Starting phenix.real_space_refine on Mon Mar 11 00:12:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utd_26767/03_2024/7utd_26767_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utd_26767/03_2024/7utd_26767.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utd_26767/03_2024/7utd_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_26767/03_2024/7utd_26767_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utd_26767/03_2024/7utd_26767_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utd_26767/03_2024/7utd_26767.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utd_26767/03_2024/7utd_26767.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utd_26767/03_2024/7utd_26767_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7utd_26767/03_2024/7utd_26767_updated.pdb" } resolution = 2.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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 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. 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-5265/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: 20.60, per 1000 atoms: 0.38 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: 17.32 Conformation dependent library (CDL) restraints added in 7.3 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: 7.87 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: 18.10 Time building geometry restraints manager: 18.98 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 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: 1.900 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: 0.050 Extract box with map and model: 11.040 Check model and map are aligned: 0.590 Set scattering table: 0.380 Process input model: 120.090 Find NCS groups from input model: 3.000 Set up NCS constraints: 0.610 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5877 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 % Allowed : 7.10 % Favored : 91.54 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP C 198 HIS 0.011 0.003 HIS H 239 PHE 0.034 0.004 PHE E 381 TYR 0.023 0.003 TYR N 229 ARG 0.006 0.001 ARG B 255 *********************** 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 : 4.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 LYS cc_start: 0.6022 (OUTLIER) cc_final: 0.5786 (pptt) REVERT: G 72 LYS cc_start: 0.6017 (OUTLIER) cc_final: 0.5783 (pptt) REVERT: M 72 LYS cc_start: 0.6019 (OUTLIER) cc_final: 0.5783 (pptt) REVERT: O 72 LYS cc_start: 0.6025 (OUTLIER) cc_final: 0.5786 (pptt) REVERT: Q 43 ASP cc_start: 0.8687 (m-30) cc_final: 0.8249 (m-30) REVERT: S 43 ASP cc_start: 0.8689 (m-30) cc_final: 0.8410 (m-30) REVERT: T 43 ASP cc_start: 0.8700 (m-30) cc_final: 0.8422 (m-30) outliers start: 77 outliers final: 14 residues processed: 815 average time/residue: 1.3564 time to fit residues: 1402.2305 Evaluate side-chains 390 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 372 time to evaluate : 4.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain C residue 72 LYS Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain F residue 287 MET Chi-restraints excluded: chain G residue 72 LYS Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain J residue 287 MET Chi-restraints excluded: chain L residue 287 MET Chi-restraints excluded: chain M residue 72 LYS Chi-restraints excluded: chain N residue 50 ASN Chi-restraints excluded: chain O residue 72 LYS Chi-restraints excluded: chain P residue 50 ASN Chi-restraints excluded: chain Q residue 23 ASP Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 23 ASP Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain S residue 23 ASP Chi-restraints excluded: chain T residue 38 LEU 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 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 80 ASN P 270 HIS Q 67 ASN R 67 ASN S 67 ASN T 67 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6042 moved from start: 0.2102 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= 0.554 Angle : 2.178 82.926 75888 Z= 0.779 Chirality : 0.076 1.775 8044 Planarity : 0.005 0.042 9932 Dihedral : 7.061 72.995 7652 Min Nonbonded Distance : 1.475 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.87 % Allowed : 10.13 % Favored : 87.00 % Cbeta Deviations : 0.00 % 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 (0.10), residues: 6852 helix: 0.38 (0.09), residues: 2708 sheet: -0.10 (0.20), residues: 544 loop : 0.02 (0.11), residues: 3600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 198 HIS 0.008 0.002 HIS F 164 PHE 0.027 0.003 PHE P 195 TYR 0.027 0.002 TYR H 301 ARG 0.013 0.001 ARG I 333 *********************** 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 527 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 364 time to evaluate : 4.613 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: 163 outliers final: 39 residues processed: 492 average time/residue: 1.2872 time to fit residues: 815.8960 Evaluate side-chains 355 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 316 time to evaluate : 4.