Starting phenix.real_space_refine on Fri Feb 16 04:28:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgc_40454/02_2024/8sgc_40454_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgc_40454/02_2024/8sgc_40454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgc_40454/02_2024/8sgc_40454.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgc_40454/02_2024/8sgc_40454.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgc_40454/02_2024/8sgc_40454_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgc_40454/02_2024/8sgc_40454_updated.pdb" } resolution = 2.9 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= 0.004 sd= 0.043 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: 8 Type Number sf(0) Gaussians Al 16 5.89 5 P 32 5.49 5 Mg 16 5.21 5 S 412 5.16 5 C 41697 2.51 5 N 11602 2.21 5 O 12914 1.98 5 F 48 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 17": "OD1" <-> "OD2" Residue "B ASP 77": "OD1" <-> "OD2" Residue "D TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 46": "OD1" <-> "OD2" Residue "D TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 67": "OD1" <-> "OD2" Residue "E ASP 231": "OD1" <-> "OD2" Residue "E PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 52": "OD1" <-> "OD2" Residue "G TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 70": "OD1" <-> "OD2" Residue "Z TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 213": "OD1" <-> "OD2" Residue "Z ASP 389": "OD1" <-> "OD2" Residue "a ASP 529": "OD1" <-> "OD2" Residue "d GLU 279": "OE1" <-> "OE2" Residue "d PHE 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 467": "OE1" <-> "OE2" Residue "e TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 17": "OE1" <-> "OE2" Residue "g GLU 293": "OE1" <-> "OE2" Residue "h ASP 70": "OD1" <-> "OD2" Residue "h ASP 251": "OD1" <-> "OD2" Residue "h TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 478": "OD1" <-> "OD2" Residue "q ASP 393": "OD1" <-> "OD2" Residue "z ASP 86": "OD1" <-> "OD2" Residue "z TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 389": "OD1" <-> "OD2" Residue "P PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 301": "OD1" <-> "OD2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 66737 Number of models: 1 Model: "" Number of chains: 50 Chain: "N" Number of atoms: 264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 264 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain breaks: 2 Chain: "A" Number of atoms: 4069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4069 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 14, 'TRANS': 521} Chain: "B" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3952 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 10, 'TRANS': 515} Chain: "D" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3923 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "E" Number of atoms: 4132 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} Conformer: "C" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} bond proxies already assigned to first conformer: 4158 Chain: "G" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4089 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "H" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4054 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 16, 'TRANS': 511} Chain: "Q" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4086 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 18, 'TRANS': 519} Chain: "Z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "a" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4041 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Chain: "b" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3943 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 10, 'TRANS': 514} Chain: "d" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3917 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 4169 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} Conformer: "B" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} bond proxies already assigned to first conformer: 4195 Chain: "g" Number of atoms: 4088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4088 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "h" Number of atoms: 4032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4032 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 16, 'TRANS': 508} Chain: "q" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4053 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 16, 'TRANS': 516} Chain: "z" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4033 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 512} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "P" Number of atoms: 1339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1339 Classifications: {'peptide': 172} Link IDs: {'PTRANS': 4, 'TRANS': 167} Chain breaks: 4 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N BPHE E 9 " occ=0.38 ... (20 atoms not shown) pdb=" CZ CPHE E 9 " occ=0.62 residue: pdb=" N APHE e 9 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE e 9 " occ=0.50 Time building chain proxies: 28.54, per 1000 atoms: 0.43 Number of scatterers: 66737 At special positions: 0 Unit cell: (181.976, 176.686, 180.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 412 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 12914 8.00 N 11602 7.00 C 41697 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 Atom "HETATM66260 O3A ADP B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66644 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66516 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66324 O3A ADP E 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66388 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66548 O3A ADP d 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66580 O3A ADP e 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66292 O3A ADP D 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.07 Conformation dependent library (CDL) restraints added in 10.2 seconds 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16150 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 321 helices and 110 sheets defined 51.0% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.31 Creating SS restraints... Processing helix chain 'A' and resid 15 through 35 removed outlier: 3.616A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N SER A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N SER A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 70 through 85 Processing helix chain 'A' and resid 90 through 110 removed outlier: 3.593A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 135 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 146 through 156 Processing helix chain 'A' and resid 163 through 179 removed outlier: 4.591A pdb=" N ASP A 166 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ALA A 169 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 257 through 281 removed outlier: 4.588A pdb=" N ASP A 261 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 280 " --> pdb=" O LYS A 277 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 382 through 404 Processing helix chain 'A' and resid 414 through 429 removed outlier: 4.411A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N SER A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 456 removed outlier: 3.749A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N ILE A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Proline residue: A 449 - end of helix removed outlier: 3.647A pdb=" N ALA A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 476 Processing helix chain 'A' and resid 478 through 485 removed outlier: 5.168A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A 484 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TRP A 485 " --> pdb=" O ASN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 507 through 526 Processing helix chain 'B' and resid 21 through 39 Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 99 through 118 Processing helix chain 'B' and resid 123 through 144 Processing helix chain 'B' and resid 153 through 168 Processing helix chain 'B' and resid 171 through 190 removed outlier: 3.586A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS B 176 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N ASP B 177 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 198 No H-bonds generated for 'chain 'B' and resid 196 through 198' Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 261 through 285 removed outlier: 3.957A pdb=" N HIS B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 317 through 327 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 380 through 402 Processing helix chain 'B' and resid 412 through 427 removed outlier: 3.782A pdb=" N ARG B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 454 Proline residue: B 447 - end of helix removed outlier: 3.624A pdb=" N ALA B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 471 Processing helix chain 'B' and resid 488 through 491 No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 497 through 515 Processing helix chain 'D' and resid 29 through 51 removed outlier: 4.423A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N SER D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 80 Processing helix chain 'D' and resid 86 through 101 Processing helix chain 'D' and resid 106 through 125 removed outlier: 4.037A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 151 Processing helix chain 'D' and resid 160 through 172 Processing helix chain 'D' and resid 180 through 193 Proline residue: D 185 - end of helix Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 269 through 293 removed outlier: 4.163A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR D 293 " --> pdb=" O GLN D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 319 Processing helix chain 'D' and resid 330 through 340 removed outlier: 4.548A pdb=" N GLU D 334 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE D 340 " --> pdb=" O CYS D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 350 No H-bonds generated for 'chain 'D' and resid 348 through 350' Processing helix chain 'D' and resid 353 through 355 No H-bonds generated for 'chain 'D' and resid 353 through 355' Processing helix chain 'D' and resid 395 through 417 Processing helix chain 'D' and resid 427 through 442 removed outlier: 3.606A pdb=" N THR D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 469 removed outlier: 3.813A pdb=" N VAL D 460 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ILE D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) Proline residue: D 462 - end of helix Processing helix chain 'D' and resid 473 through 486 Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'E' and resid 22 through 24 No H-bonds generated for 'chain 'E' and resid 22 through 24' Processing helix chain 'E' and resid 31 through 51 removed outlier: 4.189A pdb=" N THR E 50 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N SER E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 80 Processing helix chain 'E' and resid 86 through 101 Processing helix chain 'E' and resid 106 through 126 removed outlier: 4.280A pdb=" N VAL E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 151 Processing helix chain 'E' and resid 163 through 175 removed outlier: 4.652A pdb=" N SER E 175 " --> pdb=" O THR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 180 removed outlier: 3.972A pdb=" N SER E 180 " --> pdb=" O VAL E 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 177 through 180' Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 219 through 221 No H-bonds generated for 'chain 'E' and resid 219 through 221' Processing helix chain 'E' and resid 271 through 295 removed outlier: 3.841A pdb=" N THR E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 316 Processing helix chain 'E' and resid 327 through 337 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 392 through 414 Processing helix chain 'E' and resid 424 through 437 Processing helix chain 'E' and resid 442 through 465 removed outlier: 3.858A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL E 457 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N ILE E 458 " --> pdb=" O ALA E 454 " (cutoff:3.500A) Proline residue: E 459 - end of helix Processing helix chain 'E' and resid 470 through 483 Processing helix chain 'E' and resid 501 through 504 No H-bonds generated for 'chain 'E' and resid 501 through 504' Processing helix chain 'E' and resid 510 through 529 Processing helix chain 'G' and resid 20 through 40 removed outlier: 3.798A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N THR G 39 " --> pdb=" O ASP G 35 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N CYS G 40 " --> pdb=" O ILE G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 68 Processing helix chain 'G' and resid 75 through 90 Processing helix chain 'G' and resid 95 through 114 removed outlier: 3.576A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 139 Processing helix chain 'G' and resid 149 through 160 Processing helix chain 'G' and resid 169 through 183 Processing helix chain 'G' and resid 195 through 198 No H-bonds generated for 'chain 'G' and resid 195 through 198' Processing helix chain 'G' and resid 