 402 " - pdb=" SG CYS B 113 " pdb="FE3 F3S B 402 " - pdb=" SG CYS B 12 " pdb="FE4 F3S B 402 " - pdb=" SG CYS B 161 " pdb=" F3S B 403 " pdb="FE4 F3S B 403 " - pdb=" SG CYS B 242 " pdb="FE1 F3S B 403 " - pdb=" SG CYS B 263 " pdb="FE3 F3S B 403 " - pdb=" SG CYS B 260 " pdb=" F3S B 404 " pdb="FE4 F3S B 404 " - pdb=" SG CYS B 233 " pdb="FE3 F3S B 404 " - pdb=" SG CYS B 226 " pdb="FE1 F3S B 404 " - pdb=" SG CYS B 203 " pdb=" F3S D 402 " pdb="FE4 F3S D 402 " - pdb=" SG CYS D 113 " pdb="FE1 F3S D 402 " - pdb=" SG CYS D 12 " pdb="FE3 F3S D 402 " - pdb=" SG CYS D 161 " pdb=" F3S D 403 " pdb="FE1 F3S D 403 " - pdb=" SG CYS D 242 " pdb="FE3 F3S D 403 " - pdb=" SG CYS D 263 " pdb="FE4 F3S D 403 " - pdb=" SG CYS D 260 " pdb=" F3S D 404 " pdb="FE4 F3S D 404 " - pdb=" SG CYS D 233 " pdb="FE3 F3S D 404 " - pdb=" SG CYS D 226 " pdb="FE1 F3S D 404 " - pdb=" SG CYS D 203 " pdb=" F3S F 402 " pdb="FE1 F3S F 402 " - pdb=" SG CYS F 113 " pdb="FE3 F3S F 402 " - pdb=" SG CYS F 12 " pdb="FE4 F3S F 402 " - pdb=" SG CYS F 161 " pdb=" F3S F 403 " pdb="FE4 F3S F 403 " - pdb=" SG CYS F 242 " pdb="FE1 F3S F 403 " - pdb=" SG CYS F 263 " pdb="FE3 F3S F 403 " - pdb=" SG CYS F 260 " pdb=" F3S F 404 " pdb="FE4 F3S F 404 " - pdb=" SG CYS F 233 " pdb="FE3 F3S F 404 " - pdb=" SG CYS F 226 " pdb="FE1 F3S F 404 " - pdb=" SG CYS F 203 " pdb=" F3S H 402 " pdb="FE4 F3S H 402 " - pdb=" SG CYS H 113 " pdb="FE1 F3S H 402 " - pdb=" SG CYS H 12 " pdb="FE3 F3S H 402 " - pdb=" SG CYS H 161 " pdb=" F3S H 403 " pdb="FE1 F3S H 403 " - pdb=" SG CYS H 242 " pdb="FE3 F3S H 403 " - pdb=" SG CYS H 263 " pdb="FE4 F3S H 403 " - pdb=" SG CYS H 260 " pdb=" F3S H 404 " pdb="FE4 F3S H 404 " - pdb=" SG CYS H 233 " pdb="FE3 F3S H 404 " - pdb=" SG CYS H 226 " pdb="FE1 F3S H 404 " - pdb=" SG CYS H 203 " pdb=" F3S J 402 " pdb="FE1 F3S J 402 " - pdb=" SG CYS J 113 " pdb="FE3 F3S J 402 " - pdb=" SG CYS J 12 " pdb="FE4 F3S J 402 " - pdb=" SG CYS J 161 " pdb=" F3S J 403 " pdb="FE4 F3S J 403 " - pdb=" SG CYS J 242 " pdb="FE1 F3S J 403 " - pdb=" SG CYS J 263 " pdb="FE3 F3S J 403 " - pdb=" SG CYS J 260 " pdb=" F3S J 404 " pdb="FE4 F3S J 404 " - pdb=" SG CYS J 233 " pdb="FE3 F3S J 404 " - pdb=" SG CYS J 226 " pdb="FE1 F3S J 404 " - pdb=" SG CYS J 203 " pdb=" F3S L 402 " pdb="FE1 F3S L 402 " - pdb=" SG CYS L 113 " pdb="FE3 F3S L 402 " - pdb=" SG CYS L 12 " pdb="FE4 F3S L 402 " - pdb=" SG CYS L 161 " pdb=" F3S L 403 " pdb="FE4 F3S L 403 " - pdb=" SG CYS L 242 " pdb="FE1 F3S L 403 " - pdb=" SG CYS L 263 " pdb="FE3 F3S L 403 " - pdb=" SG CYS L 260 " pdb=" F3S L 404 " pdb="FE4 F3S L 404 " - pdb=" SG CYS L 233 " pdb="FE3 F3S L 404 " - pdb=" SG CYS L 226 " pdb="FE1 F3S L 404 " - pdb=" SG CYS L 203 " pdb=" F3S N 402 " pdb="FE4 F3S N 402 " - pdb=" SG CYS N 113 " pdb="FE1 F3S N 402 " - pdb=" SG CYS N 12 " pdb="FE3 F3S N 402 " - pdb=" SG CYS N 161 " pdb=" F3S N 403 " pdb="FE1 F3S N 403 " - pdb=" SG CYS N 242 " pdb="FE3 F3S N 403 " - pdb=" SG CYS N 263 " pdb="FE4 F3S N 403 " - pdb=" SG CYS N 260 " pdb=" F3S N 404 " pdb="FE4 F3S N 404 " - pdb=" SG CYS N 233 " pdb="FE3 F3S N 404 " - pdb=" SG CYS N 226 " pdb="FE1 F3S N 404 " - pdb=" SG CYS N 203 " pdb=" F3S P 402 " pdb="FE4 F3S P 402 " - pdb=" SG CYS P 113 " pdb="FE1 F3S P 402 " - pdb=" SG CYS P 12 " pdb="FE3 F3S P 402 " - pdb=" SG CYS P 161 " pdb=" F3S P 403 " pdb="FE1 F3S P 403 " - pdb=" SG CYS P 242 " pdb="FE3 F3S P 403 " - pdb=" SG CYS P 263 " pdb="FE4 F3S P 403 " - pdb=" SG CYS P 260 " pdb=" F3S P 404 " pdb="FE4 F3S P 404 " - pdb=" SG CYS P 233 " pdb="FE3 F3S P 404 " - pdb=" SG CYS P 226 " pdb="FE1 F3S P 404 " - pdb=" SG CYS P 203 " Number of angles added : 216 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DHI A 166 " pdb=" CB DHI C 166 " pdb=" CB DHI E 166 " pdb=" CB DHI G 166 " pdb=" CB DHI I 166 " pdb=" CB DHI K 166 " pdb=" CB DHI M 166 " pdb=" CB DHI O 166 " Number of C-beta restraints generated: 12512 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 352 helices and 40 sheets defined 41.8% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.49 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 53 through 61 Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 66 through 80 Processing helix chain 'A' and resid 87 through 111 Proline residue: A 106 - end of helix Processing helix chain 'A' and resid 114 through 118 Processing helix chain 'A' and resid 120 through 122 No H-bonds generated for 'chain 'A' and resid 120 through 122' Processing helix chain 'A' and resid 128 through 135 Processing helix chain 'A' and resid 143 through 161 removed outlier: 4.017A pdb=" N ALA A 151 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS A 152 " --> pdb=" O VAL A 148 " (cutoff:3.500A) Proline residue: A 153 - end of helix Processing helix chain 'A' and resid 181 through 197 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 217 through 226 Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 234 through 245 Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 277 through 280 No H-bonds generated for 'chain 'A' and resid 277 through 280' Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 318 through 320 No H-bonds generated for 'chain 'A' and resid 318 through 320' Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 359 through 367 Processing helix chain 'A' and resid 380 through 387 Processing helix chain 'A' and resid 392 through 416 removed outlier: 3.850A pdb=" N GLY A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Proline residue: A 404 - end of helix Processing helix chain 'A' and resid 465 through 470 Processing helix chain 'A' and resid 481 through 486 Processing helix chain 'A' and resid 498 through 507 removed outlier: 3.536A pdb=" N PHE A 507 " --> pdb=" O VAL A 503 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'B' and resid 14 through 21 Processing helix chain 'B' and resid 27 through 33 Processing helix chain 'B' and resid 49 through 61 Processing helix chain 'B' and resid 93 through 103 Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 119 through 121 No H-bonds generated for 'chain 'B' and resid 119 through 121' Processing helix chain 'B' and resid 165 through 176 removed outlier: 4.384A pdb=" N ILE B 171 " --> pdb=" O TRP B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 182 No H-bonds generated for 'chain 'B' and resid 180 through 182' Processing helix chain 'B' and resid 192 through 195 No H-bonds generated for 'chain 'B' and resid 192 through 195' Processing helix chain 'B' and resid 206 through 210 Processing helix chain 'B' and resid 219 through 223 Processing helix chain 'B' and resid 235 through 237 No H-bonds generated for 'chain 'B' and resid 235 through 237' Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 253 through 256 No H-bonds generated for 'chain 'B' and resid 253 through 256' Processing helix chain 'B' and resid 270 through 273 Processing helix chain 'B' and resid 298 through 311 Processing helix chain 'B' and resid 314 through 317 Processing helix chain 'C' and resid 42 through 46 Processing helix chain 'C' and resid 53 through 61 Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 66 through 80 Processing helix chain 'C' and resid 87 through 111 Proline residue: C 106 - end of helix Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 120 through 122 No H-bonds generated for 'chain 'C' and resid 120 through 122' Processing helix chain 'C' and resid 128 through 135 Processing helix chain 'C' and resid 143 through 161 removed outlier: 4.017A pdb=" N ALA C 151 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS C 152 " --> pdb=" O VAL C 148 " (cutoff:3.500A) Proline residue: C 153 - end of helix Processing helix chain 'C' and resid 181 through 197 Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 217 through 226 Processing helix chain 'C' and resid 228 through 232 Processing helix chain 'C' and resid 234 through 245 Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'C' and resid 277 through 280 No H-bonds generated for 'chain 'C' and resid 277 through 