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain C residue 82 ARG Chi-restraints excluded: chain C residue 313 ASN Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain E residue 509 SER Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 313 ASN Chi-restraints excluded: chain G residue 476 SER Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 313 ASN Chi-restraints excluded: chain I residue 509 SER Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain K residue 104 SER Chi-restraints excluded: chain K residue 313 ASN Chi-restraints excluded: chain K residue 509 SER Chi-restraints excluded: chain L residue 23 ASP Chi-restraints excluded: chain L residue 187 ASP Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain M residue 313 ASN Chi-restraints excluded: chain M residue 476 SER Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain O residue 82 ARG Chi-restraints excluded: chain O residue 313 ASN Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 184 THR Chi-restraints excluded: chain Q residue 23 ASP Chi-restraints excluded: chain R residue 23 ASP Chi-restraints excluded: chain S residue 23 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 345 optimal weight: 20.0000 chunk 192 optimal weight: 4.9990 chunk 516 optimal weight: 7.9990 chunk 422 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 chunk 622 optimal weight: 0.9980 chunk 672 optimal weight: 1.9990 chunk 554 optimal weight: 7.9990 chunk 617 optimal weight: 0.3980 chunk 212 optimal weight: 5.9990 chunk 499 optimal weight: 20.0000 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 193 HIS ** J 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5948 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.180 55708 Z= 0.366 Angle : 2.001 84.734 75888 Z= 0.705 Chirality : 0.081 1.966 8044 Planarity : 0.004 0.045 9932 Dihedral : 6.817 73.437 7610 Min Nonbonded Distance : 1.520 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.52 % Allowed : 10.59 % Favored : 86.89 % Cbeta Deviations : 0.00 % 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 (0.10), residues: 6852 helix: 0.55 (0.10), residues: 2748 sheet: -0.37 (0.21), residues: 560 loop : 0.09 (0.12), residues: 3544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 198 HIS 0.004 0.001 HIS F 270 PHE 0.041 0.002 PHE J 56 TYR 0.014 0.002 TYR A 71 ARG 0.008 0.000 ARG I 292 *********************** 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 519 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 376 time to evaluate : 4.738 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 outliers start: 143 outliers final: 39 residues processed: 476 average time/residue: 1.2776 time to fit residues: 784.5781 Evaluate side-chains 365 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 326 time to evaluate : 4.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 313 ASN Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain C residue 82 ARG Chi-restraints excluded: chain C residue 313 ASN Chi-restraints excluded: chain C residue 334 GLN Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 313 ASN Chi-restraints excluded: chain E residue 509 SER Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 313 ASN Chi-restraints excluded: chain G residue 334 GLN Chi-restraints excluded: chain G residue 476 SER Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 313 ASN Chi-restraints excluded: chain I residue 509 SER Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain K residue 104 SER Chi-restraints excluded: chain K residue 313 ASN Chi-restraints excluded: chain K residue 509 SER Chi-restraints excluded: chain L residue 187 ASP Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain M residue 313 ASN Chi-restraints excluded: chain M residue 334 GLN Chi-restraints excluded: chain M residue 476 SER Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain O residue 82 ARG Chi-restraints excluded: chain O residue 313 ASN Chi-restraints excluded: chain O residue 334 GLN Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 184 THR Chi-restraints excluded: chain Q residue 23 ASP Chi-restraints excluded: chain R residue 23 ASP Chi-restraints excluded: chain S residue 23 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 614 optimal weight: 4.9990 chunk 467 optimal weight: 1.9990 chunk 322 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 296 optimal weight: 9.9990 chunk 417 optimal weight: 30.0000 chunk 624 optimal weight: 6.9990 chunk 661 optimal weight: 3.9990 chunk 326 optimal weight: 0.7980 chunk 591 optimal weight: 5.9990 chunk 178 optimal weight: 20.