209 through 211 No H-bonds generated for 'chain 'G' and resid 209 through 211' Processing helix chain 'G' and resid 261 through 285 removed outlier: 4.187A pdb=" N PHE G 264 " --> pdb=" O GLU G 261 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR G 265 " --> pdb=" O GLU G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 307 removed outlier: 3.577A pdb=" N ALA G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 327 Processing helix chain 'G' and resid 335 through 337 No H-bonds generated for 'chain 'G' and resid 335 through 337' Processing helix chain 'G' and resid 381 through 403 Processing helix chain 'G' and resid 413 through 428 removed outlier: 3.529A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 455 removed outlier: 3.557A pdb=" N TRP G 435 " --> pdb=" O VAL G 432 " (cutoff:3.500A) Proline residue: G 436 - end of helix removed outlier: 4.006A pdb=" N ILE G 447 " --> pdb=" O LEU G 444 " (cutoff:3.500A) Proline residue: G 448 - end of helix Processing helix chain 'G' and resid 459 through 471 Processing helix chain 'G' and resid 490 through 493 No H-bonds generated for 'chain 'G' and resid 490 through 493' Processing helix chain 'G' and resid 499 through 517 Processing helix chain 'H' and resid 19 through 39 removed outlier: 3.954A pdb=" N VAL H 36 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N THR H 38 " --> pdb=" O GLU H 34 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N THR H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 68 Processing helix chain 'H' and resid 76 through 89 removed outlier: 3.687A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 113 removed outlier: 4.001A pdb=" N THR H 98 " --> pdb=" O THR H 94 " (cutoff:3.500A) Proline residue: H 110 - end of helix Processing helix chain 'H' and resid 118 through 139 Processing helix chain 'H' and resid 148 through 163 Processing helix chain 'H' and resid 169 through 184 removed outlier: 5.383A pdb=" N ALA H 173 " --> pdb=" O GLN H 170 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE H 175 " --> pdb=" O LYS H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'H' and resid 205 through 207 No H-bonds generated for 'chain 'H' and resid 205 through 207' Processing helix chain 'H' and resid 260 through 283 Processing helix chain 'H' and resid 297 through 305 Processing helix chain 'H' and resid 316 through 326 Processing helix chain 'H' and resid 379 through 401 Processing helix chain 'H' and resid 411 through 426 removed outlier: 4.062A pdb=" N THR H 426 " --> pdb=" O ASP H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 453 removed outlier: 4.106A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ILE H 444 " --> pdb=" O LYS H 440 " (cutoff:3.500A) removed outlier: 5.320A pdb=" N ILE H 445 " --> pdb=" O ALA H 441 " (cutoff:3.500A) Proline residue: H 446 - end of helix Processing helix chain 'H' and resid 457 through 469 Processing helix chain 'H' and resid 496 through 514 Processing helix chain 'Q' and resid 11 through 14 No H-bonds generated for 'chain 'Q' and resid 11 through 14' Processing helix chain 'Q' and resid 24 through 46 removed outlier: 4.189A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ALA Q 46 " --> pdb=" O THR Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 74 Processing helix chain 'Q' and resid 81 through 96 Processing helix chain 'Q' and resid 101 through 121 Processing helix chain 'Q' and resid 125 through 146 Proline residue: Q 144 - end of helix Processing helix chain 'Q' and resid 158 through 167 removed outlier: 4.091A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 177 through 189 Processing helix chain 'Q' and resid 199 through 201 No H-bonds generated for 'chain 'Q' and resid 199 through 201' Processing helix chain 'Q' and resid 212 through 214 No H-bonds generated for 'chain 'Q' and resid 212 through 214' Processing helix chain 'Q' and resid 262 through 286 removed outlier: 4.886A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N THR Q 286 " --> pdb=" O ALA Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 299 through 307 Processing helix chain 'Q' and resid 318 through 328 Processing helix chain 'Q' and resid 382 through 404 Processing helix chain 'Q' and resid 414 through 429 removed outlier: 3.708A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 456 removed outlier: 3.561A pdb=" N TYR Q 436 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) Proline residue: Q 449 - end of helix Processing helix chain 'Q' and resid 460 through 473 Processing helix chain 'Q' and resid 492 through 495 No H-bonds generated for 'chain 'Q' and resid 492 through 495' Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'Z' and resid 3 through 7 Processing helix chain 'Z' and resid 16 through 37 removed outlier: 3.717A pdb=" N ARG Z 35 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR Z 36 " --> pdb=" O VAL Z 33 " (cutoff:3.500A) Processing helix chain 'Z' and resid 60 through 66 Processing helix chain 'Z' and resid 72 through 87 Processing helix chain 'Z' and resid 92 through 112 removed outlier: 3.558A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLU Z 112 " --> pdb=" O LEU Z 108 " (cutoff:3.500A) Processing helix chain 'Z' and resid 116 through 137 Processing helix chain 'Z' and resid 145 through 159 removed outlier: 4.100A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 162 through 179 removed outlier: 3.647A pdb=" N GLU Z 170 " --> pdb=" O ASP Z 166 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 190 No H-bonds generated for 'chain 'Z' and resid 188 through 190' Processing helix chain 'Z' and resid 201 through 203 No H-bonds generated for 'chain 'Z' and resid 201 through 203' Processing helix chain 'Z' and resid 253 through 263 Processing helix chain 'Z' and resid 265 through 281 removed outlier: 3.631A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 299 through 308 removed outlier: 3.749A pdb=" N GLU Z 308 " --> pdb=" O ALA Z 304 " (cutoff:3.500A) Processing helix chain 'Z' and resid 318 through 327 removed outlier: 4.426A pdb=" N GLU Z 322 " --> pdb=" O ARG Z 318 " (cutoff:3.500A) Processing helix chain 'Z' and resid 341 through 343 No H-bonds generated for 'chain 'Z' and resid 341 through 343' Processing helix chain 'Z' and resid 381 through 403 Processing helix chain 'Z' and resid 413 through 428 Proline residue: Z 427 - end of helix Processing helix chain 'Z' and resid 431 through 455 removed outlier: 3.979A pdb=" N GLN Z 434 " --> pdb=" O GLY Z 431 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE Z 447 " --> pdb=" O LEU Z 444 " (cutoff:3.500A) Proline residue: Z 448 - end of helix Processing helix chain 'Z' and resid 459 through 473 Processing helix chain 'Z' and resid 489 through 492 No H-bonds generated for 'chain 'Z' and resid 489 through 492' Processing helix chain 'Z' and resid 498 through 516 Processing helix chain 'a' and resid 15 through 35 removed outlier: 3.684A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N SER a 34 " --> pdb=" O ASN a 30 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N SER a 35 " --> pdb=" O ILE a 31 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 64 Processing helix chain 'a' and resid 70 through 85 Processing helix chain 'a' and resid 90 through 109 removed outlier: 4.003A pdb=" N VAL a 94 " --> pdb=" O THR a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 114 through 135 Processing helix chain 'a' and resid 144 through 156 Processing helix chain 'a' and resid 163 through 178 removed outlier: 4.302A pdb=" N ASP a 166 " --> pdb=" O ILE a 163 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ALA a 169 " --> pdb=" O ASP a 166 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 186 No H-bonds generated for 'chain 'a' and resid 184 through 186' Processing helix chain 'a' and resid 205 through 207 No H-bonds generated for 'chain 'a' and resid 205 through 207' Processing helix chain 'a' and resid 257 through 281 removed outlier: 4.634A pdb=" N ASP a 261 " --> pdb=" O GLU a 258 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ILE a 270 " --> pdb=" O GLU a 267 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR a 281 " --> pdb=" O ILE a 278 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 302 Processing helix chain 'a' and resid 313 through 323 Processing helix chain 'a' and resid 342 through 344 No H-bonds generated for 'chain 'a' and resid 342 through 344' Processing helix chain 'a' and resid 382 through 404 Processing helix chain 'a' and resid 414 through 428 removed outlier: 4.556A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) Processing helix chain 'a' and resid 434 through 455 removed outlier: 3.683A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ILE a 448 " --> pdb=" O SER a 444 " (cutoff:3.500A) Proline residue: a 449 - end of helix Processing helix chain 'a' and resid 460 through 476 Processing helix chain 'a' and resid 481 through 485 removed outlier: 3.909A pdb=" N TRP a 485 " --> pdb=" O ASN a 482 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 501 No H-bonds generated for 'chain 'a' and resid 498 through 501' Processing helix chain 'a' and resid 507 through 525 Processing helix chain 'b' and resid 21 through 39 Processing helix chain 'b' and resid 67 through 72 Processing helix chain 'b' and resid 79 through 94 Processing helix chain 'b' and resid 99 through 118 Processing helix chain 'b' and resid 123 through 144 Processing helix chain 'b' and resid 152 through 168 Processing helix chain 'b' and resid 171 through 190 removed outlier: 3.615A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS b 176 " --> pdb=" O THR b 173 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N ASP b 177 " --> pdb=" O HIS b 174 " (cutoff:3.500A) Processing helix chain 'b' and resid 196 through 198 No H-bonds generated for 'chain 'b' and resid 196 through 198' Processing helix chain 'b' and resid 209 through 211 No H-bonds generated for 'chain 'b' and resid 209 through 211' Processing helix chain 'b' and resid 261 through 285 removed outlier: 3.999A pdb=" N HIS b 285 " --> pdb=" O ARG b 281 " (cutoff:3.500A) Processing helix chain 'b' and resid 298 through 306 Processing helix chain 'b' and resid 317 through 327 Processing helix chain 'b' and resid 338 through 340 No H-bonds generated for 'chain 'b' and resid 338 through 340' Processing helix chain 'b' and resid 380 through 402 Processing helix chain 'b' and resid 412 through 427 removed outlier: 3.804A pdb=" N ARG b 427 " --> pdb=" O GLN b 423 " (cutoff:3.500A) Processing helix chain 'b' and resid 431 through 454 Proline residue: b 447 - end of helix removed outlier: 3.718A pdb=" N ALA b 454 " --> pdb=" O ILE b 450 " (cutoff:3.500A) Processing helix chain 'b' and resid 458 through 471 Processing helix chain 'b' and resid 488 through 491 No H-bonds generated for 'chain 'b' and resid 488 through 491' Processing helix chain 'b' and resid 497 through 515 Processing helix chain 'd' and resid 29 through 49 Processing helix chain 'd' and resid 74 through 80 Processing helix chain 'd' and resid 86 through 101 Processing helix chain 'd' and resid 106 through 125 removed outlier: 3.652A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 132 through 151 Processing helix chain 'd' and resid 160 through 172 Processing helix chain 'd' and resid 175 through 177 No H-bonds generated for 'chain 'd' and resid 175 through 177' Processing helix chain 'd' and resid 179 through 194 removed outlier: 5.106A pdb=" N SER d 184 " --> pdb=" O SER d 181 " (cutoff:3.500A) Proline residue: d 185 - end of helix removed outlier: 3.672A pdb=" N LYS d 193 " --> pdb=" O ALA d 190 " (cutoff:3.500A) Processing helix chain 'd' and resid 205 through 207 No H-bonds generated for 'chain 'd' and resid 205 through 207' Processing helix chain 'd' and resid 218 through 220 No H-bonds generated for 'chain 'd' and resid 218 through 220' Processing helix chain 'd' and resid 269 through 293 removed outlier: 3.920A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR d 293 " --> pdb=" O GLN d 289 " (cutoff:3.500A) Processing helix chain 'd' and resid 311 through 319 Processing helix chain 'd' and resid 330 through 340 removed outlier: 4.272A pdb=" N GLU d 334 " --> pdb=" O GLU d 331 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE d 340 " --> pdb=" O CYS d 337 " (cutoff:3.500A) Processing helix chain 'd' and resid 348 through 350 No H-bonds generated for 'chain 'd' and resid 348 through 350' Processing helix chain 'd' and resid 353 through 355 No H-bonds generated for 'chain 'd' and resid 353 through 355' Processing helix chain 'd' and resid 395 through 416 Processing helix chain 'd' and resid 427 through 442 Processing helix chain 'd' and resid 446 through 466 removed outlier: 3.941A pdb=" N VAL d 460 " --> pdb=" O ASP d 456 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ILE d 461 " --> pdb=" O ALA d 457 " (cutoff:3.500A) Proline residue: d 462 - end of helix Processing helix chain 'd' and resid 473 through 485 Processing helix chain 'd' and resid 512 through 530 removed outlier: 4.912A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 51 removed outlier: 3.612A pdb=" N ARG e 49 " --> pdb=" O ASN e 46 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR e 50 " --> pdb=" O THR e 47 " (cutoff:3.500A) Processing