280' Processing helix chain 'C' and resid 298 through 300 No H-bonds generated for 'chain 'C' and resid 298 through 300' Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 328 through 333 Processing helix chain 'C' and resid 359 through 367 Processing helix chain 'C' and resid 380 through 387 Processing helix chain 'C' and resid 392 through 416 removed outlier: 3.850A pdb=" N GLY C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) Proline residue: C 404 - end of helix Processing helix chain 'C' and resid 465 through 470 Processing helix chain 'C' and resid 481 through 486 Processing helix chain 'C' and resid 498 through 507 removed outlier: 3.535A pdb=" N PHE C 507 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'D' and resid 14 through 21 Processing helix chain 'D' and resid 27 through 33 Processing helix chain 'D' and resid 49 through 61 Processing helix chain 'D' and resid 93 through 103 Processing helix chain 'D' and resid 112 through 116 Processing helix chain 'D' and resid 119 through 121 No H-bonds generated for 'chain 'D' and resid 119 through 121' Processing helix chain 'D' and resid 165 through 176 removed outlier: 4.385A pdb=" N ILE D 171 " --> pdb=" O TRP D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 182 No H-bonds generated for 'chain 'D' and resid 180 through 182' Processing helix chain 'D' and resid 192 through 195 No H-bonds generated for 'chain 'D' and resid 192 through 195' Processing helix chain 'D' and resid 206 through 210 Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 235 through 237 No H-bonds generated for 'chain 'D' and resid 235 through 237' Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 253 through 256 No H-bonds generated for 'chain 'D' and resid 253 through 256' Processing helix chain 'D' and resid 270 through 273 Processing helix chain 'D' and resid 298 through 310 Processing helix chain 'D' and resid 315 through 317 No H-bonds generated for 'chain 'D' and resid 315 through 317' Processing helix chain 'E' and resid 42 through 46 Processing helix chain 'E' and resid 53 through 61 Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 66 through 80 Processing helix chain 'E' and resid 87 through 111 Proline residue: E 106 - end of helix Processing helix chain 'E' and resid 114 through 118 Processing helix chain 'E' and resid 120 through 122 No H-bonds generated for 'chain 'E' and resid 120 through 122' Processing helix chain 'E' and resid 128 through 135 Processing helix chain 'E' and resid 143 through 161 removed outlier: 4.017A pdb=" N ALA E 151 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS E 152 " --> pdb=" O VAL E 148 " (cutoff:3.500A) Proline residue: E 153 - end of helix Processing helix chain 'E' and resid 181 through 197 Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 217 through 226 Processing helix chain 'E' and resid 228 through 232 Processing helix chain 'E' and resid 234 through 245 Processing helix chain 'E' and resid 266 through 268 No H-bonds generated for 'chain 'E' and resid 266 through 268' Processing helix chain 'E' and resid 277 through 280 No H-bonds generated for 'chain 'E' and resid 277 through 280' Processing helix chain 'E' and resid 298 through 300 No H-bonds generated for 'chain 'E' and resid 298 through 300' Processing helix chain 'E' and resid 318 through 320 No H-bonds generated for 'chain 'E' and resid 318 through 320' Processing helix chain 'E' and resid 328 through 333 Processing helix chain 'E' and resid 359 through 367 Processing helix chain 'E' and resid 380 through 387 Processing helix chain 'E' and resid 392 through 416 removed outlier: 3.850A pdb=" N GLY E 403 " --> pdb=" O ARG E 399 " (cutoff:3.500A) Proline residue: E 404 - end of helix Processing helix chain 'E' and resid 465 through 470 Processing helix chain 'E' and resid 481 through 486 Processing helix chain 'E' and resid 498 through 507 removed outlier: 3.536A pdb=" N PHE E 507 " --> pdb=" O VAL E 503 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 515 Processing helix chain 'F' and resid 14 through 21 Processing helix chain 'F' and resid 27 through 33 Processing helix chain 'F' and resid 49 through 61 Processing helix chain 'F' and resid 93 through 103 Processing helix chain 'F' and resid 112 through 116 Processing helix chain 'F' and resid 119 through 121 No H-bonds generated for 'chain 'F' and resid 119 through 121' Processing helix chain 'F' and resid 165 through 176 removed outlier: 4.384A pdb=" N ILE F 171 " --> pdb=" O TRP F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 182 No H-bonds generated for 'chain 'F' and resid 180 through 182' Processing helix chain 'F' and resid 192 through 195 No H-bonds generated for 'chain 'F' and resid 192 through 195' Processing helix chain 'F' and resid 206 through 210 Processing helix chain 'F' and resid 219 through 223 Processing helix chain 'F' and resid 235 through 237 No H-bonds generated for 'chain 'F' and resid 235 through 237' Processing helix chain 'F' and resid 247 through 249 No H-bonds generated for 'chain 'F' and resid 247 through 249' Processing helix chain 'F' and resid 253 through 256 No H-bonds generated for 'chain 'F' and resid 253 through 256' Processing helix chain 'F' and resid 270 through 273 Processing helix chain 'F' and resid 298 through 311 Processing helix chain 'F' and resid 314 through 317 Processing helix chain 'G' and resid 42 through 46 Processing helix chain 'G' and resid 53 through 61 Proline residue: G 59 - end of helix Processing helix chain 'G' and resid 66 through 80 Processing helix chain 'G' and resid 87 through 111 Proline residue: G 106 - end of helix Processing helix chain 'G' and resid 114 through 118 Processing helix chain 'G' and resid 120 through 122 No H-bonds generated for 'chain 'G' and resid 120 through 122' Processing helix chain 'G' and resid 128 through 135 Processing helix chain 'G' and resid 143 through 161 removed outlier: 4.017A pdb=" N ALA G 151 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS G 152 " --> pdb=" O VAL G 148 " (cutoff:3.500A) Proline residue: G 153 - end of helix Processing helix chain 'G' and resid 181 through 197 Processing helix chain 'G' and resid 208 through 213 Processing helix chain 'G' and resid 217 through 226 Processing helix chain 'G' and resid 228 through 232 Processing helix chain 'G' and resid 234 through 245 Processing helix chain 'G' and resid 266 through 268 No H-bonds generated for 'chain 'G' and resid 266 through 268' Processing helix chain 'G' and resid 277 through 280 No H-bonds generated for 'chain 'G' and resid 277 through 280' Processing helix chain 'G' and resid 298 through 300 No H-bonds generated for 'chain 'G' and resid 298 through 300' Processing helix chain 'G' and resid 318 through 320 No H-bonds generated for 'chain 'G' and resid 318 through 320' Processing helix chain 'G' and resid 328 through 333 Processing helix chain 'G' and resid 359 through 367 Processing helix chain 'G' and resid 380 through 387 Processing helix chain 'G' and resid 392 through 416 removed outlier: 3.850A pdb=" N GLY G 403 " --> pdb=" O ARG G 399 " (cutoff:3.500A) Proline residue: G 404 - end of helix Processing helix chain 'G' and resid 465 through 470 Processing helix chain 'G' and resid 481 through 486 Processing helix chain 'G' and resid 498 through 507 removed outlier: 3.535A pdb=" N PHE G 507 " --> pdb=" O VAL G 503 " (cutoff:3.500A) Processing helix chain 'G' and resid 511 through 515 Processing helix chain 'H' and resid 14 through 21 Processing helix chain 'H' and resid 27 through 33 Processing helix chain 'H' and resid 49 through 61 Processing helix chain 'H' and resid 93 through 103 Processing helix chain 'H' and resid 112 through 116 Processing helix chain 'H' and resid 119 through 121 No H-bonds generated for 'chain 'H' and resid 119 through 121' Processing helix chain 'H' and resid 165 through 176 removed outlier: 4.385A pdb=" N ILE H 171 " --> pdb=" O TRP