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 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 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 97 GLN ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 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 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 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: 0.6022 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.168 55708 Z= 0.415 Angle : 1.970 84.941 75888 Z= 0.697 Chirality : 0.080 1.568 8044 Planarity : 0.004 0.031 9932 Dihedral : 6.718 74.969 7610 Min Nonbonded Distance : 1.523 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.15 % Allowed : 11.43 % Favored : 86.42 % Cbeta Deviations : 0.00 % 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: 0.27 (0.11), residues: 6852 helix: 0.60 (0.10), residues: 2748 sheet: -0.28 (0.21), residues: 560 loop : 0.06 (0.12), residues: 3544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 198 HIS 0.007 0.002 HIS B 164 PHE 0.024 0.002 PHE L 56 TYR 0.018 0.002 TYR H 301 ARG 0.011 0.001 ARG K 333 *********************** 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 459 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 337 time to evaluate : 4.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 PHE cc_start: 0.6130 (OUTLIER) cc_final: 0.5830 (m-80) REVERT: E 319 PHE cc_start: 0.6130 (OUTLIER) cc_final: 0.5830 (m-80) REVERT: I 319 PHE cc_start: 0.6130 (OUTLIER) cc_final: 0.5831 (m-80) REVERT: K 319 PHE cc_start: 0.6126 (OUTLIER) cc_final: 0.5827 (m-80) outliers start: 122 outliers final: 51 residues processed: 419 average time/residue: 1.2032 time to fit residues: 658.3981 Evaluate side-chains 351 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 296 time to evaluate : 4.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain C residue 82 ARG Chi-restraints excluded: chain C residue 313 ASN Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 319 PHE Chi-restraints excluded: chain E residue 509 SER Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 313 ASN Chi-restraints excluded: chain G residue 476 SER Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain I residue 38 MET Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain I residue 319 PHE Chi-restraints excluded: chain I residue 509 SER Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 119 ILE Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 104 SER Chi-restraints excluded: chain K residue 316 LEU Chi-restraints excluded: chain K residue 319 PHE Chi-restraints excluded: chain K residue 509 SER Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 187 ASP Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain M residue 313 ASN Chi-restraints excluded: chain M residue 476 SER Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain O residue 82 ARG Chi-restraints excluded: chain O residue 313 ASN Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 184 THR Chi-restraints excluded: chain Q residue 23 ASP Chi-restraints excluded: chain R residue 23 ASP Chi-restraints excluded: chain S residue 23 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 550 optimal weight: 1.9990 chunk 375 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 492 optimal weight: 5.9990 chunk 272 optimal weight: 20.0000 chunk 564 optimal weight: 7.9990 chunk 457 optimal weight: 3.9990 chunk 0 optimal weight: 40.0000 chunk 337 optimal weight: 0.8980 chunk 593 optimal weight: 6.9990 chunk 166 optimal weight: 40.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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** ** C 502 HIS ** 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 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 GLN ** F 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 282 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 502 HIS ** 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 8 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 8 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** ** M 502 HIS ** 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** ** O 502 HIS ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6053 moved from start: 0.3288 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= 0.444 Angle : 1.966 85.086 75888 Z= 0.697 Chirality : 0.082 1.538 8044 Planarity : 0.004 0.037 9932 Dihedral : 6.759 78.310 7610 Min Nonbonded Distance : 1.519 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.52 % Allowed : 12.09 % Favored : 85.39 % Cbeta Deviations : 0.00 % 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: 0.21 (0.11), residues: 6852 helix: 0.57 (0.10), residues: 2748 sheet: -0.21 (0.22), residues: 544 loop : -0.02 (0.12), residues: 3560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 198 HIS 0.007 0.002 HIS L 164 PHE 0.023 0.002 PHE F 56 TYR 0.017 0.002 TYR N 301 ARG 0.006 0.000 ARG E 333 *********************** 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 473 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 330 time to evaluate : 4.699 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: A 319 PHE cc_start: 0.6103 (OUTLIER) cc_final: 0.5799 (m-80) REVERT: E 319 PHE cc_start: 0.6102 (OUTLIER) cc_final: 0.5797 (m-80) REVERT: I 319 PHE cc_start: 0.6105 (OUTLIER) cc_final: 0.5800 (m-80) REVERT: K 319 PHE cc_start: 0.6101 (OUTLIER) cc_final: 0.5795 (m-80) outliers start: 143 outliers final: 54 residues processed: 432 average time/residue: 1.1684 time to fit residues: 666.8007 Evaluate side-chains 374 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 316 time to evaluate : 4.