helix chain 'e' and resid 74 through 80 Processing helix chain 'e' and resid 86 through 101 Processing helix chain 'e' and resid 106 through 125 removed outlier: 4.274A pdb=" N VAL e 110 " --> pdb=" O THR e 106 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN e 122 " --> pdb=" O GLU e 118 " (cutoff:3.500A) Processing helix chain 'e' and resid 130 through 150 Processing helix chain 'e' and resid 163 through 175 removed outlier: 4.703A pdb=" N SER e 175 " --> pdb=" O THR e 171 " (cutoff:3.500A) Processing helix chain 'e' and resid 177 through 195 removed outlier: 3.955A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N ARG e 183 " --> pdb=" O SER e 180 " (cutoff:3.500A) Processing helix chain 'e' and resid 206 through 208 No H-bonds generated for 'chain 'e' and resid 206 through 208' Processing helix chain 'e' and resid 219 through 221 No H-bonds generated for 'chain 'e' and resid 219 through 221' Processing helix chain 'e' and resid 271 through 294 Processing helix chain 'e' and resid 308 through 316 Processing helix chain 'e' and resid 327 through 337 Processing helix chain 'e' and resid 345 through 347 No H-bonds generated for 'chain 'e' and resid 345 through 347' Processing helix chain 'e' and resid 350 through 352 No H-bonds generated for 'chain 'e' and resid 350 through 352' Processing helix chain 'e' and resid 392 through 414 Processing helix chain 'e' and resid 424 through 439 removed outlier: 3.998A pdb=" N LYS e 439 " --> pdb=" O GLN e 435 " (cutoff:3.500A) Processing helix chain 'e' and resid 442 through 465 removed outlier: 3.899A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N VAL e 457 " --> pdb=" O ASP e 453 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ILE e 458 " --> pdb=" O ALA e 454 " (cutoff:3.500A) Proline residue: e 459 - end of helix Processing helix chain 'e' and resid 470 through 483 Processing helix chain 'e' and resid 501 through 504 No H-bonds generated for 'chain 'e' and resid 501 through 504' Processing helix chain 'e' and resid 510 through 529 Processing helix chain 'g' and resid 20 through 37 removed outlier: 3.822A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 69 removed outlier: 3.735A pdb=" N GLU g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 75 through 90 Processing helix chain 'g' and resid 95 through 114 Processing helix chain 'g' and resid 119 through 139 Processing helix chain 'g' and resid 149 through 160 Processing helix chain 'g' and resid 164 through 167 removed outlier: 3.832A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 164 through 167' Processing helix chain 'g' and resid 169 through 183 Processing helix chain 'g' and resid 209 through 211 No H-bonds generated for 'chain 'g' and resid 209 through 211' Processing helix chain 'g' and resid 263 through 285 removed outlier: 4.306A pdb=" N LEU g 285 " --> pdb=" O ASP g 281 " (cutoff:3.500A) Processing helix chain 'g' and resid 298 through 307 removed outlier: 3.570A pdb=" N ALA g 307 " --> pdb=" O TYR g 303 " (cutoff:3.500A) Processing helix chain 'g' and resid 317 through 327 Processing helix chain 'g' and resid 335 through 337 No H-bonds generated for 'chain 'g' and resid 335 through 337' Processing helix chain 'g' and resid 381 through 403 Processing helix chain 'g' and resid 413 through 428 removed outlier: 3.642A pdb=" N LYS g 427 " --> pdb=" O THR g 423 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ALA g 428 " --> pdb=" O GLU g 424 " (cutoff:3.500A) Processing helix chain 'g' and resid 434 through 455 removed outlier: 3.925A pdb=" N LEU g 444 " --> pdb=" O VAL g 440 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N GLU g 445 " --> pdb=" O ALA g 441 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL g 446 " --> pdb=" O GLN g 442 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N ILE g 447 " --> pdb=" O ALA g 443 " (cutoff:3.500A) Proline residue: g 448 - end of helix Processing helix chain 'g' and resid 459 through 471 Processing helix chain 'g' and resid 490 through 493 No H-bonds generated for 'chain 'g' and resid 490 through 493' Processing helix chain 'g' and resid 499 through 517 Processing helix chain 'h' and resid 19 through 36 removed outlier: 3.595A pdb=" N ALA h 35 " --> pdb=" O VAL h 31 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N VAL h 36 " --> pdb=" O ILE h 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 68 Processing helix chain 'h' and resid 76 through 89 removed outlier: 3.702A pdb=" N GLU h 89 " --> pdb=" O GLN h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 113 removed outlier: 4.158A pdb=" N THR h 98 " --> pdb=" O THR h 94 " (cutoff:3.500A) Proline residue: h 110 - end of helix Processing helix chain 'h' and resid 118 through 139 Processing helix chain 'h' and resid 148 through 163 Processing helix chain 'h' and resid 172 through 185 removed outlier: 3.596A pdb=" N MET h 185 " --> pdb=" O ASP h 181 " (cutoff:3.500A) Processing helix chain 'h' and resid 192 through 194 No H-bonds generated for 'chain 'h' and resid 192 through 194' Processing helix chain 'h' and resid 205 through 207 No H-bonds generated for 'chain 'h' and resid 205 through 207' Processing helix chain 'h' and resid 225 through 227 No H-bonds generated for 'chain 'h' and resid 225 through 227' Processing helix chain 'h' and resid 260 through 284 removed outlier: 3.576A pdb=" N SER h 284 " --> pdb=" O LYS h 280 " (cutoff:3.500A) Processing helix chain 'h' and resid 297 through 305 Processing helix chain 'h' and resid 316 through 326 Processing helix chain 'h' and resid 339 through 341 No H-bonds generated for 'chain 'h' and resid 339 through 341' Processing helix chain 'h' and resid 379 through 401 Processing helix chain 'h' and resid 411 through 426 removed outlier: 4.032A pdb=" N THR h 426 " --> pdb=" O ASP h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 430 through 453 removed outlier: 4.139A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU h 443 " --> pdb=" O ALA h 439 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE h 444 " --> pdb=" O LYS h 440 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N ILE h 445 " --> pdb=" O ALA h 441 " (cutoff:3.500A) Proline residue: h 446 - end of helix Processing helix chain 'h' and resid 457 through 470 Processing helix chain 'h' and resid 496 through 515 Processing helix chain 'q' and resid 11 through 14 No H-bonds generated for 'chain 'q' and resid 11 through 14' Processing helix chain 'q' and resid 25 through 46 removed outlier: 4.132A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ALA q 46 " --> pdb=" O THR q 42 " (cutoff:3.500A) Processing helix chain 'q' and resid 69 through 75 Processing helix chain 'q' and resid 81 through 96 Processing helix chain 'q' and resid 101 through 121 Processing helix chain 'q' and resid 125 through 146 Proline residue: q 144 - end of helix Processing helix chain 'q' and resid 158 through 167 removed outlier: 4.302A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N SER q 167 " --> pdb=" O LEU q 163 " (cutoff:3.500A) Processing helix chain 'q' and resid 177 through 189 Processing helix chain 'q' and resid 199 through 201 No H-bonds generated for 'chain 'q' and resid 199 through 201' Processing helix chain 'q' and resid 212 through 214 No H-bonds generated for 'chain 'q' and resid 212 through 214' Processing helix chain 'q' and resid 262 through 286 removed outlier: 4.865A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR q 286 " --> pdb=" O ALA q 282 " (cutoff:3.500A) Processing helix chain 'q' and resid 299 through 307 Processing helix chain 'q' and resid 318 through 328 Processing helix chain 'q' and resid 382 through 404 Processing helix chain 'q' and resid 414 through 429 removed outlier: 3.788A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 456 removed outlier: 3.563A pdb=" N TYR q 436 " --> pdb=" O LEU q 433 " (cutoff:3.500A) Proline residue: q 449 - end of helix Processing helix chain 'q' and resid 460 through 473 Processing helix chain 'q' and resid 492 through 495 No H-bonds generated for 'chain 'q' and resid 492 through 495' Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'z' and resid 3 through 7 removed outlier: 3.744A pdb=" N LEU z 7 " --> pdb=" O ALA z 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 3 through 7' Processing helix chain 'z' and resid 16 through 37 removed outlier: 3.701A pdb=" N ARG z 35 " --> pdb=" O ASP z 32 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR z 36 " --> pdb=" O VAL z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 60 through 65 Processing helix chain 'z' and resid 72 through 87 Processing helix chain 'z' and resid 92 through 112 removed outlier: 3.547A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLU z 112 " --> pdb=" O LEU z 108 " (cutoff:3.500A) Processing helix chain 'z' and resid 116 through 137 Processing helix chain 'z' and resid 145 through 159 removed outlier: 4.234A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 162 through 179 removed outlier: 3.577A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) Processing helix chain 'z' and resid 188 through 190 No H-bonds generated for 'chain 'z' and resid 188 through 190' Processing helix chain 'z' and resid 201 through 203 No H-bonds generated for 'chain 'z' and resid 201 through 203' Processing helix chain 'z' and resid 253 through 281 removed outlier: 4.203A pdb=" N ARG z 264 " --> pdb=" O VAL z 260 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS z 265 " --> pdb=" O LYS z 261 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N PHE z 266 " --> pdb=" O ALA z 262 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE z 267 " --> pdb=" O GLU z 263 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 299 through 308 removed outlier: 3.807A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 318 through 328 removed outlier: 4.344A pdb=" N GLU z 322 " --> pdb=" O ARG z 318 " (cutoff:3.500A) Processing helix chain 'z' and resid 341 through 343 No H-bonds generated for 'chain 'z' and resid 341 through 343' Processing helix chain 'z' and resid 381 through 403 Processing helix chain 'z' and resid 413 through 428 Proline residue: z 427 - end of helix Processing helix chain 'z' and resid 431 through 455 removed outlier: 4.113A pdb=" N GLN z 434 " --> pdb=" O GLY z 431 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ILE z 447 " --> pdb=" O LEU z 444 " (cutoff:3.500A) Proline residue: z 448 - end of helix Processing helix chain 'z' and resid 459 through 473 Processing helix chain 'z' and resid 489 through 492 No H-bonds generated for 'chain 'z' and resid 489 through 492' Processing helix chain 'z' and resid 498 through 516 Processing helix chain 'P' and resid 57 through 61 Processing helix chain 'P' and resid 63 through 84 removed outlier: 3.720A pdb=" N GLU P 79 " --> pdb=" O GLU P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 175 Processing helix chain 'P' and resid 195 through 208 Processing helix chain 'P' and resid 219 through 222 No H-bonds generated for 'chain 'P' and resid 219 through 222' Processing helix chain 'P' and resid 226 through 231 Processing helix chain 'P' and resid 252 through 255 No H-bonds generated for 'chain 'P' and resid 252 through 255' Processing helix chain 'P' and resid 261 through 271 removed outlier: 4.052A pdb=" N PHE P 271 " --> pdb=" O PHE P 267 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'N' and resid 253 through 255 removed outlier: 3.698A pdb=" N PHE N 254 " --> pdb=" O TRP N 266 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'N' and resid 220 through 222 removed outlier: 3.513A pdb=" N GLN N 231 " --> pdb=" O LEU N 221 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 9 through 13 Processing sheet with id= D, first strand: chain 'A' and resid 43 through 46 Processing sheet with id= E, first strand: chain 'A' and resid 180 through 182 removed outlier: 3.774A pdb=" N TYR A 181 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 196 through 199 Processing sheet with id= G, first strand: chain 'A' and resid 213 through 216 Processing sheet with id= H, first strand: chain 'A' and resid 346 through 348 removed outlier: 6.499A pdb=" N VAL A 285 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LEU A 237 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU A 287 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET A 306 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N THR A 288 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A 308 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 408 through 410 Processing sheet with id= J, first strand: chain 'A' and resid 486 through 489 Processing sheet with id= K, first strand: chain 'B' and resid 17 through 19 Processing sheet with id= L, first strand: chain 'B' and resid 50 through 53 Processing sheet with id= M, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.359A pdb=" N CYS B 371 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N ILE B 202 " --> pdb=" O CYS B 371 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ILE B 373 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LYS B 204 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N LEU B 375 " --> pdb=" O LYS B 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'B' and resid 218 through 220 Processing