H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 182 No H-bonds generated for 'chain 'H' and resid 180 through 182' Processing helix chain 'H' and resid 192 through 195 No H-bonds generated for 'chain 'H' and resid 192 through 195' Processing helix chain 'H' and resid 206 through 210 Processing helix chain 'H' and resid 219 through 223 Processing helix chain 'H' and resid 235 through 237 No H-bonds generated for 'chain 'H' and resid 235 through 237' Processing helix chain 'H' and resid 247 through 249 No H-bonds generated for 'chain 'H' and resid 247 through 249' Processing helix chain 'H' and resid 253 through 256 No H-bonds generated for 'chain 'H' and resid 253 through 256' Processing helix chain 'H' and resid 270 through 273 Processing helix chain 'H' and resid 298 through 310 Processing helix chain 'H' and resid 315 through 317 No H-bonds generated for 'chain 'H' and resid 315 through 317' Processing helix chain 'I' and resid 42 through 46 Processing helix chain 'I' and resid 53 through 61 Proline residue: I 59 - end of helix Processing helix chain 'I' and resid 66 through 80 Processing helix chain 'I' and resid 87 through 111 Proline residue: I 106 - end of helix Processing helix chain 'I' and resid 114 through 118 Processing helix chain 'I' and resid 120 through 122 No H-bonds generated for 'chain 'I' and resid 120 through 122' Processing helix chain 'I' and resid 128 through 135 Processing helix chain 'I' and resid 143 through 161 removed outlier: 4.017A pdb=" N ALA I 151 " --> pdb=" O VAL I 147 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS I 152 " --> pdb=" O VAL I 148 " (cutoff:3.500A) Proline residue: I 153 - end of helix Processing helix chain 'I' and resid 181 through 197 Processing helix chain 'I' and resid 208 through 213 Processing helix chain 'I' and resid 217 through 226 Processing helix chain 'I' and resid 228 through 232 Processing helix chain 'I' and resid 234 through 245 Processing helix chain 'I' and resid 266 through 268 No H-bonds generated for 'chain 'I' and resid 266 through 268' Processing helix chain 'I' and resid 277 through 280 No H-bonds generated for 'chain 'I' and resid 277 through 280' Processing helix chain 'I' and resid 298 through 300 No H-bonds generated for 'chain 'I' and resid 298 through 300' Processing helix chain 'I' and resid 318 through 320 No H-bonds generated for 'chain 'I' and resid 318 through 320' Processing helix chain 'I' and resid 328 through 333 Processing helix chain 'I' and resid 359 through 367 Processing helix chain 'I' and resid 380 through 387 Processing helix chain 'I' and resid 392 through 416 removed outlier: 3.850A pdb=" N GLY I 403 " --> pdb=" O ARG I 399 " (cutoff:3.500A) Proline residue: I 404 - end of helix Processing helix chain 'I' and resid 465 through 470 Processing helix chain 'I' and resid 481 through 486 Processing helix chain 'I' and resid 498 through 507 removed outlier: 3.536A pdb=" N PHE I 507 " --> pdb=" O VAL I 503 " (cutoff:3.500A) Processing helix chain 'I' and resid 511 through 515 Processing helix chain 'J' and resid 14 through 21 Processing helix chain 'J' and resid 27 through 33 Processing helix chain 'J' and resid 49 through 61 Processing helix chain 'J' and resid 93 through 103 Processing helix chain 'J' and resid 112 through 116 Processing helix chain 'J' and resid 119 through 121 No H-bonds generated for 'chain 'J' and resid 119 through 121' Processing helix chain 'J' and resid 165 through 176 removed outlier: 4.384A pdb=" N ILE J 171 " --> pdb=" O TRP J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 180 through 182 No H-bonds generated for 'chain 'J' and resid 180 through 182' Processing helix chain 'J' and resid 192 through 195 No H-bonds generated for 'chain 'J' and resid 192 through 195' Processing helix chain 'J' and resid 206 through 210 Processing helix chain 'J' and resid 219 through 223 Processing helix chain 'J' and resid 235 through 237 No H-bonds generated for 'chain 'J' and resid 235 through 237' Processing helix chain 'J' and resid 247 through 249 No H-bonds generated for 'chain 'J' and resid 247 through 249' Processing helix chain 'J' and resid 253 through 256 No H-bonds generated for 'chain 'J' and resid 253 through 256' Processing helix chain 'J' and resid 270 through 273 Processing helix chain 'J' and resid 298 through 311 Processing helix chain 'J' and resid 314 through 317 Processing helix chain 'K' and resid 42 through 46 Processing helix chain 'K' and resid 53 through 61 Proline residue: K 59 - end of helix Processing helix chain 'K' and resid 66 through 80 Processing helix chain 'K' and resid 87 through 111 Proline residue: K 106 - end of helix Processing helix chain 'K' and resid 114 through 118 Processing helix chain 'K' and resid 120 through 122 No H-bonds generated for 'chain 'K' and resid 120 through 122' Processing helix chain 'K' and resid 128 through 135 Processing helix chain 'K' and resid 143 through 161 removed outlier: 4.017A pdb=" N ALA K 151 " --> pdb=" O VAL K 147 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N LYS K 152 " --> pdb=" O VAL K 148 " (cutoff:3.500A) Proline residue: K 153 - end of helix Processing helix chain 'K' and resid 181 through 197 Processing helix chain 'K' and resid 208 through 213 Processing helix chain 'K' and resid 217 through 226 Processing helix chain 'K' and resid 228 through 232 Processing helix chain 'K' and resid 234 through 245 Processing helix chain 'K' and resid 266 through 268 No H-bonds generated for 'chain 'K' and resid 266 through 268' Processing helix chain 'K' and resid 277 through 280 No H-bonds generated for 'chain 'K' and resid 277 through 280' Processing helix chain 'K' and resid 298 through 300 No H-bonds generated for 'chain 'K' and resid 298 through 300' Processing helix chain 'K' and resid 318 through 320 No H-bonds generated for 'chain 'K' and resid 318 through 320' Processing helix chain 'K' and resid 328 through 333 Processing helix chain 'K' and resid 359 through 367 Processing helix chain 'K' and resid 380 through 387 Processing helix chain 'K' and resid 392 through 416 removed outlier: 3.850A pdb=" N GLY K 403 " --> pdb=" O ARG K 399 " (cutoff:3.500A) Proline residue: K 404 - end of helix Processing helix chain 'K' and resid 465 through 470 Processing helix chain 'K' and resid 481 through 486 Processing helix chain 'K' and resid 498 through 507 removed outlier: 3.536A pdb=" N PHE K 507 " --> pdb=" O VAL K 503 " (cutoff:3.500A) Processing helix chain 'K' and resid 511 through 515 Processing helix chain 'L' and resid 14 through 21 Processing helix chain 'L' and resid 27 through 33 Processing helix chain 'L' and resid 49 through 61 Processing helix chain 'L' and resid 93 through 103 Processing helix chain 'L' and resid 112 through 116 Processing helix chain 'L' and resid 119 through 121 No H-bonds generated for 'chain 'L' and resid 119 through 121' Processing helix chain 'L' and resid 165 through 176 removed outlier: 4.384A pdb=" N ILE L 171 " --> pdb=" O TRP L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 180 through 182 No H-bonds generated for 'chain 'L' and resid 180 through 182' Processing helix chain 'L' and resid 192 through 195 No H-bonds generated for 'chain 'L' and resid 192 through 195' Processing helix chain 'L' and resid 206 through 210 Processing helix chain 'L' and resid 219 through 223 Processing helix chain 'L' and resid 235 through 237 No H-bonds generated for 'chain 'L' and resid 235 through 237' Processing helix chain 'L' and resid 247 through 249 No H-bonds generated for 'chain 'L' and resid 247 through 249' Processing helix chain 'L' and resid 253 through 256 No H-bonds generated for 'chain 'L' and resid 253 through 256' Processing helix chain 'L' and resid 270 through 273 Processing helix chain 'L' and resid 298 through 311 Processing helix chain 'L' and resid 314 through 317 Processing helix chain 'M' and resid 42 through 46 Processing helix chain 'M' and resid 53 through 61 Proline