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 82 ARG Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 72 LYS Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 319 PHE Chi-restraints excluded: chain E residue 453 GLU Chi-restraints excluded: chain E residue 509 SER Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 476 SER Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain I residue 38 MET Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain I residue 319 PHE Chi-restraints excluded: chain I residue 453 GLU Chi-restraints excluded: chain I residue 509 SER Chi-restraints excluded: chain I residue 514 THR Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 72 LYS Chi-restraints excluded: chain K residue 104 SER Chi-restraints excluded: chain K residue 316 LEU Chi-restraints excluded: chain K residue 319 PHE Chi-restraints excluded: chain K residue 453 GLU Chi-restraints excluded: chain K residue 509 SER Chi-restraints excluded: chain K residue 514 THR Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 187 ASP Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain M residue 476 SER Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain O residue 82 ARG Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 184 THR Chi-restraints excluded: chain R residue 23 ASP Chi-restraints excluded: chain S residue 23 ASP 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: 9.9990 chunk 130 optimal weight: 8.9990 chunk 388 optimal weight: 6.9990 chunk 163 optimal weight: 3.9990 chunk 661 optimal weight: 1.9990 chunk 549 optimal weight: 8.9990 chunk 306 optimal weight: 1.9990 chunk 55 optimal weight: 20.0000 chunk 218 optimal weight: 4.9990 chunk 347 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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** ** H 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 502 HIS ** J 8 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** K 502 HIS ** L 8 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** ** 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** S 33 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6023 moved from start: 0.3520 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= 0.376 Angle : 1.912 84.859 75888 Z= 0.677 Chirality : 0.086 1.660 8044 Planarity : 0.004 0.038 9932 Dihedral : 6.661 80.967 7608 Min Nonbonded Distance : 1.523 Molprobity Statistics. All-atom Clashscore : 15.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.34 % Allowed : 12.56 % Favored : 85.10 % Cbeta Deviations : 0.00 % 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: 0.21 (0.11), residues: 6852 helix: 0.57 (0.10), residues: 2748 sheet: -0.10 (0.23), residues: 544 loop : -0.04 (0.11), residues: 3560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 198 HIS 0.005 0.001 HIS P 270 PHE 0.023 0.002 PHE B 56 TYR 0.014 0.002 TYR C 71 ARG 0.007 0.000 ARG I 333 *********************** 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 472 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 339 time to evaluate : 4.600 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: A 319 PHE cc_start: 0.6168 (OUTLIER) cc_final: 0.5865 (m-80) REVERT: E 319 PHE cc_start: 0.6168 (OUTLIER) cc_final: 0.5865 (m-80) REVERT: I 319 PHE cc_start: 0.6154 (OUTLIER) cc_final: 0.5854 (m-80) REVERT: K 319 PHE cc_start: 0.6167 (OUTLIER) cc_final: 0.5863 (m-80) outliers start: 133 outliers final: 55 residues processed: 439 average time/residue: 1.2116 time to fit residues: 695.7458 Evaluate side-chains 369 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 310 time to evaluate : 4.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 82 ARG Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 72 LYS Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 319 PHE Chi-restraints excluded: chain E residue 453 GLU Chi-restraints excluded: chain E residue 482 ILE Chi-restraints excluded: chain E residue 509 SER Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 476 SER Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain I residue 38 MET Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain I residue 319 PHE Chi-restraints excluded: chain I residue 453 GLU Chi-restraints excluded: chain I residue 482 ILE Chi-restraints excluded: chain I residue 509 SER Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 72 LYS Chi-restraints excluded: chain K residue 104 SER Chi-restraints