sheet with id= O, first strand: chain 'B' and resid 344 through 346 removed outlier: 3.539A pdb=" N CYS B 346 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N CYS B 289 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ALA B 240 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE B 291 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N MET B 310 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N ASN B 292 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE B 312 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 406 through 408 Processing sheet with id= Q, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= R, first strand: chain 'D' and resid 59 through 62 Processing sheet with id= S, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.740A pdb=" N VAL D 386 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N VAL D 211 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE D 388 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LYS D 213 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL D 390 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 227 through 229 Processing sheet with id= U, first strand: chain 'D' and resid 357 through 359 removed outlier: 6.970A pdb=" N VAL D 297 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ILE D 249 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU D 299 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N MET D 323 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N ILE D 300 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE D 325 " --> pdb=" O ILE D 300 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 421 through 423 Processing sheet with id= W, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.712A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 59 through 62 Processing sheet with id= Y, first strand: chain 'E' and resid 209 through 215 removed outlier: 7.011A pdb=" N VAL E 383 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N GLU E 212 " --> pdb=" O VAL E 383 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE E 385 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LYS E 214 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE E 387 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 228 through 230 Processing sheet with id= AA, first strand: chain 'E' and resid 354 through 356 removed outlier: 7.212A pdb=" N LEU E 299 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 418 through 420 Processing sheet with id= AC, first strand: chain 'G' and resid 15 through 17 Processing sheet with id= AD, first strand: chain 'G' and resid 48 through 51 Processing sheet with id= AE, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.483A pdb=" N CYS G 372 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N GLU G 202 " --> pdb=" O CYS G 372 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILE G 374 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE G 204 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU G 376 " --> pdb=" O ILE G 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'G' and resid 238 through 241 removed outlier: 6.530A pdb=" N VAL G 289 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N LEU G 241 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ILE G 291 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR G 310 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 8.086A pdb=" N THR G 292 " --> pdb=" O THR G 310 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE G 312 " --> pdb=" O THR G 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'G' and resid 351 through 355 Processing sheet with id= AH, first strand: chain 'G' and resid 407 through 409 Processing sheet with id= AI, first strand: chain 'G' and resid 478 through 480 Processing sheet with id= AJ, first strand: chain 'H' and resid 14 through 17 Processing sheet with id= AK, first strand: chain 'H' and resid 47 through 50 Processing sheet with id= AL, first strand: chain 'H' and resid 195 through 201 removed outlier: 6.243A pdb=" N CYS H 370 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LYS H 198 " --> pdb=" O CYS H 370 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N PHE H 372 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL H 200 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N LEU H 374 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR H 371 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'H' and resid 214 through 217 Processing sheet with id= AN, first strand: chain 'H' and resid 237 through 240 removed outlier: 6.911A pdb=" N VAL H 288 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU H 240 " --> pdb=" O VAL H 288 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU H 290 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N PHE H 309 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N SER H 291 " --> pdb=" O PHE H 309 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA H 311 " --> pdb=" O SER H 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain 'H' and resid 405 through 407 Processing sheet with id= AP, first strand: chain 'H' and resid 475 through 478 Processing sheet with id= AQ, first strand: chain 'Q' and resid 20 through 23 Processing sheet with id= AR, first strand: chain 'Q' and resid 54 through 57 removed outlier: 3.519A pdb=" N THR Q 66 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'Q' and resid 202 through 206 removed outlier: 6.707A pdb=" N SER Q 373 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N CYS Q 205 " --> pdb=" O SER Q 373 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE Q 375 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Q' and resid 220 through 223 Processing sheet with id= AU, first strand: chain 'Q' and resid 240 through 242 removed outlier: 5.994A pdb=" N MET Q 311 " --> pdb=" O VAL Q 291 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR Q 293 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N VAL Q 313 " --> pdb=" O THR Q 293 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'Q' and resid 498 through 500 removed outlier: 3.949A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N VAL Q 147 " --> pdb=" O PRO Q 410 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id= AX, first strand: chain 'Z' and resid 12 through 15 removed outlier: 3.561A pdb=" N GLU Z 12 " --> pdb=" O ARG Z 523 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'Z' and resid 45 through 48 Processing sheet with id= AZ, first strand: chain 'Z' and resid 191 through 196 removed outlier: 7.134A pdb=" N VAL Z 372 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N MET Z 194 " --> pdb=" O VAL Z 372 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU Z 374 " --> pdb=" O MET Z 194 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N MET Z 196 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ILE Z 376 " --> pdb=" O MET Z 196 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER Z 205 " --> pdb=" O LEU Z 375 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id= BB, first strand: chain 'Z' and resid 345 through 347 Processing sheet with id= BC, first strand: chain 'Z' and resid 477 through 479 removed outlier: 3.643A pdb=" N MET Z 487 " --> pdb=" O GLY Z 478 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'a' and resid 9 through 13 Processing sheet with id= BE, first strand: chain 'a' and resid 43 through 46 Processing sheet with id= BF, first strand: chain 'a' and resid 137 through 139 Processing sheet with id= BG, first strand: chain 'a' and resid 180 through 182 Processing sheet with id= BH, first strand: chain 'a' and resid 196 through 201 removed outlier: 3.689A pdb=" N GLY a 379 " --> pdb=" O ALA a 200 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'a' and resid 213 through 216 Processing sheet with id= BJ, first strand: chain 'a' and resid 346 through 348 removed outlier: 6.520A pdb=" N VAL a 285 " --> pdb=" O ALA a 235 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU a 237 " --> pdb=" O VAL a 285 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU a 287 " --> pdb=" O LEU a 237 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N MET a 306 " --> pdb=" O ILE a 286 " (cutoff:3.500A) removed outlier: 8.307A pdb=" N THR a 288 " --> pdb=" O MET a 306 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL a 308 " --> pdb=" O THR a 288 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'a' and resid 486 through 489 Processing sheet with id= BL, first strand: chain 'b' and resid 17 through 19 Processing sheet with id= BM, first strand: chain 'b' and resid 50 through 53 Processing sheet with id= BN, first strand: chain 'b' and resid 199 through 205 removed outlier: 6.268A pdb=" N CYS b 371 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE b 202 " --> pdb=" O CYS b 371 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ILE b 373 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LYS b 204 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N LEU b 375 " --> pdb=" O LYS b 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= BN Processing sheet with id= BO, first strand: chain 'b' and resid 218 through 220 Processing sheet with id= BP, first strand: chain 'b' and resid 344 through 346 removed outlier: 6.907A pdb=" N CYS b 289 " --> pdb=" O LEU b 238 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ALA b 240 " --> pdb=" O CYS b 289 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ILE b 291 " --> pdb=" O ALA b 240 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET b 310 " --> pdb=" O PHE b 290 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASN b 292 " --> pdb=" O MET b 310 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE b 312 " --> pdb=" O ASN b 292 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'b' and resid 406 through 408 Processing sheet with id= BR, first strand: chain 'b' and resid 476 through 479 Processing sheet with id= BS, first strand: chain 'd' and resid 59 through 62 Processing sheet with id= BT, first strand: chain 'd' and resid 208 through 214 removed outlier: 6.694A pdb=" N VAL d 386 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N VAL d 211 " --> pdb=" O VAL d 386 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ILE d 388 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LYS d 213 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N VAL d 390 " --> pdb=" O LYS d 213 " (cutoff:3.500A) No H-bonds generated for sheet with id= BT Processing sheet with id= BU, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.526A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'd' and resid 357 through 359 removed outlier: 6.549A pdb=" N VAL d 297 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N ILE d 249 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU d 299 " --> pdb=" O ILE d 249 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N MET d 323 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ILE d 300 " --> pdb=" O MET d 323 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE d 325 " --> pdb=" O ILE d 300 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'd' and resid 421 through 423 Processing sheet with id= BX, first strand: chain 'd' and resid 491 through 494 Processing sheet with id= BY, first strand: chain 'e' and resid 59 through 62 Processing sheet with id= BZ, first strand: chain 'e' and resid 209 through 215 removed outlier: 7.238A pdb=" N VAL e 383 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N GLU e 212 " --> pdb=" O VAL e 383 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE e 385 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LYS e 214 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE e 387 " --> pdb=" O LYS e 214 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'e' and resid 228 through 230 Processing sheet with id= CB, first strand: chain 'e' and resid 354 through 356 removed outlier: 6.979A pdb=" N LEU e 299 " --> pdb=" O ALA e 249 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU e 251 " --> pdb=" O LEU e 299 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE e 301 " --> pdb=" O LEU e 251 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N CYS e 302 " --> pdb=" O PRO e 320 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL e 322 " --> pdb=" O CYS e 302 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'e' and resid 418 through 420 Processing sheet with id= CD, first strand: chain 'g' and resid 15 through 18 Processing sheet with id= CE, first strand: chain 'g' and resid 48 through 51 Processing sheet with id= CF, first strand: chain 'g' and resid 185 through 187 Processing sheet with id= CG, first strand: chain 'g' and resid 200 through 205 removed outlier: 3.912A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'g' and resid 218 through 220 Processing sheet with id= CI, first strand: chain 'g' and resid 238 through 241 removed outlier: 6.468A pdb=" N VAL g 289 " --> pdb=" O VAL g 239 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LEU g 241 " --> pdb=" O VAL g 289 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE g 291 " --> pdb=" O LEU g 241 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR g 310 " --> pdb=" O VAL g 290 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N THR g 292 " --> pdb=" O