residue: M 59 - end of helix Processing helix chain 'M' and resid 66 through 80 Processing helix chain 'M' and resid 87 through 111 Proline residue: M 106 - end of helix Processing helix chain 'M' and resid 114 through 118 Processing helix chain 'M' and resid 120 through 122 No H-bonds generated for 'chain 'M' and resid 120 through 122' Processing helix chain 'M' and resid 128 through 135 Processing helix chain 'M' and resid 143 through 161 removed outlier: 4.017A pdb=" N ALA M 151 " --> pdb=" O VAL M 147 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS M 152 " --> pdb=" O VAL M 148 " (cutoff:3.500A) Proline residue: M 153 - end of helix Processing helix chain 'M' and resid 181 through 197 Processing helix chain 'M' and resid 208 through 213 Processing helix chain 'M' and resid 217 through 226 Processing helix chain 'M' and resid 228 through 232 Processing helix chain 'M' and resid 234 through 245 Processing helix chain 'M' and resid 266 through 268 No H-bonds generated for 'chain 'M' and resid 266 through 268' Processing helix chain 'M' and resid 277 through 280 No H-bonds generated for 'chain 'M' and resid 277 through 280' Processing helix chain 'M' and resid 298 through 300 No H-bonds generated for 'chain 'M' and resid 298 through 300' Processing helix chain 'M' and resid 318 through 320 No H-bonds generated for 'chain 'M' and resid 318 through 320' Processing helix chain 'M' and resid 328 through 333 Processing helix chain 'M' and resid 359 through 367 Processing helix chain 'M' and resid 380 through 387 Processing helix chain 'M' and resid 392 through 416 removed outlier: 3.850A pdb=" N GLY M 403 " --> pdb=" O ARG M 399 " (cutoff:3.500A) Proline residue: M 404 - end of helix Processing helix chain 'M' and resid 465 through 470 Processing helix chain 'M' and resid 481 through 486 Processing helix chain 'M' and resid 498 through 507 removed outlier: 3.535A pdb=" N PHE M 507 " --> pdb=" O VAL M 503 " (cutoff:3.500A) Processing helix chain 'M' and resid 511 through 515 Processing helix chain 'N' and resid 14 through 21 Processing helix chain 'N' and resid 27 through 33 Processing helix chain 'N' and resid 49 through 61 Processing helix chain 'N' and resid 93 through 103 Processing helix chain 'N' and resid 112 through 116 Processing helix chain 'N' and resid 119 through 121 No H-bonds generated for 'chain 'N' and resid 119 through 121' Processing helix chain 'N' and resid 165 through 176 removed outlier: 4.385A pdb=" N ILE N 171 " --> pdb=" O TRP N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 180 through 182 No H-bonds generated for 'chain 'N' and resid 180 through 182' Processing helix chain 'N' and resid 192 through 195 No H-bonds generated for 'chain 'N' and resid 192 through 195' Processing helix chain 'N' and resid 206 through 210 Processing helix chain 'N' and resid 219 through 223 Processing helix chain 'N' and resid 235 through 237 No H-bonds generated for 'chain 'N' and resid 235 through 237' Processing helix chain 'N' and resid 247 through 249 No H-bonds generated for 'chain 'N' and resid 247 through 249' Processing helix chain 'N' and resid 253 through 256 No H-bonds generated for 'chain 'N' and resid 253 through 256' Processing helix chain 'N' and resid 270 through 273 Processing helix chain 'N' and resid 298 through 310 Processing helix chain 'N' and resid 315 through 317 No H-bonds generated for 'chain 'N' and resid 315 through 317' Processing helix chain 'O' and resid 42 through 46 Processing helix chain 'O' and resid 53 through 61 Proline residue: O 59 - end of helix Processing helix chain 'O' and resid 66 through 80 Processing helix chain 'O' and resid 87 through 111 Proline residue: O 106 - end of helix Processing helix chain 'O' and resid 114 through 118 Processing helix chain 'O' and resid 120 through 122 No H-bonds generated for 'chain 'O' and resid 120 through 122' Processing helix chain 'O' and resid 128 through 135 Processing helix chain 'O' and resid 143 through 161 removed outlier: 4.017A pdb=" N ALA O 151 " --> pdb=" O VAL O 147 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LYS O 152 " --> pdb=" O VAL O 148 " (cutoff:3.500A) Proline residue: O 153 - end of helix Processing helix chain 'O' and resid 181 through 197 Processing helix chain 'O' and resid 208 through 213 Processing helix chain 'O' and resid 217 through 226 Processing helix chain 'O' and resid 228 through 232 Processing helix chain 'O' and resid 234 through 245 Processing helix chain 'O' and resid 266 through 268 No H-bonds generated for 'chain 'O' and resid 266 through 268' Processing helix chain 'O' and resid 277 through 280 No H-bonds generated for 'chain 'O' and resid 277 through 280' Processing helix chain 'O' and resid 298 through 300 No H-bonds generated for 'chain 'O' and resid 298 through 300' Processing helix chain 'O' and resid 318 through 320 No H-bonds generated for 'chain 'O' and resid 318 through 320' Processing helix chain 'O' and resid 328 through 333 Processing helix chain 'O' and resid 359 through 367 Processing helix chain 'O' and resid 380 through 387 Processing helix chain 'O' and resid 392 through 416 removed outlier: 3.850A pdb=" N GLY O 403 " --> pdb=" O ARG O 399 " (cutoff:3.500A) Proline residue: O 404 - end of helix Processing helix chain 'O' and resid 465 through 470 Processing helix chain 'O' and resid 481 through 486 Processing helix chain 'O' and resid 498 through 507 removed outlier: 3.535A pdb=" N PHE O 507 " --> pdb=" O VAL O 503 " (cutoff:3.500A) Processing helix chain 'O' and resid 511 through 515 Processing helix chain 'P' and resid 14 through 21 Processing helix chain 'P' and resid 27 through 33 Processing helix chain 'P' and resid 49 through 61 Processing helix chain 'P' and resid 93 through 103 Processing helix chain 'P' and resid 112 through 116 Processing helix chain 'P' and resid 119 through 121 No H-bonds generated for 'chain 'P' and resid 119 through 121' Processing helix chain 'P' and resid 165 through 176 removed outlier: 4.385A pdb=" N ILE P 171 " --> pdb=" O TRP P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 180 through 182 No H-bonds generated for 'chain 'P' and resid 180 through 182' Processing helix chain 'P' and resid 192 through 195 No H-bonds generated for 'chain 'P' and resid 192 through 195' Processing helix chain 'P' and resid 206 through 210 Processing helix chain 'P' and resid 219 through 223 Processing helix chain 'P' and resid 235 through 237 No H-bonds generated for 'chain 'P' and resid 235 through 237' Processing helix chain 'P' and resid 247 through 249 No H-bonds generated for 'chain 'P' and resid 247 through 249' Processing helix chain 'P' and resid 253 through 256 No H-bonds generated for 'chain 'P' and resid 253 through 256' Processing helix chain 'P' and resid 270 through 273 Processing helix chain 'P' and resid 298 through 310 Processing helix chain 'P' and resid 315 through 317 No H-bonds generated for 'chain 'P' and resid 315 through 317' Processing helix chain 'Q' and resid 21 through 30 Processing helix chain 'Q' and resid 32 through 43 Processing helix chain 'Q' and resid 45 through 60 Processing helix chain 'Q' and resid 62 through 77 Processing helix chain 'R' and resid 21 through 30 Processing helix chain 'R' and resid 32 through 43 Processing helix chain 'R' and resid 45 through 60 Processing helix chain 'R' and resid 62 through 77 Processing helix chain 'S' and resid 21 through 30 Processing helix chain 'S' and resid 32 through 43 Processing helix chain 'S' and resid 45 through 60 Processing helix chain 'S' and resid 62 through 77 Processing helix chain 'T' and resid 21 through 30 Processing helix chain 'T' and resid 32 through 43 Processing helix chain 'T' and resid 45 through 60 Processing helix chain 'T' and resid 62 through 77 Processing sheet with id= A, first strand: chain 'A' and resid 5 through 8 removed outlier: 6.137A pdb=" N ASN A 25 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL A 29 " --> pdb=" O ASN A 25 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 257 through 259 Processing sheet with id= C, first strand: chain 'A' and resid 301 through 304 Processing sheet with id= D, first strand: chain 'A' and resid 433 through 441 removed outlier: 5.871A pdb=" N GLU A 453 " --> pdb=" O ILE A 457 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILE A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.260A pdb=" N ASP B 37 " --> pdb=" O VAL B 4 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N TRP B 6 " --> pdb=" O ASP B 37 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LEU B 39 " --> pdb=" O TRP B 6 " (cutoff:3.500A) removed outlier: 12.229A pdb=" N GLN B 8 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N HIS B 41 " --> pdb=" O GLN B 8 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 5 through 8 removed outlier: 6.137A pdb=" N ASN C 25 " --> pdb=" O VAL C 29 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N VAL C 29 " --> pdb=" O ASN C 25 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 257 through 259 Processing sheet with id= H, first strand: chain 'C' and resid 301 through 304 Processing sheet with id= I, first strand: chain 'C' and resid 433 through 441 removed outlier: 5.873A pdb=" N GLU C 453 " --> pdb=" O ILE C 457 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ILE C 457 " --> pdb=" O GLU C 453 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 156 through 158 removed outlier: 6.260A pdb=" N ASP D 37 " --> pdb=" O VAL D 4 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N TRP D 6 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LEU D 39 " --> pdb=" O TRP D 6 " (cutoff:3.500A) removed outlier: 12.230A pdb=" N GLN D 8 " --> pdb=" O LEU D 39 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N HIS D 41 " --> pdb=" O GLN D 8 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 5 through 8 removed outlier: 6.137A pdb=" N ASN E 25 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL E 29 " --> pdb=" O ASN E 25 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 257 through 259 Processing sheet with id= M, first strand: chain 'E' and resid 301 through 304 Processing sheet with id= N, first strand: chain 'E' and resid 433 through 441 removed outlier: 5.871A pdb=" N GLU E 453 " --> pdb=" O ILE E 457 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILE E 457 " --> pdb=" O GLU E 453 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'F' and resid 156 through 158 removed outlier: 6.260A pdb=" N ASP F 37 " --> pdb=" O VAL F 4 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N TRP F 6 " --> pdb=" O ASP F 37 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LEU F 39 " --> pdb=" O TRP F 6 " (cutoff:3.500A) removed outlier: 12.229A pdb=" N GLN F 8 " --> pdb=" O LEU F 39 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N HIS F 41 " --> pdb=" O GLN F 8 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 5 through 8 removed outlier: 6.137A pdb=" N ASN G 25 " --> pdb=" O VAL G 29 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N VAL G 29 " --> pdb=" O ASN G 25 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'G' and resid 257 through 259 Processing sheet with id= R, first strand: chain 'G' and resid 301 through 304 Processing sheet with id= S, first strand: chain 'G' and resid 433 through 441 removed outlier: 5.873A pdb=" N GLU G 453 " --> pdb=" O ILE G 457 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ILE G 457 " --> pdb=" O GLU G 453 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 156 through 158 removed outlier: 6.260A pdb=" N ASP H 37 " --> pdb=" O VAL H 4 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N TRP H 6 " --> pdb=" O ASP H 37 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LEU H 39 " --> pdb=" O TRP H 6 " (cutoff:3.500A) removed outlier: 12.230A pdb=" N GLN H 8 " --> pdb=" O LEU H 39 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N HIS H 41 " --> pdb=" O GLN H 8 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 5 through 8 removed outlier: 6.137A pdb=" N ASN I 25 " --> pdb=" O VAL I 29 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL I 29 " --> pdb=" O ASN I 25 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'I' and resid 257 through 259 Processing sheet with id= W, first strand: chain 'I' and resid 301 through 304 Processing sheet with id= X, first strand: chain 'I' and resid 433 through 441 removed outlier: 5.871A pdb=" N GLU I 453 " --> pdb=" O ILE I 457 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILE I 457 " --> pdb=" O GLU I 453 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'J' and resid 156 through 158 removed outlier: 6.260A pdb=" N ASP J 37 " --> pdb=" O VAL J 4 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N TRP J 6 " --> pdb=" O ASP J 37 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LEU J 39 " --> pdb=" O TRP J 6 " (cutoff:3.500A) removed outlier: 12.229A pdb=" N GLN J 8 " --> pdb=" O LEU J 39 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N HIS J 41 " --> pdb=" O GLN J 8 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'K' and resid 5 through 8 removed outlier: 6.137A pdb=" N ASN K 25 " --> pdb=" O VAL K 29 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N VAL K 29 " --> pdb=" O ASN K 25 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'K' and resid 257 through 259 Processing sheet with id= AB, first strand: chain 'K' and resid 301 through 304 Processing sheet with id= AC, first strand: chain 'K' and resid 433 through 441 removed outlier: 5.871A pdb=" N GLU K 453 " --> pdb=" O ILE K 457 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N ILE K 457 " --> pdb=" O GLU K 453 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'L' and resid 156 through 158 removed outlier: 6.260A pdb=" N ASP L 37 " --> pdb=" O VAL L 4 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N TRP L 6 " --> pdb=" O ASP L 37 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LEU L 39 " --> pdb=" O TRP L 6 " (cutoff:3.500A) removed outlier: 12.229A pdb=" N GLN L 8 " --> pdb=" O LEU L 39 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N HIS L 41 " --> pdb=" O GLN L 8 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'M' and resid 5 through 8 removed outlier: 6.137A pdb=" N ASN M 25 " --> pdb=" O VAL M 29 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N VAL M 29 " --> pdb=" O ASN M 25 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'M' and resid 257 through 259 Processing sheet with id= AG, first strand: chain 'M' and resid 301 through 304 Processing sheet with id= AH, first strand: chain 'M' and resid 433 through 441 removed outlier: 5.873A pdb=" N GLU M 453 " --> pdb=" O ILE M 457 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ILE M 457 " --> pdb=" O GLU M 453 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'N' and resid 156 through 158 removed outlier: 6.260A pdb=" N ASP N 37 " --> pdb=" O VAL N 4 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N TRP N 6 " --> pdb=" O ASP N 37 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LEU N 39 " --> pdb=" O TRP N 6 " (cutoff:3.500A) removed outlier: 12.230A pdb=" N GLN N 8 " --> pdb=" O LEU N 39 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N HIS N 41 " --> pdb=" O GLN N 8 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'O' and resid 5 through 8 removed outlier: 6.137A pdb=" N ASN O 25 " --> pdb=" O VAL O 29 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N VAL O 29 " --> pdb=" O ASN O 25 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'O' and resid 257 through 259 Processing sheet with id= AL, first strand: chain 'O' and resid 301 through 304 Processing sheet with id= AM, first strand: chain 'O' and resid 433 through 441 removed outlier: 5.873A pdb=" N GLU O 453 " --> pdb=" O ILE O 457 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ILE O 457 " --> pdb=" O GLU O 453 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'P' and resid 156 through 158 removed outlier: 6.260A pdb=" N ASP P 37 " --> pdb=" O VAL P 4 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N TRP P 6 " --> pdb=" O ASP P 37 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N LEU P 39 " --> pdb=" O TRP P 6 " (cutoff:3.500A) removed outlier: 12.230A pdb=" N GLN P 8 " --> pdb=" O LEU P 39 " (cutoff:3.500A) removed outlier: 10.246A pdb=" N HIS P 41 " --> pdb=" O GLN P 8 " (cutoff:3.500A) 1872 hydrogen bonds defined for protein. 