excluded: chain K residue 316 LEU Chi-restraints excluded: chain K residue 319 PHE Chi-restraints excluded: chain K residue 453 GLU Chi-restraints excluded: chain K residue 482 ILE Chi-restraints excluded: chain K residue 509 SER Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 187 ASP Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain M residue 476 SER Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain O residue 82 ARG Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 184 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 638 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 377 optimal weight: 10.0000 chunk 483 optimal weight: 4.9990 chunk 374 optimal weight: 1.9990 chunk 557 optimal weight: 0.8980 chunk 369 optimal weight: 3.9990 chunk 659 optimal weight: 3.9990 chunk 412 optimal weight: 2.9990 chunk 401 optimal weight: 8.9990 chunk 304 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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** ** 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 8 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 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 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6014 moved from start: 0.3639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.171 55708 Z= 0.352 Angle : 1.911 85.380 75888 Z= 0.676 Chirality : 0.084 1.592 8044 Planarity : 0.004 0.041 9932 Dihedral : 6.399 81.702 7604 Min Nonbonded Distance : 1.526 Molprobity Statistics. All-atom Clashscore : 15.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.66 % Allowed : 13.44 % Favored : 84.90 % Cbeta Deviations : 0.00 % 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: 0.30 (0.11), residues: 6852 helix: 0.65 (0.10), residues: 2748 sheet: -0.06 (0.23), residues: 544 loop : 0.00 (0.12), residues: 3560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 198 HIS 0.005 0.001 HIS B 270 PHE 0.032 0.002 PHE L 56 TYR 0.014 0.001 TYR L 229 ARG 0.011 0.000 ARG I 333 *********************** 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 418 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 324 time to evaluate : 4.614 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: A 319 PHE cc_start: 0.6166 (OUTLIER) cc_final: 0.5896 (m-80) REVERT: C 400 MET cc_start: 0.5254 (mmt) cc_final: 0.5038 (mmt) REVERT: E 319 PHE cc_start: 0.6162 (OUTLIER) cc_final: 0.5893 (m-80) REVERT: G 400 MET cc_start: 0.5262 (mmt) cc_final: 0.5046 (mmt) REVERT: I 319 PHE cc_start: 0.6166 (OUTLIER) cc_final: 0.5860 (m-80) REVERT: K 319 PHE cc_start: 0.6164 (OUTLIER) cc_final: 0.5894 (m-80) REVERT: M 400 MET cc_start: 0.5260 (mmt) cc_final: 0.5046 (mmt) REVERT: O 400 MET cc_start: 0.5257 (mmt) cc_final: 0.5039 (mmt) outliers start: 94 outliers final: 60 residues processed: 392 average time/residue: 1.2253 time to fit residues: 627.7925 Evaluate side-chains 369 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 305 time to evaluate : 4.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 82 ARG Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 72 LYS Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 319 PHE Chi-restraints excluded: chain E residue 453 GLU Chi-restraints excluded: chain E residue 509 SER Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 476 SER Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain I residue 38 MET Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 72 LYS Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain I residue 319 PHE Chi-restraints excluded: chain I residue 453 GLU Chi-restraints excluded: chain I residue 509 SER Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 72 LYS Chi-restraints excluded: chain K residue 104 SER Chi-restraints excluded: chain K residue 316 LEU Chi-restraints excluded: chain K residue 319 PHE Chi-restraints excluded: chain K residue 453 GLU Chi-restraints excluded: chain K residue 509 SER Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 187 ASP Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain M residue 476 SER Chi-restraints excluded: chain N residue 50 ASN Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain O residue 82 ARG Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 50 ASN Chi-restraints excluded: chain P residue 184 THR Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain T residue 50 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 407 optimal weight: 0.6980 chunk 263 optimal weight: 5.9990 chunk 393 optimal weight: 10.0000 chunk 198 optimal weight: 5.9990 chunk 129 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 419 optimal weight: 9.9990 chunk 449 optimal weight: 0.9990 chunk 325 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 518 optimal weight: 10.0000 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 ** 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 ** I 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 8 