THR g 310 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE g 312 " --> pdb=" O THR g 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= CI Processing sheet with id= CJ, first strand: chain 'g' and resid 407 through 409 Processing sheet with id= CK, first strand: chain 'g' and resid 478 through 481 removed outlier: 3.537A pdb=" N VAL g 488 " --> pdb=" O GLY g 479 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR g 486 " --> pdb=" O ASN g 481 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain 'h' and resid 14 through 17 Processing sheet with id= CM, first strand: chain 'h' and resid 47 through 50 Processing sheet with id= CN, first strand: chain 'h' and resid 195 through 201 removed outlier: 6.471A pdb=" N CYS h 370 " --> pdb=" O GLY h 196 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N LYS h 198 " --> pdb=" O CYS h 370 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N PHE h 372 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N VAL h 200 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU h 374 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR h 371 " --> pdb=" O VAL h 211 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'h' and resid 214 through 217 Processing sheet with id= CP, first strand: chain 'h' and resid 237 through 240 removed outlier: 6.777A pdb=" N VAL h 288 " --> pdb=" O ALA h 238 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU h 240 " --> pdb=" O VAL h 288 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU h 290 " --> pdb=" O LEU h 240 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N PHE h 309 " --> pdb=" O VAL h 289 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N SER h 291 " --> pdb=" O PHE h 309 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ALA h 311 " --> pdb=" O SER h 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= CP Processing sheet with id= CQ, first strand: chain 'h' and resid 405 through 407 Processing sheet with id= CR, first strand: chain 'h' and resid 475 through 478 Processing sheet with id= CS, first strand: chain 'q' and resid 20 through 23 Processing sheet with id= CT, first strand: chain 'q' and resid 54 through 57 Processing sheet with id= CU, first strand: chain 'q' and resid 202 through 208 removed outlier: 6.548A pdb=" N SER q 373 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N CYS q 205 " --> pdb=" O SER q 373 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE q 375 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N ILE q 207 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N LEU q 377 " --> pdb=" O ILE q 207 " (cutoff:3.500A) Processing sheet with id= CV, first strand: chain 'q' and resid 220 through 223 Processing sheet with id= CW, first strand: chain 'q' and resid 240 through 242 removed outlier: 6.077A pdb=" N MET q 311 " --> pdb=" O VAL q 291 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR q 293 " --> pdb=" O MET q 311 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL q 313 " --> pdb=" O THR q 293 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain 'q' and resid 498 through 500 removed outlier: 3.879A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N VAL q 147 " --> pdb=" O PRO q 410 " (cutoff:3.500A) Processing sheet with id= CY, first strand: chain 'q' and resid 478 through 480 Processing sheet with id= CZ, first strand: chain 'z' and resid 12 through 15 Processing sheet with id= DA, first strand: chain 'z' and resid 45 through 48 Processing sheet with id= DB, first strand: chain 'z' and resid 192 through 196 Processing sheet with id= DC, first strand: chain 'z' and resid 210 through 212 Processing sheet with id= DD, first strand: chain 'z' and resid 345 through 347 Processing sheet with id= DE, first strand: chain 'z' and resid 477 through 479 Processing sheet with id= DF, first strand: chain 'P' and resid 215 through 218 removed outlier: 3.566A pdb=" N CYS P 215 " --> pdb=" O MET P 184 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE P 187 " --> pdb=" O ALA P 235 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA P 235 " --> pdb=" O ILE P 187 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY P 246 " --> pdb=" O ILE P 238 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N LYS P 240 " --> pdb=" O LEU P 244 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N LEU P 244 " --> pdb=" O LYS P 240 " (cutoff:3.500A) 3457 hydrogen bonds defined for protein. 9126 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: 28.07 Time building geometry restraints manager: 24.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 22417 1.34 - 1.46: 7414 1.46 - 1.57: 36881 1.57 - 1.69: 48 1.69 - 1.81: 730 Bond restraints: 67490 Sorted by residual: bond pdb=" F2 AF3 z 603 " pdb="AL AF3 z 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.43e+01 bond pdb=" F2 AF3 Z 603 " pdb="AL AF3 Z 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.40e+01 bond pdb=" F2 AF3 G 603 " pdb="AL AF3 G 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.38e+01 bond pdb=" F2 AF3 b 603 " pdb="AL AF3 b 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.34e+01 bond pdb=" F2 AF3 e 603 " pdb="AL AF3 e 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.33e+01 ... (remaining 67485 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.60: 1132 105.60 - 113.29: 39188 113.29 - 120.97: 32569 120.97 - 128.66: 17948 128.66 - 136.35: 288 Bond angle restraints: 91125 Sorted by residual: angle pdb=" C GLY h 18 " pdb=" N ILE h 19 " pdb=" CA ILE h 19 " ideal model delta sigma weight residual 120.24 123.99 -3.75 6.30e-01 2.52e+00 3.55e+01 angle pdb=" C LYS P 176 " pdb=" N GLU P 177 " pdb=" CA GLU P 177 " ideal model delta sigma weight residual 121.54 128.65 -7.11 1.91e+00 2.74e-01 1.38e+01 angle pdb=" N ILE G 165 " pdb=" CA ILE G 165 " pdb=" C ILE G 165 " ideal model delta sigma weight residual 112.29 108.99 3.30 9.40e-01 1.13e+00 1.23e+01 angle pdb=" CA MET E 4 " pdb=" CB MET E 4 " pdb=" CG MET E 4 " ideal model delta sigma weight residual 114.10 120.31 -6.21 2.00e+00 2.50e-01 9.64e+00 angle pdb=" N GLU z 121 " pdb=" CA GLU z 121 " pdb=" CB GLU z 121 " ideal model delta sigma weight residual 110.12 114.58 -4.46 1.47e+00 4.63e-01 9.20e+00 ... (remaining 91120 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.69: 41021 34.69 - 69.38: 638 69.38 - 104.07: 55 104.07 - 138.76: 9 138.76 - 173.45: 8 Dihedral angle restraints: 41731 sinusoidal: 16798 harmonic: 24933 Sorted by residual: dihedral pdb=" O2A ADP z 601 " pdb=" O3A ADP z 601 " pdb=" PA ADP z 601 " pdb=" PB ADP z 601 " ideal model delta sinusoidal sigma weight residual -60.00 113.45 -173.45 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP q 601 " pdb=" O3A ADP q 601 " pdb=" PA ADP q 601 " pdb=" PB ADP q 601 " ideal model delta sinusoidal sigma weight residual 300.00 127.38 172.63 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP g 601 " pdb=" O3A ADP g 601 " pdb=" PA ADP g 601 " pdb=" PB ADP g 601 " ideal model delta sinusoidal sigma weight residual -60.00 110.29 -170.29 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 41728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 7177 0.031 - 0.062: 2346 0.062 - 0.092: 704 0.092 - 0.123: 592 0.123 - 0.154: 41 Chirality restraints: 10860 Sorted by residual: chirality pdb=" CA ILE B 11 " pdb=" N ILE B 11 " pdb=" C ILE B 11 " pdb=" CB ILE B 11 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA ILE g 363 " pdb=" N ILE g 363 " pdb=" C ILE g 363 " pdb=" CB ILE g 363 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA GLU A 77 " pdb=" N GLU A 77 " pdb=" C GLU A 77 " pdb=" CB GLU A 77 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.20e-01 ... (remaining 10857 not shown) Planarity restraints: 11630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 7 " -0.044 5.00e-02 4.00e+02 6.75e-02 7.29e+00 pdb=" N PRO B 8 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO B 8 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 8 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 73 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.03e+00 pdb=" C LYS A 73 " 0.042 2.00e-02 2.50e+03 pdb=" O LYS A 73 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL A 74 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO e 441 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.027 5.00e-02 4.00e+02 ... (remaining 11627 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 663 2.56 - 3.15: 53721 3.15 - 3.73: 106289 3.73 - 4.32: 147172 4.32 - 4.90: 250288 Nonbonded interactions: 558133 Sorted by model distance: nonbonded pdb="MG MG z 602 " pdb=" F1 AF3 z 603 " model vdw 1.975 2.120 nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.975 2.120 nonbonded pdb=" O1A ADP q 601 " pdb="MG MG q 602 " model vdw 1.980 2.170 nonbonded pdb="MG MG e 602 " pdb=" F1 AF3 e 603 " model vdw 1.982 2.120 nonbonded pdb="MG MG H 602 " pdb=" F2 AF3 H 603 " model vdw 1.984 2.120 ... (remaining 558128 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' and (resid 4 through 535 or resid 601 through 603)) selection = chain 'a' } ncs_group { reference = (chain 'B' and (resid 2 through 526 or resid 601 through 603)) selection = chain 'b' } ncs_group { reference = (chain 'D' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 538 or resid 601 through 603)) selection = chain 'd' } ncs_group { reference = (chain 'E' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) selection = (chain 'e' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) } ncs_group { reference = (chain 'G' and (resid 5 through 528 or resid 601 through 603)) selection = (chain 'g' and (resid 5 through 528 or resid 601 through 603)) } ncs_group { reference = (chain 'H' and (resid 1 through 525 or resid 601 through 603)) selection = chain 'h' } ncs_group { reference = (chain 'Q' and (resid 2 through 534 or resid 601 through 603)) selection = chain 'q' } ncs_group { reference = chain 'Z' selection = (chain 'z' and (resid 2 through 526 or resid 601 through 603)) } 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=0.00 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: 1.550 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: 0.070 Extract box with map and model: 8.170 Check model and map are aligned: 0.720 Set scattering table: 0.460 Process input model: 148.120 Find NCS groups from input model: 6.600 Set up NCS constraints: 0.630 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:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 178.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.160 67490 Z= 0.247 Angle : 0.514 10.248 91125 Z= 0.251 Chirality : 0.040 0.154 10860 Planarity : 0.003 0.068 11630 Dihedral : 14.017 173.453 25581 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.21 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.91 (0.09), residues: 8626 helix: 2.51 (0.08), residues: 4455 sheet: 0.34 (0.16), residues: 1141 loop : -0.23 (0.11), residues: 3030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 266 HIS 0.004 0.001 HIS G 470 PHE 0.017 0.001 PHE e 386 TYR 0.019 0.001 TYR G 274 ARG 0.007 0.000 ARG e 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 554 time to evaluate : 5.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 268 MET cc_start: 0.8401 (pmm) cc_final: 0.8091 (pmm) REVERT: A 51 ASP cc_start: 0.8550 (m-30) cc_final: 0.7431 (m-30) REVERT: D 25 GLN cc_start: 0.8705 (tp-100) cc_final: 0.8351 (tp-100) REVERT: D 67 ASP cc_start: 0.8537 (m-30) cc_final: 0.8288 (m-30) REVERT: D 307 ASP cc_start: 0.8372 (t0) cc_final: 0.8139 (t0) REVERT: E 39 MET cc_start: 0.8891 (ttm) cc_final: 0.8628 (ttp) REVERT: E 474 MET cc_start: 0.8199 (tmm) cc_final: 0.7951 (tmm) REVERT: G 21 LYS cc_start: 0.8418 (tptp) cc_final: 0.8111 (tptt) REVERT: Q 42 THR cc_start: 0.8017 (m) cc_final: 0.7707 (m) REVERT: Q 200 ASP cc_start: 0.8800 (m-30) cc_final: 0.8571 (t0) REVERT: Q 357 ASP cc_start: 0.8478 (t0) cc_final: 0.8218 (t0) REVERT: Z 238 GLU cc_start: 0.8969 (pt0) cc_final: 0.8565 (pt0) REVERT: b 13 LYS cc_start: 0.8798 (mtmt) cc_final: 0.8310 (mtpp) REVERT: d 192 MET cc_start: 0.9124 (mmm) cc_final: 0.8854 (mmm) REVERT: d 232 LYS cc_start: 0.8877 (pttp) cc_final: 0.8596 (ptmm) REVERT: g 47 MET cc_start: 0.9098 (mmp) cc_final: 0.8856 (mmp) REVERT: h 324 MET cc_start: 0.9120 (mmm) cc_final: 0.8849 (mmm) REVERT: h 440 LYS cc_start: 0.9152 (ttmt) cc_final: 0.8925 (tppp) REVERT: q 41 GLN cc_start: 0.8795 (tp-100) cc_final: 0.8538 (tp-100) REVERT: q 130 GLU cc_start: 0.8346 (tp30) cc_final: 0.7861 (tp30) REVERT: z 17 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8429 (mp10) outliers start: 0 outliers final: 2 residues processed: 554 average time/residue: 1.5695 time to fit residues: 1119.5061 Evaluate side-chains 437 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 435 time to evaluate : 5.