5268 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: 17.46 Time building geometry restraints manager: 21.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.67: 55012 1.67 - 2.24: 480 2.24 - 2.82: 144 2.82 - 3.40: 0 3.40 - 3.97: 72 Bond restraints: 55708 Sorted by residual: bond pdb=" S4 F3S D 403 " pdb="FE1 F3S D 403 " ideal model delta sigma weight residual 2.233 3.973 -1.740 2.00e-02 2.50e+03 7.57e+03 bond pdb=" S4 F3S H 403 " pdb="FE1 F3S H 403 " ideal model delta sigma weight residual 2.233 3.973 -1.740 2.00e-02 2.50e+03 7.57e+03 bond pdb=" S4 F3S P 403 " pdb="FE1 F3S P 403 " ideal model delta sigma weight residual 2.233 3.973 -1.740 2.00e-02 2.50e+03 7.57e+03 bond pdb=" S4 F3S N 403 " pdb="FE1 F3S N 403 " ideal model delta sigma weight residual 2.233 3.973 -1.740 2.00e-02 2.50e+03 7.57e+03 bond pdb=" S1 F3S L 403 " pdb="FE4 F3S L 403 " ideal model delta sigma weight residual 2.258 3.974 -1.716 2.00e-02 2.50e+03 7.36e+03 ... (remaining 55703 not shown) Histogram of bond angle deviations from ideal: 39.83 - 66.48: 140 66.48 - 93.14: 164 93.14 - 119.79: 50568 119.79 - 146.44: 24992 146.44 - 173.10: 24 Bond angle restraints: 75888 Sorted by residual: angle pdb=" S1 F3S F 403 " pdb="FE4 F3S F 403 " pdb=" S3 F3S F 403 " ideal model delta sigma weight residual 114.75 63.83 50.92 3.00e+00 1.11e-01 2.88e+02 angle pdb=" S1 F3S L 403 " pdb="FE4 F3S L 403 " pdb=" S3 F3S L 403 " ideal model delta sigma weight residual 114.75 63.83 50.92 3.00e+00 1.11e-01 2.88e+02 angle pdb=" S1 F3S J 403 " pdb="FE4 F3S J 403 " pdb=" S3 F3S J 403 " ideal model delta sigma weight residual 114.75 63.83 50.92 3.00e+00 1.11e-01 2.88e+02 angle pdb=" S1 F3S B 403 " pdb="FE4 F3S B 403 " pdb=" S3 F3S B 403 " ideal model delta sigma weight residual 114.75 63.83 50.92 3.00e+00 1.11e-01 2.88e+02 angle pdb=" S1 F3S D 404 " pdb="FE4 F3S D 404 " pdb=" S3 F3S D 404 " ideal model delta sigma weight residual 114.75 64.32 50.43 3.00e+00 1.11e-01 2.83e+02 ... (remaining 75883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.49: 29382 17.49 - 34.97: 2318 34.97 - 52.46: 452 52.46 - 69.94: 212 69.94 - 87.43: 104 Dihedral angle restraints: 32468 sinusoidal: 12836 harmonic: 19632 Sorted by residual: dihedral pdb=" C ARG T 60 " pdb=" N ARG T 60 " pdb=" CA ARG T 60 " pdb=" CB ARG T 60 " ideal model delta harmonic sigma weight residual -122.60 -135.82 13.22 0 2.50e+00 1.60e-01 2.79e+01 dihedral pdb=" C ARG S 60 " pdb=" N ARG S 60 " pdb=" CA ARG S 60 " pdb=" CB ARG S 60 " ideal model delta harmonic sigma weight residual -122.60 -135.80 13.20 0 2.50e+00 1.60e-01 2.79e+01 dihedral pdb=" C ARG Q 60 " pdb=" N ARG Q 60 " pdb=" CA ARG Q 60 " pdb=" CB ARG Q 60 " ideal model delta harmonic sigma weight residual -122.60 -135.80 13.20 0 2.50e+00 1.60e-01 2.79e+01 ... (remaining 32465 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.838: 8020 3.838 - 7.676: 0 7.676 - 11.515: 0 11.515 - 15.353: 0 15.353 - 19.191: 24 Chirality restraints: 8044 Sorted by residual: chirality pdb=" S2 F3S B 402 " pdb="FE1 F3S B 402 " pdb="FE3 F3S B 402 " pdb="FE4 F3S B 402 " both_signs ideal model delta sigma weight residual False 10.77 -8.42 19.19 2.00e-01 2.50e+01 9.21e+03 chirality pdb=" S2 F3S F 402 " pdb="FE1 F3S F 402 " pdb="FE3 F3S F 402 " pdb="FE4 F3S F 402 " both_signs ideal model delta sigma weight residual False 10.77 -8.42 19.19 2.00e-01 2.50e+01 9.21e+03 chirality pdb=" S2 F3S L 402 " pdb="FE1 F3S L 402 " pdb="FE3 F3S L 402 " pdb="FE4 F3S L 402 " both_signs ideal model delta sigma weight residual False 10.77 -8.42 19.19 2.00e-01 2.50e+01 9.21e+03 ... (remaining 8041 not shown) Planarity restraints: 9932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 MQ9 J 401 " -0.552 2.00e-02 2.50e+03 4.72e-01 2.79e+03 pdb=" C13 MQ9 J 401 " 0.700 2.00e-02 2.50e+03 pdb=" C14 MQ9 J 401 " 0.405 2.00e-02 2.50e+03 pdb=" C15 MQ9 J 401 " -0.241 2.00e-02 2.50e+03 pdb=" C16 MQ9 J 401 " -0.313 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 MQ9 F 401 " -0.552 2.00e-02 2.50e+03 4.72e-01 2.79e+03 pdb=" C13 MQ9 F 401 " 0.700 2.00e-02 2.50e+03 pdb=" C14 MQ9 F 401 " 0.405 2.00e-02 2.50e+03 pdb=" C15 MQ9 F 401 " -0.241 2.00e-02 2.50e+03 pdb=" C16 MQ9 F 401 " -0.313 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 MQ9 L 401 " -0.552 2.00e-02 2.50e+03 4.72e-01 2.79e+03 pdb=" C13 MQ9 L 401 " 0.700 2.00e-02 2.50e+03 pdb=" C14 MQ9 L 401 " 0.405 2.00e-02 2.50e+03 pdb=" C15 MQ9 L 401 " -0.241 2.00e-02 2.50e+03 pdb=" C16 MQ9 L 401 " -0.313 2.00e-02 2.50e+03 ... (remaining 9929 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 563 2.55 - 3.14: 49945 3.14 - 3.73: 102944 3.73 - 4.31: 152156 4.31 - 4.90: 239920 Nonbonded interactions: 545528 Sorted by model distance: nonbonded pdb=" O VAL E 462 " pdb="MG MG E 603 " model vdw 1.964 2.170 nonbonded pdb=" O VAL A 462 " pdb="MG MG A 603 " model vdw 1.964 2.170 nonbonded pdb=" O VAL I 462 " pdb="MG MG I 603 " model vdw 1.964 2.170 nonbonded pdb=" O VAL K 462 " pdb="MG MG K 603 " model vdw 1.964 2.170 nonbonded pdb=" O VAL O 462 " pdb="MG MG O 603 " model vdw 1.964 2.170 ... (remaining 545523 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 80 7.16 5 Ni 8 6.56 5 Mg 8 5.21 5 S 408 5.16 5 C 34452 2.51 5 N 9160 2.21 5 O 10084 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.080 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: 12.570 Check model and map are aligned: 0.600 Process input model: 117.140 Find NCS groups from input model: 3.150 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Set scattering table: 0.370 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6124 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 : 0.060 1.740 55708 Z= 3.857 Angle : 2.356 50.915 75888 Z= 0.990 Chirality : 1.002 19.191 8044 Planarity : 0.018 0.472 9932 Dihedral : 15.033 87.430 19956 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.17 % Favored : 97.71 % Rotamer Outliers : 1.36 % Cbeta Deviations : 0.45 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.10), residues: 6852 helix: 0.09 (0.09), residues: 2820 sheet: -0.17 (0.20), residues: 544 loop : 0.08 (0.11), residues: 3488 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 768 time to evaluate : 4.986 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 14 residues processed: 815 average time/residue: 1.3717 time to fit residues: 1421.3185 Evaluate side-chains 386 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 372 time to evaluate : 4.724 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 10 average time/residue: 0.7808 time to fit residues: 17.6655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 577 optimal weight: 5.9990 chunk 518 optimal weight: 10.0000 chunk 287 optimal weight: 6.9990 chunk 177 optimal weight: 8.9990 chunk 349 optimal weight: 7.9990 chunk 276 optimal weight: 10.0000 chunk 536 optimal weight: 7.9990 chunk 207 optimal weight: 6.9990 chunk 325 optimal weight: 5.9990 chunk 399 optimal weight: 5.9990 chunk 621 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 97 GLN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 197 ASN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 HIS ** E 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 197 ASN ** F 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 270 HIS ** I 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 197 ASN ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 GLN ** K 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 197 ASN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 270 HIS ** O 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 270 HIS Q 67 ASN R 67 ASN S 67 ASN T 67 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.182 55708 Z= 0.562 Angle : 2.168 79.713 75888 Z= 0.775 Chirality : 0.079 2.060 8044 Planarity : 0.005 0.042 9932 Dihedral : 6.918 73.042 7604 Min Nonbonded Distance : 1.541 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.10), residues: 6852 helix: 0.39 (0.09), residues: 2708 sheet: -0.10 (0.20), residues: 544 loop : 0.03 (0.11), residues: 3600 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 363 time to evaluate : 4.