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 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 ** N 15 ASN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5968 moved from start: 0.3795 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= 0.322 Angle : 1.890 84.523 75888 Z= 0.666 Chirality : 0.085 1.601 8044 Planarity : 0.004 0.054 9932 Dihedral : 6.464 81.894 7604 Min Nonbonded Distance : 1.524 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.90 % Allowed : 13.44 % Favored : 84.65 % Cbeta Deviations : 0.00 % 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: 0.43 (0.11), residues: 6852 helix: 0.83 (0.10), residues: 2700 sheet: -0.02 (0.23), residues: 544 loop : 0.04 (0.11), residues: 3608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 468 HIS 0.005 0.001 HIS J 270 PHE 0.024 0.001 PHE J 56 TYR 0.014 0.001 TYR C 71 ARG 0.008 0.000 ARG I 333 *********************** 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 441 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 333 time to evaluate : 4.693 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: A 319 PHE cc_start: 0.6141 (OUTLIER) cc_final: 0.5867 (m-80) REVERT: C 400 MET cc_start: 0.5208 (mmt) cc_final: 0.4940 (mmt) REVERT: E 319 PHE cc_start: 0.6136 (OUTLIER) cc_final: 0.5865 (m-80) REVERT: G 400 MET cc_start: 0.5213 (mmt) cc_final: 0.4949 (mmt) REVERT: I 319 PHE cc_start: 0.6139 (OUTLIER) cc_final: 0.5864 (m-80) REVERT: K 319 PHE cc_start: 0.6139 (OUTLIER) cc_final: 0.5866 (m-80) REVERT: M 400 MET cc_start: 0.5212 (mmt) cc_final: 0.4949 (mmt) REVERT: O 400 MET cc_start: 0.5206 (mmt) cc_final: 0.4994 (mmt) REVERT: T 43 ASP cc_start: 0.8632 (m-30) cc_final: 0.8339 (m-30) outliers start: 108 outliers final: 71 residues processed: 416 average time/residue: 1.2497 time to fit residues: 675.4328 Evaluate side-chains 405 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 330 time to evaluate : 4.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 64 ILE Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 82 ARG Chi-restraints excluded: chain C residue 313 ASN Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 72 LYS Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 319 PHE Chi-restraints excluded: chain E residue 509 SER Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 313 ASN Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 476 SER Chi-restraints excluded: chain H residue 50 ASN Chi-restraints excluded: chain H residue 122 MET Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain I residue 38 MET Chi-restraints excluded: chain I residue 64 ILE Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain I residue 319 PHE Chi-restraints excluded: chain I residue 509 SER Chi-restraints excluded: chain I residue 514 THR Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 64 ILE Chi-restraints excluded: chain K residue 72 LYS Chi-restraints excluded: chain K residue 104 SER Chi-restraints excluded: chain K residue 316 LEU Chi-restraints excluded: chain K residue 319 PHE Chi-restraints excluded: chain K residue 509 SER Chi-restraints excluded: chain K residue 514 THR Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 187 ASP Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain M residue 313 ASN Chi-restraints excluded: chain M residue 326 VAL Chi-restraints excluded: chain M residue 476 SER Chi-restraints excluded: chain N residue 50 ASN Chi-restraints excluded: chain N residue 122 MET Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain O residue 82 ARG Chi-restraints excluded: chain O residue 313 ASN Chi-restraints excluded: chain O residue 326 VAL Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 50 ASN Chi-restraints excluded: chain P residue 122 MET Chi-restraints excluded: chain P residue 184 THR Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain T residue 50 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 599 optimal weight: 10.0000 chunk 631 optimal weight: 0.9990 chunk 576 optimal weight: 3.9990 chunk 614 optimal weight: 9.9990 chunk 369 optimal weight: 30.0000 chunk 267 optimal weight: 10.0000 chunk 482 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 555 optimal weight: 2.9990 chunk 581 optimal weight: 30.0000 chunk 612 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 ** 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 8 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 8 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: 0.6050 moved from start: 0.3847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.164 55708 Z= 0.423 Angle : 1.927 86.186 75888 Z= 0.684 Chirality : 0.085 1.676 8044 Planarity : 0.004 0.046 9932 Dihedral : 6.467 85.108 7604 Min Nonbonded Distance : 1.525 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.73 % Allowed : 13.60 % Favored : 84.67 % Cbeta Deviations : 0.00 % 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: 0.40 (0.11), residues: 6852 helix: 0.77 (0.10), residues: 2700 sheet: 0.06 (0.23), residues: 544 loop : 0.03 (0.12), residues: 3608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 198 HIS 0.007 0.002 HIS B 164 PHE 0.019 0.002 PHE M 381 TYR 0.017 0.002 TYR H 301 ARG 0.014 0.001 ARG I 333 *********************** 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 436 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 338 time to evaluate : 4.