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 292 ILE Chi-restraints excluded: chain h residue 81 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 725 optimal weight: 10.0000 chunk 651 optimal weight: 0.0040 chunk 361 optimal weight: 0.9980 chunk 222 optimal weight: 0.9990 chunk 439 optimal weight: 2.9990 chunk 347 optimal weight: 8.9990 chunk 673 optimal weight: 20.0000 chunk 260 optimal weight: 0.3980 chunk 409 optimal weight: 0.9990 chunk 501 optimal weight: 7.9990 chunk 780 optimal weight: 0.7980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 526 HIS H 283 HIS H 470 GLN ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 227 ASN z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.0610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 67490 Z= 0.136 Angle : 0.507 11.427 91125 Z= 0.251 Chirality : 0.040 0.157 10860 Planarity : 0.004 0.050 11630 Dihedral : 7.405 173.138 9375 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.84 % Favored : 97.15 % Rotamer: Outliers : 0.72 % Allowed : 5.71 % Favored : 93.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.76 (0.09), residues: 8626 helix: 2.33 (0.08), residues: 4450 sheet: 0.34 (0.16), residues: 1135 loop : -0.24 (0.11), residues: 3041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 266 HIS 0.012 0.001 HIS z 161 PHE 0.013 0.001 PHE g 362 TYR 0.013 0.001 TYR G 437 ARG 0.008 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 483 time to evaluate : 5.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 268 MET cc_start: 0.8355 (pmm) cc_final: 0.8074 (pmm) REVERT: A 51 ASP cc_start: 0.8447 (m-30) cc_final: 0.8203 (m-30) REVERT: B 445 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8193 (tpp) REVERT: D 25 GLN cc_start: 0.8698 (tp-100) cc_final: 0.8337 (tp-100) REVERT: D 28 ASP cc_start: 0.8527 (t70) cc_final: 0.8098 (t70) REVERT: D 67 ASP cc_start: 0.8443 (m-30) cc_final: 0.8208 (m-30) REVERT: D 307 ASP cc_start: 0.8421 (t0) cc_final: 0.8060 (t0) REVERT: E 39 MET cc_start: 0.8857 (ttm) cc_final: 0.8578 (ttp) REVERT: E 448 MET cc_start: 0.8987 (mtt) cc_final: 0.8689 (mtm) REVERT: E 474 MET cc_start: 0.8230 (tmm) cc_final: 0.7843 (tmm) REVERT: H 2 MET cc_start: 0.6701 (mmt) cc_final: 0.6329 (mmt) REVERT: H 14 ASP cc_start: 0.8671 (t0) cc_final: 0.8238 (t0) REVERT: H 470 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8638 (pp30) REVERT: Q 357 ASP cc_start: 0.8454 (t0) cc_final: 0.8207 (t0) REVERT: Q 526 MET cc_start: 0.9140 (mtm) cc_final: 0.8907 (mtm) REVERT: Z 238 GLU cc_start: 0.8953 (pt0) cc_final: 0.8514 (pt0) REVERT: Z 357 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8359 (mm-30) REVERT: b 13 LYS cc_start: 0.8950 (mtmt) cc_final: 0.8719 (mttp) REVERT: b 310 MET cc_start: 0.8700 (ttm) cc_final: 0.8476 (ttm) REVERT: d 186 MET cc_start: 0.8427 (ttm) cc_final: 0.8082 (ttm) REVERT: d 232 LYS cc_start: 0.8861 (pttp) cc_final: 0.8572 (ptmm) REVERT: e 48 MET cc_start: 0.9179 (tpt) cc_final: 0.8935 (mmm) REVERT: e 526 MET cc_start: 0.9301 (ttt) cc_final: 0.8835 (ttt) REVERT: g 47 MET cc_start: 0.9068 (mmp) cc_final: 0.8825 (mmp) REVERT: g 133 MET cc_start: 0.9144 (mtp) cc_final: 0.8941 (mtp) REVERT: h 324 MET cc_start: 0.9122 (mmm) cc_final: 0.8835 (mmm) REVERT: q 41 GLN cc_start: 0.8784 (tp-100) cc_final: 0.8520 (tp-100) REVERT: q 130 GLU cc_start: 0.8311 (tp30) cc_final: 0.7828 (tp30) REVERT: z 194 MET cc_start: 0.9252 (tpp) cc_final: 0.8909 (tpp) REVERT: P 196 GLU cc_start: 0.5274 (pt0) cc_final: 0.3816 (tm-30) outliers start: 52 outliers final: 10 residues processed: 502 average time/residue: 1.6113 time to fit residues: 1043.5451 Evaluate side-chains 452 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 440 time to evaluate : 5.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 445 MET Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 470 GLN Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain q residue 266 MET Chi-restraints excluded: chain z residue 358 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 433 optimal weight: 4.9990 chunk 242 optimal weight: 9.9990 chunk 649 optimal weight: 1.9990 chunk 531 optimal weight: 9.9990 chunk 215 optimal weight: 7.9990 chunk 781 optimal weight: 0.9980 chunk 844 optimal weight: 4.9990 chunk 695 optimal weight: 4.9990 chunk 774 optimal weight: 9.9990 chunk 266 optimal weight: 0.8980 chunk 626 optimal weight: 0.9980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 GLN ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS e 139 GLN z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.0700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 67490 Z= 0.199 Angle : 0.508 9.226 91125 Z= 0.250 Chirality : 0.040 0.154 10860 Planarity : 0.003 0.050 11630 Dihedral : 7.207 175.396 9371 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.11 % Favored : 96.88 % Rotamer: Outliers : 0.82 % Allowed : 7.57 % Favored : 91.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.66 (0.09), residues: 8626 helix: 2.24 (0.08), residues: 4457 sheet: 0.26 (0.16), residues: 1133 loop : -0.26 (0.11), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 266 HIS 0.009 0.001 HIS z 161 PHE 0.016 0.001 PHE e 386 TYR 0.014 0.001 TYR Z 353 ARG 0.009 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 454 time to evaluate : 6.767 Fit side-chains revert: symmetry clash REVERT: D 25 GLN cc_start: 0.8774 (tp-100) cc_final: 0.8394 (tp-100) REVERT: D 28 ASP cc_start: 0.8536 (t70) cc_final: 0.8120 (t70) REVERT: D 67 ASP cc_start: 0.8441 (m-30) cc_final: 0.8173 (m-30) REVERT: D 248 LEU cc_start: 0.9451 (OUTLIER) cc_final: 0.9130 (tt) REVERT: D 307 ASP cc_start: 0.8512 (t0) cc_final: 0.8082 (t0) REVERT: E 39 MET cc_start: 0.8876 (ttm) cc_final: 0.8616 (ttp) REVERT: E 448 MET cc_start: 0.9015 (mtt) cc_final: 0.8735 (mtm) REVERT: E 474 MET cc_start: 0.8273 (tmm) cc_final: 0.8035 (tmm) REVERT: E 501 MET cc_start: 0.9122 (mmt) cc_final: 0.8762 (mmp) REVERT: G 17 GLU cc_start: 0.7225 (tp30) cc_final: 0.6946 (tp30) REVERT: G 20 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7417 (ttp-110) REVERT: G 21 LYS cc_start: 0.8312 (tmtt) cc_final: 0.7932 (tptt) REVERT: G 152 MET cc_start: 0.8914 (mmt) cc_final: 0.8508 (mmt) REVERT: H 11 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7699 (tm-30) REVERT: H 14 ASP cc_start: 0.8690 (t0) cc_final: 0.8205 (t0) REVERT: H 283 HIS cc_start: 0.8119 (m90) cc_final: 0.7799 (m-70) REVERT: H 497 MET cc_start: 0.8082 (ptp) cc_final: 0.7761 (ppp) REVERT: Q 357 ASP cc_start: 0.8447 (t0) cc_final: 0.8231 (t0) REVERT: Z 238 GLU cc_start: 0.8956 (pt0) cc_final: 0.8530 (pt0) REVERT: Z 244 VAL cc_start: 0.8352 (OUTLIER) cc_final: 0.8119 (t) REVERT: b 139 GLU cc_start: 0.8232 (tp30) cc_final: 0.8005 (tp30) REVERT: b 310 MET cc_start: 0.8737 (ttm) cc_final: 0.8483 (ttm) REVERT: d 60 MET cc_start: 0.8931 (ttm) cc_final: 0.8706 (tpp) REVERT: d 186 MET cc_start: 0.8419 (ttm) cc_final: 0.8056 (ttm) REVERT: d 232 LYS cc_start: 0.8858 (pttp) cc_final: 0.8612 (ptmm) REVERT: e 48 MET cc_start: 0.9222 (tpt) cc_final: 0.8995 (mmm) REVERT: e 526 MET cc_start: 0.9275 (ttt) cc_final: 0.8851 (ttt) REVERT: g 47 MET cc_start: 0.9104 (mmp) cc_final: 0.8850 (mmp) REVERT: g 133 MET cc_start: 0.9152 (mtp) cc_final: 0.8927 (mtp) REVERT: h 11 GLU cc_start: 0.8405 (tp30) cc_final: 0.8075 (tp30) REVERT: h 324 MET cc_start: 0.9147 (mmm) cc_final: 0.8846 (mmm) REVERT: h 455 PHE cc_start: 0.7601 (m-10) cc_final: 0.7306 (m-10) REVERT: h 482 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.7894 (tp30) REVERT: q 41 GLN cc_start: 0.8836 (tp-100) cc_final: 0.8553 (tp-100) REVERT: q 130 GLU cc_start: 0.8335 (tp30) cc_final: 0.7861 (tp30) REVERT: q 276 MET cc_start: 0.9167 (tpp) cc_final: 0.8919 (tpp) REVERT: z 194 MET cc_start: 0.9269 (tpp) cc_final: 0.8748 (tpp) REVERT: z 487 MET cc_start: 0.8486 (ppp) cc_final: 0.8211 (ppp) REVERT: P 196 GLU cc_start: 0.5407 (pt0) cc_final: 0.3927 (tm-30) outliers start: 59 outliers final: 18 residues processed: 480 average time/residue: 1.5535 time to fit residues: 968.7214 Evaluate side-chains 456 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 434 time to evaluate : 5.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 239 MET Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 482 GLU Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain z residue 7 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 772 optimal weight: 2.9990 chunk 587 optimal weight: 8.9990 chunk 405 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 372 optimal weight: 7.9990 chunk 524 optimal weight: 8.9990 chunk 784 optimal weight: 9.9990 chunk 830 optimal weight: 0.0980 chunk 409 optimal weight: 7.9990 chunk 743 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 overall best weight: 5.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 472 ASN G 13 ASN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 470 GLN Q 53 ASN Z 161 HIS a 69 HIS e 139 GLN h 117 HIS z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 67490 Z= 0.470 Angle : 0.626 10.254 91125 Z= 0.312 Chirality : 0.044 0.217 10860 Planarity : 0.004 0.052 11630 Dihedral : 7.433 177.984 9371 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.82 % Favored : 96.17 % Rotamer: Outliers : 1.16 % Allowed : 8.95 % Favored : 89.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.34 (0.09), residues: 8626 helix: 1.96 (0.08), residues: 4462 sheet: 0.11 (0.16), residues: 1133 loop : -0.37 (0.11), residues: 3031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 168 HIS 0.012 0.001 HIS Z 161 PHE 0.023 0.002 PHE e 386 TYR 0.014 0.002 TYR Q 304 ARG 0.006 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 430 time to evaluate : 6.036 Fit side-chains revert: symmetry clash REVERT: A 164 ASN cc_start: 0.6917 (m-40) cc_final: 0.6700 (m-40) REVERT: D 25 GLN cc_start: 0.8977 (tp-100) cc_final: 0.8604 (tp-100) REVERT: D 67 ASP cc_start: 0.8408 (m-30) cc_final: 0.8127 (m-30) REVERT: D 307 ASP cc_start: 0.8591 (t0) cc_final: 0.8132 (t0) REVERT: D 374 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9009 (tm) REVERT: E 39 MET cc_start: 0.8866 (ttm) cc_final: 0.8615 (ttp) REVERT: E 474 MET cc_start: 0.8398 (tmm) cc_final: 0.8114 (tmm) REVERT: G 17 GLU cc_start: 0.7170 (tp30) cc_final: 0.6858 (tp30) REVERT: G 21 LYS cc_start: 0.8539 (tmtt) cc_final: 0.8056 (tptt) REVERT: G 114 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8441 (mm-30) REVERT: H 14 ASP cc_start: 0.8757 (t0) cc_final: 0.8272 (t0) REVERT: H 470 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8717 (pp30) REVERT: Q 526 MET cc_start: 0.9153 (mtm) cc_final: 0.8912 (mtm) REVERT: Z 196 MET cc_start: 0.8210 (mtm) cc_final: 0.7981 (mtp) REVERT: Z 238 GLU cc_start: 0.8983 (pt0) cc_final: 0.8626 (pt0) REVERT: Z 357 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8431 (mm-30) REVERT: a 106 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8221 (tp30) REVERT: a 156 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8466 (mtp) REVERT: b 310 MET cc_start: 0.8892 (ttm) cc_final: 0.8533 (ttm) REVERT: b 415 MET cc_start: 0.9393 (mmm) cc_final: 0.8980 (mmp) REVERT: d 186 MET cc_start: 0.8767 (ttm) cc_final: 0.8388 (ttm) REVERT: d 232 LYS cc_start: 0.8894 (pttp) cc_final: 0.8615 (ptmm) REVERT: e 526 MET cc_start: 0.9298 (ttt) cc_final: 0.8964 (ttt) REVERT: g 133 MET cc_start: 0.9160 (mtp) cc_final: 0.8880 (mtp) REVERT: h 11 GLU cc_start: 0.8472 (tp30) cc_final: 0.8175 (tp30) REVERT: h 324 MET cc_start: 0.9142 (mmm) cc_final: 0.8831 (mmm) REVERT: h 440 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8817 (tppp) REVERT: q 41 GLN cc_start: 0.8851 (tp-100) cc_final: 0.8288 (tp40) REVERT: q 130 GLU cc_start: 0.8383 (tp30) cc_final: 0.7853 (tp30) outliers start: 84 outliers final: 24 residues processed: 475 average time/residue: 1.5419 time to fit residues: 955.1936 Evaluate side-chains 445 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 416 time to evaluate : 5.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 265 VAL Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 470 GLN Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Q residue 482 ILE Chi-restraints excluded: chain Z residue 358 GLU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain e residue 11 GLU Chi-restraints excluded: chain e residue 367 THR Chi-restraints excluded: chain g residue 255 ASP Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 440 LYS Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 193 ASP Chi-restraints excluded: chain z residue 7 LEU Chi-restraints excluded: chain P residue 296 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 691 optimal weight: 0.9990 chunk 471 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 618 optimal weight: 0.9980 chunk 342 optimal weight: 9.9990 chunk 708 optimal weight: 2.9990 chunk 573 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 423 optimal weight: 1.9990 chunk 745 optimal weight: 1.9990 chunk 209 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 481 ASN ** H 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN Z 161 HIS e 139 GLN z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 67490 Z= 0.161 Angle : 0.517 13.609 91125 Z= 0.255 Chirality : 0.040 0.157 10860 Planarity : 0.003 0.050 11630 Dihedral : 7.207 178.048 9371 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.09 % Favored : 96.90 % Rotamer: Outliers : 0.83 % Allowed : 10.09 % Favored : 89.