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 162 outliers final: 37 residues processed: 490 average time/residue: 1.2991 time to fit residues: 824.8626 Evaluate side-chains 354 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 317 time to evaluate : 4.633 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 33 residues processed: 5 average time/residue: 0.5095 time to fit residues: 10.5172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 345 optimal weight: 9.9990 chunk 192 optimal weight: 2.9990 chunk 516 optimal weight: 7.9990 chunk 422 optimal weight: 0.7980 chunk 171 optimal weight: 0.9990 chunk 622 optimal weight: 1.9990 chunk 672 optimal weight: 0.9980 chunk 554 optimal weight: 7.9990 chunk 617 optimal weight: 4.9990 chunk 212 optimal weight: 5.9990 chunk 499 optimal weight: 20.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 HIS B 8 GLN ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 HIS C 197 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 ASN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 HIS F 8 GLN ** F 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 193 HIS G 197 ASN ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 25 ASN ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 HIS J 8 GLN ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN ** K 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 HIS L 8 GLN ** L 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 193 HIS M 197 ASN ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 193 HIS O 197 ASN ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 GLN T 33 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6216 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.170 55708 Z= 0.391 Angle : 1.968 85.226 75888 Z= 0.695 Chirality : 0.095 2.364 8044 Planarity : 0.004 0.047 9932 Dihedral : 6.697 73.417 7604 Min Nonbonded Distance : 1.514 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.10), residues: 6852 helix: 0.56 (0.10), residues: 2748 sheet: -0.30 (0.21), residues: 560 loop : 0.09 (0.11), residues: 3544 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 379 time to evaluate : 4.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 136 outliers final: 36 residues processed: 475 average time/residue: 1.2972 time to fit residues: 800.8518 Evaluate side-chains 348 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 312 time to evaluate : 4.717 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 32 residues processed: 4 average time/residue: 0.5286 time to fit residues: 9.8524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 614 optimal weight: 20.0000 chunk 467 optimal weight: 1.9990 chunk 322 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 296 optimal weight: 8.9990 chunk 417 optimal weight: 7.9990 chunk 624 optimal weight: 6.9990 chunk 661 optimal weight: 3.9990 chunk 326 optimal weight: 0.6980 chunk 591 optimal weight: 5.9990 chunk 178 optimal weight: 20.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 97 GLN ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 97 GLN ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 97 GLN ** K 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6287 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.169 55708 Z= 0.418 Angle : 1.964 84.925 75888 Z= 0.696 Chirality : 0.082 1.609 8044 Planarity : 0.004 0.032 9932 Dihedral : 6.748 75.209 7604 Min Nonbonded Distance : 1.526 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.11), residues: 6852 helix: 0.61 (0.10), residues: 2732 sheet: -0.21 (0.21), residues: 560 loop : 0.11 (0.12), residues: 3560 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 329 time to evaluate : 4.736 Fit side-chains revert: symmetry clash outliers start: 132 outliers final: 52 residues processed: 428 average time/residue: 1.2137 time to fit residues: 686.2972 Evaluate side-chains 352 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 300 time to evaluate : 4.696 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 44 residues processed: 8 average time/residue: 0.9125 time to fit residues: 16.4777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 550 optimal weight: 7.9990 chunk 375 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 492 optimal weight: 4.9990 chunk 272 optimal weight: 20.0000 chunk 564 optimal weight: 6.9990 chunk 457 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 337 optimal weight: 0.6980 chunk 593 optimal weight: 9.9990 chunk 166 optimal weight: 40.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 HIS B 282 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 ASN ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 HIS F 282 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 135 HIS J 282 GLN ** K 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 135 HIS L 282 GLN ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 300 ASN ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 300 ASN ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 33 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.3513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.169 55708 Z= 0.501 Angle : 1.936 85.110 75888 Z= 0.693 Chirality : 0.095 2.316 8044 Planarity : 0.005 0.040 9932 Dihedral : 6.888 82.350 7604 Min Nonbonded Distance : 1.513 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer Outliers : 2.63 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.11), residues: 6852 helix: 0.48 (0.10), residues: 2700 sheet: 0.08 (0.22), residues: 528 loop : -0.12 (0.11), residues: 3624 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 335 time to evaluate : 4.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 149 outliers final: 52 residues processed: 450 average time/residue: 1.2311 time to fit residues: 730.2019 Evaluate side-chains 373 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 321 time to evaluate : 4.706 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 48 residues processed: 8 average time/residue: 0.4846 time to fit residues: 13.1621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 222 optimal weight: 5.9990 chunk 595 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 388 optimal weight: 3.9990 chunk 163 optimal weight: 0.6980 chunk 661 optimal weight: 0.0270 chunk 549 optimal weight: 6.9990 chunk 306 optimal weight: 3.9990 chunk 55 optimal weight: 20.0000 chunk 218 optimal weight: 0.9980 chunk 347 optimal weight: 1.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 502 HIS ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 502 HIS ** F 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 502 HIS ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 282 GLN ** K 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 502 HIS ** L 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 282 GLN ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 300 ASN ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6260 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.174 55708 Z= 0.324 Angle : 1.899 85.588 75888 Z= 0.671 Chirality : 0.083 1.560 8044 Planarity : 0.004 0.036 9932 Dihedral : 6.604 83.621 7604 Min Nonbonded Distance : 1.525 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer Outliers : 1.99 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.11), residues: 6852 helix: 0.58 (0.10), residues: 2748 sheet: -0.09 (0.23), residues: 544 loop : -0.01 (0.12), residues: 3560 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 331 time to evaluate : 4.