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 PHE cc_start: 0.6186 (OUTLIER) cc_final: 0.5883 (m-80) REVERT: E 319 PHE cc_start: 0.6182 (OUTLIER) cc_final: 0.5881 (m-80) REVERT: I 319 PHE cc_start: 0.6185 (OUTLIER) cc_final: 0.5881 (m-80) REVERT: K 319 PHE cc_start: 0.6184 (OUTLIER) cc_final: 0.5882 (m-80) outliers start: 98 outliers final: 67 residues processed: 419 average time/residue: 1.2315 time to fit residues: 674.3637 Evaluate side-chains 388 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 317 time to evaluate : 4.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain C residue 82 ARG Chi-restraints excluded: chain C residue 313 ASN Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 72 LYS Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 319 PHE Chi-restraints excluded: chain E residue 509 SER Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 313 ASN Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 476 SER Chi-restraints excluded: chain H residue 122 MET Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain I residue 38 MET Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain I residue 319 PHE Chi-restraints excluded: chain I residue 509 SER Chi-restraints excluded: chain I residue 514 THR Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 119 ILE Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 72 LYS Chi-restraints excluded: chain K residue 104 SER Chi-restraints excluded: chain K residue 316 LEU Chi-restraints excluded: chain K residue 319 PHE Chi-restraints excluded: chain K residue 509 SER Chi-restraints excluded: chain K residue 514 THR Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 187 ASP Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain M residue 313 ASN Chi-restraints excluded: chain M residue 326 VAL Chi-restraints excluded: chain M residue 476 SER Chi-restraints excluded: chain N residue 122 MET Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain O residue 82 ARG Chi-restraints excluded: chain O residue 313 ASN Chi-restraints excluded: chain O residue 326 VAL Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 122 MET Chi-restraints excluded: chain P residue 184 THR Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain T residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 403 optimal weight: 0.9980 chunk 649 optimal weight: 10.0000 chunk 396 optimal weight: 3.9990 chunk 308 optimal weight: 0.6980 chunk 451 optimal weight: 20.0000 chunk 681 optimal weight: 1.9990 chunk 627 optimal weight: 5.9990 chunk 542 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 419 optimal weight: 7.9990 chunk 332 optimal weight: 30.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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** ** G 103 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 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5998 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.171 55708 Z= 0.332 Angle : 1.913 84.616 75888 Z= 0.677 Chirality : 0.084 1.656 8044 Planarity : 0.004 0.052 9932 Dihedral : 6.461 86.184 7604 Min Nonbonded Distance : 1.528 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.44 % Allowed : 13.97 % Favored : 84.58 % Cbeta Deviations : 0.00 % 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: 0.41 (0.11), residues: 6852 helix: 0.77 (0.10), residues: 2700 sheet: 0.02 (0.23), residues: 544 loop : 0.05 (0.12), residues: 3608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 203 HIS 0.012 0.001 HIS G 502 PHE 0.025 0.002 PHE L 56 TYR 0.018 0.001 TYR B 229 ARG 0.008 0.000 ARG A 333 ********************** 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 424 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 342 time to evaluate : 4.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 PHE cc_start: 0.6134 (OUTLIER) cc_final: 0.5870 (m-80) REVERT: E 319 PHE cc_start: 0.6129 (OUTLIER) cc_final: 0.5866 (m-80) REVERT: I 319 PHE cc_start: 0.6125 (OUTLIER) cc_final: 0.5860 (m-80) REVERT: K 319 PHE cc_start: 0.6134 (OUTLIER) cc_final: 0.5872 (m-80) outliers start: 82 outliers final: 71 residues processed: 412 average time/residue: 1.2879 time to fit residues: 685.1824 Evaluate side-chains 390 residues out of total 5676 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 315 time to evaluate : 4.