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.48 (0.09), residues: 8626 helix: 2.10 (0.08), residues: 4450 sheet: 0.10 (0.16), residues: 1114 loop : -0.31 (0.11), residues: 3062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 168 HIS 0.015 0.001 HIS z 161 PHE 0.017 0.001 PHE H 455 TYR 0.017 0.001 TYR D 24 ARG 0.007 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 505 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 445 time to evaluate : 6.844 Fit side-chains revert: symmetry clash REVERT: D 25 GLN cc_start: 0.8868 (tp-100) cc_final: 0.8416 (tp-100) REVERT: D 67 ASP cc_start: 0.8408 (m-30) cc_final: 0.8138 (m-30) REVERT: D 307 ASP cc_start: 0.8587 (t0) cc_final: 0.8127 (t0) REVERT: D 374 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9059 (tm) REVERT: E 39 MET cc_start: 0.8825 (ttm) cc_final: 0.8540 (ttt) REVERT: E 474 MET cc_start: 0.8336 (tmm) cc_final: 0.7975 (tmm) REVERT: G 20 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7631 (ttp-170) REVERT: G 21 LYS cc_start: 0.8484 (tmtt) cc_final: 0.8009 (tptt) REVERT: H 2 MET cc_start: 0.7152 (mmt) cc_final: 0.6785 (mmt) REVERT: H 14 ASP cc_start: 0.8747 (t0) cc_final: 0.8270 (t0) REVERT: Q 357 ASP cc_start: 0.8381 (t0) cc_final: 0.8144 (OUTLIER) REVERT: Q 526 MET cc_start: 0.9126 (mtm) cc_final: 0.8889 (mtm) REVERT: Z 196 MET cc_start: 0.7993 (mtm) cc_final: 0.7682 (mtp) REVERT: Z 238 GLU cc_start: 0.8960 (pt0) cc_final: 0.8566 (pt0) REVERT: Z 357 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8394 (mm-30) REVERT: a 106 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8240 (tp30) REVERT: b 310 MET cc_start: 0.8839 (ttm) cc_final: 0.8523 (ttm) REVERT: b 415 MET cc_start: 0.9400 (mmm) cc_final: 0.9074 (mmp) REVERT: d 186 MET cc_start: 0.8595 (ttm) cc_final: 0.8204 (ttm) REVERT: e 371 MET cc_start: 0.9198 (mtt) cc_final: 0.8943 (mtt) REVERT: g 133 MET cc_start: 0.9126 (mtp) cc_final: 0.8911 (mtp) REVERT: h 11 GLU cc_start: 0.8435 (tp30) cc_final: 0.8116 (tp30) REVERT: h 324 MET cc_start: 0.9153 (mmm) cc_final: 0.8851 (mmm) REVERT: h 440 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8865 (tppp) REVERT: q 26 GLU cc_start: 0.8253 (tm-30) cc_final: 0.7972 (tm-30) REVERT: q 41 GLN cc_start: 0.8829 (tp-100) cc_final: 0.8301 (tp40) REVERT: q 130 GLU cc_start: 0.8355 (tp30) cc_final: 0.7825 (tp30) REVERT: z 194 MET cc_start: 0.9258 (tpp) cc_final: 0.8806 (tpp) outliers start: 60 outliers final: 22 residues processed: 480 average time/residue: 1.5617 time to fit residues: 975.0379 Evaluate side-chains 453 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 429 time to evaluate : 5.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 358 GLU Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 194 VAL Chi-restraints excluded: chain h residue 440 LYS Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain z residue 232 THR Chi-restraints excluded: chain z residue 357 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 279 optimal weight: 0.0050 chunk 747 optimal weight: 8.9990 chunk 164 optimal weight: 5.9990 chunk 487 optimal weight: 8.9990 chunk 204 optimal weight: 1.9990 chunk 831 optimal weight: 6.9990 chunk 689 optimal weight: 9.9990 chunk 384 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 274 optimal weight: 2.9990 chunk 436 optimal weight: 3.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN Z 161 HIS z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 67490 Z= 0.204 Angle : 0.519 11.360 91125 Z= 0.254 Chirality : 0.041 0.158 10860 Planarity : 0.003 0.050 11630 Dihedral : 7.009 172.656 9371 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.35 % Favored : 96.63 % Rotamer: Outliers : 1.02 % Allowed : 10.67 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.50 (0.09), residues: 8626 helix: 2.12 (0.08), residues: 4451 sheet: 0.11 (0.16), residues: 1124 loop : -0.30 (0.11), residues: 3051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 168 HIS 0.013 0.001 HIS z 161 PHE 0.012 0.001 PHE g 362 TYR 0.013 0.001 TYR Z 353 ARG 0.006 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 442 time to evaluate : 6.040 Fit side-chains revert: symmetry clash REVERT: A 306 MET cc_start: 0.8899 (mtp) cc_final: 0.8404 (mtm) REVERT: D 25 GLN cc_start: 0.8864 (tp-100) cc_final: 0.8426 (tp-100) REVERT: D 28 ASP cc_start: 0.8540 (t70) cc_final: 0.8121 (t70) REVERT: D 67 ASP cc_start: 0.8417 (m-30) cc_final: 0.8134 (m-30) REVERT: D 90 MET cc_start: 0.9056 (mtp) cc_final: 0.8744 (mtp) REVERT: D 307 ASP cc_start: 0.8607 (t0) cc_final: 0.8129 (t0) REVERT: D 374 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9067 (tm) REVERT: E 39 MET cc_start: 0.8814 (ttm) cc_final: 0.8524 (ttt) REVERT: E 448 MET cc_start: 0.8939 (mtt) cc_final: 0.8704 (mmm) REVERT: E 474 MET cc_start: 0.8346 (tmm) cc_final: 0.7962 (tmm) REVERT: G 20 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7701 (ttp-170) REVERT: G 21 LYS cc_start: 0.8430 (tmtt) cc_final: 0.8046 (tptt) REVERT: G 152 MET cc_start: 0.8869 (mmt) cc_final: 0.8559 (mmt) REVERT: G 219 MET cc_start: 0.9122 (ttp) cc_final: 0.8899 (ppp) REVERT: H 2 MET cc_start: 0.7166 (mmt) cc_final: 0.6795 (mmt) REVERT: H 14 ASP cc_start: 0.8745 (t0) cc_final: 0.8264 (t0) REVERT: H 497 MET cc_start: 0.8040 (ptp) cc_final: 0.7720 (ppp) REVERT: Q 357 ASP cc_start: 0.8435 (t0) cc_final: 0.8108 (OUTLIER) REVERT: Q 526 MET cc_start: 0.9130 (mtm) cc_final: 0.8901 (mtm) REVERT: Z 17 GLN cc_start: 0.8348 (mp10) cc_final: 0.8019 (pm20) REVERT: Z 196 MET cc_start: 0.8075 (mtm) cc_final: 0.7802 (mtp) REVERT: Z 238 GLU cc_start: 0.8955 (pt0) cc_final: 0.8565 (pt0) REVERT: Z 357 GLU cc_start: 0.8684 (mm-30) cc_final: 0.8399 (mm-30) REVERT: a 106 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8153 (tp30) REVERT: b 310 MET cc_start: 0.8838 (ttm) cc_final: 0.8521 (ttm) REVERT: b 415 MET cc_start: 0.9425 (mmm) cc_final: 0.9007 (mmp) REVERT: d 186 MET cc_start: 0.8552 (ttm) cc_final: 0.8175 (ttm) REVERT: e 526 MET cc_start: 0.9287 (ttt) cc_final: 0.8817 (ttt) REVERT: g 133 MET cc_start: 0.9129 (mtp) cc_final: 0.8896 (mtp) REVERT: h 11 GLU cc_start: 0.8428 (tp30) cc_final: 0.8134 (tp30) REVERT: h 324 MET cc_start: 0.9154 (mmm) cc_final: 0.8849 (mmm) REVERT: h 440 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8867 (tppp) REVERT: q 26 GLU cc_start: 0.8236 (tm-30) cc_final: 0.7957 (tm-30) REVERT: q 41 GLN cc_start: 0.8809 (tp-100) cc_final: 0.8530 (tp-100) REVERT: q 130 GLU cc_start: 0.8339 (tp30) cc_final: 0.7873 (tp30) REVERT: z 190 MET cc_start: 0.9149 (mmp) cc_final: 0.8880 (mmp) REVERT: z 194 MET cc_start: 0.9269 (tpp) cc_final: 0.8822 (tpp) REVERT: z 352 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.7379 (tm-30) outliers start: 74 outliers final: 35 residues processed: 491 average time/residue: 1.5303 time to fit residues: 984.7087 Evaluate side-chains 463 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 425 time to evaluate : 6.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 358 GLU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 194 VAL Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain e residue 11 GLU Chi-restraints excluded: chain g residue 255 ASP Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 440 LYS Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain z residue 7 LEU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 232 THR Chi-restraints excluded: chain z residue 352 GLU Chi-restraints excluded: chain z residue 357 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 801 optimal weight: 0.0070 chunk 93 optimal weight: 2.9990 chunk 473 optimal weight: 6.9990 chunk 606 optimal weight: 5.9990 chunk 470 optimal weight: 8.9990 chunk 699 optimal weight: 7.9990 chunk 464 optimal weight: 9.9990 chunk 827 optimal weight: 5.9990 chunk 518 optimal weight: 3.9990 chunk 504 optimal weight: 4.9990 chunk 382 optimal weight: 8.9990 overall best weight: 3.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN Z 161 HIS e 139 GLN ** h 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 67490 Z= 0.317 Angle : 0.563 15.726 91125 Z= 0.276 Chirality : 0.042 0.201 10860 Planarity : 0.003 0.049 11630 Dihedral : 7.027 169.840 9371 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.59 % Favored : 96.40 % Rotamer: Outliers : 1.04 % Allowed : 11.06 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.40 (0.09), residues: 8626 helix: 2.04 (0.08), residues: 4457 sheet: 0.04 (0.16), residues: 1136 loop : -0.34 (0.11), residues: 3033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.013 0.001 HIS Z 161 PHE 0.013 0.001 PHE E 306 TYR 0.014 0.001 TYR b 297 ARG 0.005 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 436 time to evaluate : 5.866 Fit side-chains revert: symmetry clash REVERT: D 25 GLN cc_start: 0.8943 (tp-100) cc_final: 0.8485 (tp-100) REVERT: D 67 ASP cc_start: 0.8395 (m-30) cc_final: 0.8106 (m-30) REVERT: D 307 ASP cc_start: 0.8620 (t0) cc_final: 0.8125 (t0) REVERT: D 374 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9064 (tm) REVERT: E 24 ARG cc_start: 0.8688 (mtp85) cc_final: 0.8393 (mtm-85) REVERT: E 39 MET cc_start: 0.8818 (ttm) cc_final: 0.8568 (ttt) REVERT: E 448 MET cc_start: 0.8959 (mtt) cc_final: 0.8676 (mmm) REVERT: E 474 MET cc_start: 0.8398 (tmm) cc_final: 0.7991 (tmm) REVERT: G 20 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7802 (ttp-170) REVERT: G 21 LYS cc_start: 0.8505 (tmtt) cc_final: 0.8079 (tptt) REVERT: G 152 MET cc_start: 0.8912 (mmt) cc_final: 0.8647 (mmt) REVERT: G 219 MET cc_start: 0.9131 (ttp) cc_final: 0.8913 (ppp) REVERT: H 14 ASP cc_start: 0.8755 (t0) cc_final: 0.8286 (t0) REVERT: Q 357 ASP cc_start: 0.8510 (t0) cc_final: 0.8163 (OUTLIER) REVERT: Q 526 MET cc_start: 0.9142 (mtm) cc_final: 0.8914 (mtm) REVERT: Z 17 GLN cc_start: 0.8381 (mp10) cc_final: 0.8047 (pm20) REVERT: Z 196 MET cc_start: 0.8120 (mtm) cc_final: 0.7871 (mtp) REVERT: Z 238 GLU cc_start: 0.8968 (pt0) cc_final: 0.8623 (pt0) REVERT: Z 357 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8420 (mm-30) REVERT: a 106 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8087 (tp30) REVERT: a 156 MET cc_start: 0.8646 (mtp) cc_final: 0.8379 (mtp) REVERT: b 310 MET cc_start: 0.8888 (ttm) cc_final: 0.8559 (ttm) REVERT: b 415 MET cc_start: 0.9442 (mmm) cc_final: 0.9020 (mmp) REVERT: d 60 MET cc_start: 0.8972 (ttm) cc_final: 0.8761 (tpp) REVERT: d 186 MET cc_start: 0.8685 (ttm) cc_final: 0.8311 (ttm) REVERT: d 263 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8227 (mp10) REVERT: e 371 MET cc_start: 0.9209 (mtt) cc_final: 0.8916 (mtt) REVERT: g 133 MET cc_start: 0.9144 (mtp) cc_final: 0.8882 (mtp) REVERT: h 11 GLU cc_start: 0.8427 (tp30) cc_final: 0.8153 (tp30) REVERT: h 324 MET cc_start: 0.9144 (mmm) cc_final: 0.8859 (mmm) REVERT: h 440 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8877 (tppp) REVERT: q 26 GLU cc_start: 0.8307 (tm-30) cc_final: 0.8003 (tm-30) REVERT: q 41 GLN cc_start: 0.8813 (tp-100) cc_final: 0.8264 (tp40) REVERT: q 130 GLU cc_start: 0.8354 (tp30) cc_final: 0.7896 (tp30) REVERT: z 194 MET cc_start: 0.9283 (tpp) cc_final: 0.8848 (tpp) outliers start: 75 outliers final: 44 residues processed: 483 average time/residue: 1.5144 time to fit residues: 954.2283 Evaluate side-chains 469 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 422 time to evaluate : 5.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 114 GLU Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 358 GLU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 194 VAL Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 263 GLN Chi-restraints excluded: chain e residue 11 GLU Chi-restraints excluded: chain g residue 255 ASP Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 440 LYS Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain q residue 193 ASP Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain z residue 7 LEU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 232 THR Chi-restraints excluded: chain z residue 357 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 512 optimal weight: 10.0000 chunk 330 optimal weight: 8.9990 chunk 494 optimal weight: 1.9990 chunk 249 optimal weight: 0.9990 chunk 162 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 526 optimal weight: 0.9980 chunk 564 optimal weight: 3.9990 chunk 409 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 650 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN Z 161 HIS z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 67490 Z= 0.216 Angle : 0.531 13.768 91125 Z= 0.260 Chirality : 0.041 0.250 10860 Planarity : 0.003 0.050 11630 Dihedral : 6.933 166.978 9371 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.28 % Favored : 96.70 % Rotamer: Outliers : 0.95 % Allowed : 11.54 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.46 (0.09), residues: 8626 helix: 2.09 (0.08), residues: 4446 sheet: 0.06 (0.16), residues: 1116 loop : -0.31 (0.11), residues: 3064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 168 HIS 0.017 0.001 HIS z 161 PHE 0.012 0.001 PHE g 362 TYR 0.014 0.001 TYR b 297 ARG 0.006 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 431 time to evaluate : 5.