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 113 outliers final: 60 residues processed: 414 average time/residue: 1.2379 time to fit residues: 675.5486 Evaluate side-chains 369 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 309 time to evaluate : 4.693 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 52 residues processed: 8 average time/residue: 0.9101 time to fit residues: 16.5548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 638 optimal weight: 6.9990 chunk 74 optimal weight: 1.9990 chunk 377 optimal weight: 9.9990 chunk 483 optimal weight: 9.9990 chunk 374 optimal weight: 5.9990 chunk 557 optimal weight: 8.9990 chunk 369 optimal weight: 6.9990 chunk 659 optimal weight: 5.9990 chunk 412 optimal weight: 3.9990 chunk 401 optimal weight: 8.9990 chunk 304 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 282 GLN ** K 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 282 GLN ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6345 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.169 55708 Z= 0.485 Angle : 1.934 86.656 75888 Z= 0.691 Chirality : 0.086 1.635 8044 Planarity : 0.004 0.041 9932 Dihedral : 6.600 86.810 7604 Min Nonbonded Distance : 1.518 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 2.31 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.11), residues: 6852 helix: 0.61 (0.10), residues: 2700 sheet: 0.20 (0.23), residues: 528 loop : -0.07 (0.11), residues: 3624 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 324 time to evaluate : 4.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 131 outliers final: 69 residues processed: 425 average time/residue: 1.2549 time to fit residues: 700.5854 Evaluate side-chains 373 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 304 time to evaluate : 4.673 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 60 residues processed: 13 average time/residue: 0.8012 time to fit residues: 21.5658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 407 optimal weight: 0.5980 chunk 263 optimal weight: 2.9990 chunk 393 optimal weight: 6.9990 chunk 198 optimal weight: 0.8980 chunk 129 optimal weight: 0.7980 chunk 127 optimal weight: 7.9990 chunk 419 optimal weight: 6.9990 chunk 449 optimal weight: 10.0000 chunk 325 optimal weight: 0.1980 chunk 61 optimal weight: 0.9980 chunk 518 optimal weight: 8.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 282 GLN ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6239 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.176 55708 Z= 0.311 Angle : 1.896 84.465 75888 Z= 0.669 Chirality : 0.083 1.547 8044 Planarity : 0.004 0.033 9932 Dihedral : 6.596 88.263 7604 Min Nonbonded Distance : 1.525 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.11), residues: 6852 helix: 0.74 (0.10), residues: 2700 sheet: -0.09 (0.23), residues: 544 loop : 0.04 (0.11), residues: 3608 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 321 time to evaluate : 4.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 51 residues processed: 394 average time/residue: 1.2749 time to fit residues: 663.9539 Evaluate side-chains 358 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 307 time to evaluate : 4.703 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 48 residues processed: 3 average time/residue: 1.3032 time to fit residues: 11.3070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 599 optimal weight: 9.9990 chunk 631 optimal weight: 1.9990 chunk 576 optimal weight: 0.4980 chunk 614 optimal weight: 20.0000 chunk 369 optimal weight: 20.0000 chunk 267 optimal weight: 9.9990 chunk 482 optimal weight: 0.9990 chunk 188 optimal weight: 10.0000 chunk 555 optimal weight: 6.9990 chunk 581 optimal weight: 30.0000 chunk 612 optimal weight: 7.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 282 GLN ** K 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 282 GLN ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6319 moved from start: 0.3978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.166 55708 Z= 0.413 Angle : 1.931 85.942 75888 Z= 0.687 Chirality : 0.084 1.623 8044 Planarity : 0.004 0.036 9932 Dihedral : 6.499 89.974 7604 Min Nonbonded Distance : 1.525 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer Outliers : 1.39 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.11), residues: 6852 helix: 0.71 (0.10), residues: 2700 sheet: 0.00 (0.23), residues: 544 loop : 0.01 (0.12), residues: 3608 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 316 time to evaluate : 4.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 59 residues processed: 380 average time/residue: 1.3134 time to fit residues: 654.1753 Evaluate side-chains 352 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 293 time to evaluate : 4.702 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 48 residues processed: 11 average time/residue: 1.0736 time to fit residues: 22.6893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 403 optimal weight: 0.9990 chunk 649 optimal weight: 9.9990 chunk 396 optimal weight: 5.9990 chunk 308 optimal weight: 20.0000 chunk 451 optimal weight: 20.0000 chunk 681 optimal weight: 4.9990 chunk 627 optimal weight: 0.6980 chunk 542 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 419 optimal weight: 7.9990 chunk 332 optimal weight: 40.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 282 GLN ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6326 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.169 55708 Z= 0.422 Angle : 1.932 85.800 75888 Z= 0.688 Chirality : 0.084 1.633 8044 Planarity : 0.005 0.091 9932 Dihedral : 6.535 88.819 7604 Min Nonbonded Distance : 1.520 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.11), residues: 6852 helix: 0.63 (0.10), residues: 2700 sheet: -0.02 (0.23), residues: 544 loop : -0.06 (0.11), residues: 3608 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13704 Ramachandran restraints generated. 6852 Oldfield, 0 Emsley, 6852 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 306 time to evaluate : 4.845 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 52 residues processed: 362 average time/residue: 1.2759 time to fit residues: 614.7743 Evaluate side-chains 345 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 293 time to evaluate : 4.707 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 52 residues processed: 0 time to fit residues: 6.2899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 431 optimal weight: 0.7980 chunk 578 optimal weight: 0.0970 chunk 166 optimal weight: 40.0000 chunk 500 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 150 optimal weight: 0.9990 chunk 543 optimal weight: 9.9990 chunk 227 optimal weight: 20.0000 chunk 558 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 282 GLN ** K 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 282 GLN ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 8 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.116683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.088101 restraints weight = 132126.574| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.29 r_work: 0.3446 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.175 55708 Z= 0.308 Angle : 1.909 84.257 75888 Z= 0.674 Chirality : 0.082 1.556 8044 Planarity : 0.004 0.077 9932 Dihedral : 6.736 89.254 7604 Min Nonbonded Distance : 1.523 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer Outliers : 1.20 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.11), residues: 6852 helix: 0.73 (0.10), residues: 2700 sheet: -0.07 (0.23), residues: 544 loop : 0.04 (0.11), residues: 3608 =============================================================================== Job complete usr+sys time: 15379.58 seconds wall clock time: 271 minutes 5.84 seconds (16265.84 seconds total)