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 MET Chi-restraints excluded: chain A residue 72 LYS Chi-restraints excluded: chain A residue 104 SER Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 319 PHE Chi-restraints excluded: chain A residue 509 SER Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 187 ASP Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 272 ASP Chi-restraints excluded: chain C residue 82 ARG Chi-restraints excluded: chain C residue 313 ASN Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 476 SER Chi-restraints excluded: chain D residue 122 MET Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain E residue 72 LYS Chi-restraints excluded: chain E residue 104 SER Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 319 PHE Chi-restraints excluded: chain E residue 509 SER Chi-restraints excluded: chain E residue 514 THR Chi-restraints excluded: chain F residue 27 VAL Chi-restraints excluded: chain F residue 119 ILE Chi-restraints excluded: chain F residue 187 ASP Chi-restraints excluded: chain F residue 215 THR Chi-restraints excluded: chain F residue 272 ASP Chi-restraints excluded: chain G residue 82 ARG Chi-restraints excluded: chain G residue 313 ASN Chi-restraints excluded: chain G residue 326 VAL Chi-restraints excluded: chain G residue 476 SER Chi-restraints excluded: chain H residue 122 MET Chi-restraints excluded: chain H residue 184 THR Chi-restraints excluded: chain I residue 38 MET Chi-restraints excluded: chain I residue 104 SER Chi-restraints excluded: chain I residue 316 LEU Chi-restraints excluded: chain I residue 319 PHE Chi-restraints excluded: chain I residue 509 SER Chi-restraints excluded: chain I residue 514 THR Chi-restraints excluded: chain J residue 27 VAL Chi-restraints excluded: chain J residue 119 ILE Chi-restraints excluded: chain J residue 187 ASP Chi-restraints excluded: chain J residue 215 THR Chi-restraints excluded: chain J residue 272 ASP Chi-restraints excluded: chain K residue 38 MET Chi-restraints excluded: chain K residue 72 LYS Chi-restraints excluded: chain K residue 104 SER Chi-restraints excluded: chain K residue 316 LEU Chi-restraints excluded: chain K residue 319 PHE Chi-restraints excluded: chain K residue 509 SER Chi-restraints excluded: chain K residue 514 THR Chi-restraints excluded: chain L residue 27 VAL Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 187 ASP Chi-restraints excluded: chain L residue 215 THR Chi-restraints excluded: chain L residue 272 ASP Chi-restraints excluded: chain M residue 82 ARG Chi-restraints excluded: chain M residue 313 ASN Chi-restraints excluded: chain M residue 326 VAL Chi-restraints excluded: chain M residue 476 SER Chi-restraints excluded: chain N residue 122 MET Chi-restraints excluded: chain N residue 184 THR Chi-restraints excluded: chain O residue 82 ARG Chi-restraints excluded: chain O residue 313 ASN Chi-restraints excluded: chain O residue 326 VAL Chi-restraints excluded: chain O residue 476 SER Chi-restraints excluded: chain P residue 122 MET Chi-restraints excluded: chain P residue 184 THR Chi-restraints excluded: chain Q residue 50 VAL Chi-restraints excluded: chain R residue 50 VAL Chi-restraints excluded: chain S residue 50 VAL Chi-restraints excluded: chain T residue 50 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 684 random chunks: chunk 431 optimal weight: 0.9980 chunk 578 optimal weight: 2.9990 chunk 166 optimal weight: 30.0000 chunk 500 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 543 optimal weight: 8.9990 chunk 227 optimal weight: 20.0000 chunk 558 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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** ** C 502 HIS ** 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** ** G 502 HIS ** 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 8 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 8 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** ** M 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 502 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.115511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.086310 restraints weight = 133780.263| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.29 r_work: 0.3397 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.171 55708 Z= 0.338 Angle : 1.915 84.755 75888 Z= 0.678 Chirality : 0.084 1.653 8044 Planarity : 0.005 0.080 9932 Dihedral : 6.290 86.471 7604 Min Nonbonded Distance : 1.527 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.43 % Allowed : 13.99 % Favored : 84.58 % Cbeta Deviations : 0.00 % 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: 0.44 (0.11), residues: 6852 helix: 0.80 (0.10), residues: 2700 sheet: 0.04 (0.23), residues: 544 loop : 0.06 (0.12), residues: 3608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 198 HIS 0.004 0.001 HIS P 270 PHE 0.026 0.002 PHE B 56 TYR 0.022 0.001 TYR B 229 ARG 0.020 0.001 ARG G 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15902.32 seconds wall clock time: 280 minutes 8.64 seconds (16808.64 seconds total)