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 268 MET cc_start: 0.7840 (pmt) cc_final: 0.7639 (pmm) REVERT: D 25 GLN cc_start: 0.8892 (tp-100) cc_final: 0.8434 (tp-100) REVERT: D 67 ASP cc_start: 0.8403 (m-30) cc_final: 0.8113 (m-30) REVERT: D 307 ASP cc_start: 0.8616 (t0) cc_final: 0.8100 (t0) REVERT: D 374 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9090 (tm) REVERT: E 24 ARG cc_start: 0.8690 (mtp85) cc_final: 0.8399 (mtm-85) REVERT: E 39 MET cc_start: 0.8811 (ttm) cc_final: 0.8539 (ttt) REVERT: E 474 MET cc_start: 0.8387 (tmm) cc_final: 0.7976 (tmm) REVERT: G 20 ARG cc_start: 0.8106 (OUTLIER) cc_final: 0.7752 (ttp-170) REVERT: G 21 LYS cc_start: 0.8475 (tmtt) cc_final: 0.8105 (tptt) REVERT: G 152 MET cc_start: 0.8858 (mmt) cc_final: 0.8585 (mmt) REVERT: H 14 ASP cc_start: 0.8758 (t0) cc_final: 0.8297 (t0) REVERT: H 283 HIS cc_start: 0.8231 (m-70) cc_final: 0.7944 (m-70) REVERT: Q 357 ASP cc_start: 0.8544 (t0) cc_final: 0.8152 (OUTLIER) REVERT: Q 526 MET cc_start: 0.9130 (mtm) cc_final: 0.8904 (mtm) REVERT: Z 17 GLN cc_start: 0.8399 (mp10) cc_final: 0.8083 (pm20) REVERT: Z 46 MET cc_start: 0.8423 (tpp) cc_final: 0.7811 (ttm) REVERT: Z 196 MET cc_start: 0.8057 (mtm) cc_final: 0.7729 (mtp) REVERT: Z 238 GLU cc_start: 0.8953 (pt0) cc_final: 0.8577 (pt0) REVERT: a 106 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8134 (tp30) REVERT: b 310 MET cc_start: 0.8845 (ttm) cc_final: 0.8459 (ttm) REVERT: b 415 MET cc_start: 0.9433 (mmm) cc_final: 0.9022 (mmp) REVERT: d 60 MET cc_start: 0.8960 (ttm) cc_final: 0.8754 (tpp) REVERT: d 186 MET cc_start: 0.8606 (ttm) cc_final: 0.8228 (ttm) REVERT: d 320 MET cc_start: 0.9455 (mtp) cc_final: 0.9183 (mtt) REVERT: e 526 MET cc_start: 0.9274 (ttt) cc_final: 0.8762 (ttt) REVERT: g 133 MET cc_start: 0.9143 (mtp) cc_final: 0.8941 (mtp) REVERT: g 527 LYS cc_start: 0.8870 (tptp) cc_final: 0.8659 (mmmt) REVERT: h 11 GLU cc_start: 0.8412 (tp30) cc_final: 0.8112 (tp30) REVERT: h 324 MET cc_start: 0.9162 (mmm) cc_final: 0.8855 (mmm) REVERT: h 440 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8873 (tppp) REVERT: q 26 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7997 (tm-30) REVERT: q 41 GLN cc_start: 0.8822 (tp-100) cc_final: 0.8359 (tp40) REVERT: q 130 GLU cc_start: 0.8355 (tp30) cc_final: 0.7891 (tp30) REVERT: z 194 MET cc_start: 0.9273 (tpp) cc_final: 0.8844 (tpp) REVERT: P 93 MET cc_start: 0.3700 (mmp) cc_final: 0.2826 (ptt) outliers start: 69 outliers final: 43 residues processed: 471 average time/residue: 1.5387 time to fit residues: 946.8282 Evaluate side-chains 467 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 422 time to evaluate : 5.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 350 LEU Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Q residue 482 ILE Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 358 GLU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain g residue 255 ASP Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 440 LYS Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 232 THR Chi-restraints excluded: chain z residue 357 GLU Chi-restraints excluded: chain z residue 479 VAL Chi-restraints excluded: chain P residue 180 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 753 optimal weight: 6.9990 chunk 793 optimal weight: 5.9990 chunk 723 optimal weight: 4.9990 chunk 771 optimal weight: 10.0000 chunk 792 optimal weight: 0.9980 chunk 464 optimal weight: 10.0000 chunk 336 optimal weight: 0.5980 chunk 605 optimal weight: 9.9990 chunk 236 optimal weight: 0.8980 chunk 697 optimal weight: 0.8980 chunk 729 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 481 ASN ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS e 522 GLN h 459 ASN z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 67490 Z= 0.160 Angle : 0.515 14.612 91125 Z= 0.251 Chirality : 0.040 0.204 10860 Planarity : 0.003 0.051 11630 Dihedral : 6.761 162.816 9371 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.20 % Favored : 96.79 % Rotamer: Outliers : 0.75 % Allowed : 11.76 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.53 (0.09), residues: 8626 helix: 2.15 (0.08), residues: 4446 sheet: 0.11 (0.16), residues: 1105 loop : -0.29 (0.11), residues: 3075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 168 HIS 0.017 0.001 HIS z 161 PHE 0.013 0.001 PHE g 362 TYR 0.013 0.001 TYR b 297 ARG 0.006 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 445 time to evaluate : 5.829 Fit side-chains revert: symmetry clash REVERT: D 25 GLN cc_start: 0.8849 (tp-100) cc_final: 0.8416 (tp-100) REVERT: D 28 ASP cc_start: 0.8545 (t70) cc_final: 0.8102 (t70) REVERT: D 67 ASP cc_start: 0.8389 (m-30) cc_final: 0.8133 (m-30) REVERT: D 307 ASP cc_start: 0.8619 (t0) cc_final: 0.8125 (t0) REVERT: D 374 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9080 (tm) REVERT: E 39 MET cc_start: 0.8821 (ttm) cc_final: 0.8495 (ttt) REVERT: E 474 MET cc_start: 0.8365 (tmm) cc_final: 0.7909 (tmm) REVERT: G 20 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7705 (ttp-170) REVERT: G 21 LYS cc_start: 0.8434 (tmtt) cc_final: 0.8068 (tptt) REVERT: G 54 MET cc_start: 0.8264 (mpp) cc_final: 0.7993 (pmm) REVERT: G 219 MET cc_start: 0.9072 (ttp) cc_final: 0.8870 (ppp) REVERT: H 14 ASP cc_start: 0.8755 (t0) cc_final: 0.8295 (t0) REVERT: H 283 HIS cc_start: 0.8174 (m-70) cc_final: 0.7869 (m-70) REVERT: H 497 MET cc_start: 0.8091 (ptp) cc_final: 0.7726 (ppp) REVERT: Q 357 ASP cc_start: 0.8549 (t0) cc_final: 0.8200 (t0) REVERT: Q 526 MET cc_start: 0.9127 (mtm) cc_final: 0.8905 (mtm) REVERT: Z 17 GLN cc_start: 0.8354 (mp10) cc_final: 0.8046 (pm20) REVERT: Z 196 MET cc_start: 0.7929 (mtm) cc_final: 0.7616 (mtp) REVERT: Z 238 GLU cc_start: 0.8955 (pt0) cc_final: 0.8579 (pt0) REVERT: a 106 GLU cc_start: 0.8473 (tm-30) cc_final: 0.8204 (tp30) REVERT: a 156 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8008 (mtm) REVERT: b 310 MET cc_start: 0.8794 (ttm) cc_final: 0.8414 (ttm) REVERT: b 415 MET cc_start: 0.9421 (mmm) cc_final: 0.9013 (mmp) REVERT: d 186 MET cc_start: 0.8489 (ttm) cc_final: 0.8121 (ttm) REVERT: d 320 MET cc_start: 0.9387 (mtp) cc_final: 0.9063 (mtt) REVERT: h 11 GLU cc_start: 0.8414 (tp30) cc_final: 0.8122 (tp30) REVERT: h 145 LYS cc_start: 0.8741 (pptt) cc_final: 0.8525 (tptp) REVERT: h 324 MET cc_start: 0.9159 (mmm) cc_final: 0.8884 (mmm) REVERT: q 26 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7970 (tm-30) REVERT: q 41 GLN cc_start: 0.8841 (tp-100) cc_final: 0.8580 (tp-100) REVERT: q 130 GLU cc_start: 0.8339 (tp30) cc_final: 0.7867 (tp30) REVERT: z 194 MET cc_start: 0.9253 (tpp) cc_final: 0.8800 (tpp) REVERT: P 93 MET cc_start: 0.3815 (mmp) cc_final: 0.2922 (ptt) REVERT: P 196 GLU cc_start: 0.5272 (pt0) cc_final: 0.4560 (mp0) outliers start: 54 outliers final: 34 residues processed: 475 average time/residue: 1.5183 time to fit residues: 942.8993 Evaluate side-chains 469 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 432 time to evaluate : 5.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 350 LEU Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 358 GLU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 194 VAL Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain e residue 11 GLU Chi-restraints excluded: chain g residue 255 ASP Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain z residue 7 LEU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 232 THR Chi-restraints excluded: chain z residue 357 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 768 optimal weight: 10.0000 chunk 506 optimal weight: 1.9990 chunk 815 optimal weight: 0.7980 chunk 497 optimal weight: 0.6980 chunk 387 optimal weight: 0.9980 chunk 567 optimal weight: 8.9990 chunk 855 optimal weight: 30.0000 chunk 787 optimal weight: 6.9990 chunk 681 optimal weight: 6.9990 chunk 70 optimal weight: 0.7980 chunk 526 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** H 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS e 522 GLN z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 67490 Z= 0.148 Angle : 0.517 13.445 91125 Z= 0.250 Chirality : 0.040 0.213 10860 Planarity : 0.003 0.050 11630 Dihedral : 6.653 160.384 9371 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.13 % Favored : 96.86 % Rotamer: Outliers : 0.65 % Allowed : 12.02 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.56 (0.09), residues: 8626 helix: 2.18 (0.08), residues: 4445 sheet: 0.11 (0.16), residues: 1131 loop : -0.27 (0.11), residues: 3050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP e 304 HIS 0.017 0.001 HIS z 161 PHE 0.013 0.001 PHE g 362 TYR 0.018 0.001 TYR b 297 ARG 0.009 0.000 ARG E 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17252 Ramachandran restraints generated. 8626 Oldfield, 0 Emsley, 8626 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 449 time to evaluate : 5.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 156 MET cc_start: 0.8816 (mpp) cc_final: 0.8261 (mpp) REVERT: D 25 GLN cc_start: 0.8838 (tp-100) cc_final: 0.8415 (tp-100) REVERT: D 28 ASP cc_start: 0.8521 (t70) cc_final: 0.8042 (t70) REVERT: D 67 ASP cc_start: 0.8410 (m-30) cc_final: 0.8158 (m-30) REVERT: D 90 MET cc_start: 0.9014 (mtp) cc_final: 0.8776 (mtp) REVERT: D 307 ASP cc_start: 0.8608 (t0) cc_final: 0.8090 (t0) REVERT: D 374 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9083 (tm) REVERT: E 39 MET cc_start: 0.8825 (ttm) cc_final: 0.8496 (ttt) REVERT: E 501 MET cc_start: 0.9089 (mmt) cc_final: 0.8682 (mmp) REVERT: G 20 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7697 (ttp-170) REVERT: G 21 LYS cc_start: 0.8429 (tmtt) cc_final: 0.8061 (tptt) REVERT: G 219 MET cc_start: 0.9109 (ttp) cc_final: 0.8881 (ppp) REVERT: H 14 ASP cc_start: 0.8781 (t0) cc_final: 0.8311 (t0) REVERT: H 283 HIS cc_start: 0.8208 (m-70) cc_final: 0.7894 (m-70) REVERT: H 497 MET cc_start: 0.8065 (ptp) cc_final: 0.7700 (ppp) REVERT: Q 357 ASP cc_start: 0.8505 (t0) cc_final: 0.8186 (t0) REVERT: Q 526 MET cc_start: 0.9128 (mtm) cc_final: 0.8909 (mtm) REVERT: Z 17 GLN cc_start: 0.8306 (mp10) cc_final: 0.8006 (pm20) REVERT: Z 196 MET cc_start: 0.7961 (mtm) cc_final: 0.7661 (mtp) REVERT: Z 238 GLU cc_start: 0.8942 (pt0) cc_final: 0.8575 (pt0) REVERT: a 106 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8198 (tp30) REVERT: b 310 MET cc_start: 0.8764 (ttm) cc_final: 0.8406 (ttm) REVERT: b 415 MET cc_start: 0.9443 (mmm) cc_final: 0.9033 (mmp) REVERT: d 232 LYS cc_start: 0.8879 (ptmm) cc_final: 0.8637 (pttm) REVERT: d 263 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8182 (mp10) REVERT: d 320 MET cc_start: 0.9368 (mtp) cc_final: 0.9018 (mtt) REVERT: e 526 MET cc_start: 0.9256 (ttt) cc_final: 0.8693 (ttt) REVERT: g 511 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8248 (mt-10) REVERT: h 11 GLU cc_start: 0.8421 (tp30) cc_final: 0.8128 (tp30) REVERT: h 145 LYS cc_start: 0.8739 (pptt) cc_final: 0.8532 (tptp) REVERT: h 324 MET cc_start: 0.9156 (mmm) cc_final: 0.8872 (mmm) REVERT: q 26 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7958 (tm-30) REVERT: q 41 GLN cc_start: 0.8830 (tp-100) cc_final: 0.8570 (tp-100) REVERT: q 130 GLU cc_start: 0.8351 (tp30) cc_final: 0.7846 (tp30) REVERT: z 194 MET cc_start: 0.9255 (tpp) cc_final: 0.8792 (tpp) REVERT: P 93 MET cc_start: 0.3725 (mmp) cc_final: 0.2835 (ptt) REVERT: P 196 GLU cc_start: 0.5278 (pt0) cc_final: 0.4571 (mp0) outliers start: 47 outliers final: 29 residues processed: 478 average time/residue: 1.5107 time to fit residues: 950.4119 Evaluate side-chains 470 residues out of total 7225 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 438 time to evaluate : 5.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 350 LEU Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 358 GLU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 194 VAL Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 263 GLN Chi-restraints excluded: chain e residue 11 GLU Chi-restraints excluded: chain e residue 522 GLN Chi-restraints excluded: chain g residue 255 ASP Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain z residue 137 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 417 optimal weight: 5.9990 chunk 541 optimal weight: 9.9990 chunk 725 optimal weight: 9.9990 chunk 208 optimal weight: 0.2980 chunk 628 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 189 optimal weight: 10.0000 chunk 682 optimal weight: 0.6980 chunk 285 optimal weight: 10.0000 chunk 700 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** H 282 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 481 ASN ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 460 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.069568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.055755 restraints weight = 194327.149| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 3.24 r_work: 0.2538 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2546 r_free = 0.2546 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2546 r_free = 0.2546 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.317 67490 Z= 0.219 Angle : 0.586 59.130 91125 Z= 0.306 Chirality : 0.041 0.550 10860 Planarity : 0.003 0.051 11630 Dihedral : 6.652 160.399 9371 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.12 % Favored : 96.87 % Rotamer: Outliers : 0.71 % Allowed : 12.04 % Favored : 87.26 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % 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: 1.55 (0.09), residues: 8626 helix: 2.16 (0.08), residues: 4445 sheet: 0.11 (0.16), residues: 1137 loop : -0.27 (0.11), residues: 3044 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP e 304 HIS 0.015 0.001 HIS z 161 PHE 0.012 0.001 PHE g 362 TYR 0.014 0.001 TYR b 297 ARG 0.008 0.000 ARG E 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16292.86 seconds wall clock time: 287 minutes 22.53 seconds (17242.53 seconds total)