Starting phenix.real_space_refine on Fri Feb 16 14:12:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgl_40461/02_2024/8sgl_40461_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgl_40461/02_2024/8sgl_40461.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/8sgl_40461/02_2024/8sgl_40461.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgl_40461/02_2024/8sgl_40461.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgl_40461/02_2024/8sgl_40461_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgl_40461/02_2024/8sgl_40461_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= 0.048 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 420 5.16 5 C 42118 2.51 5 N 11736 2.21 5 O 13046 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 ASP 42": "OD1" <-> "OD2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 529": "OD1" <-> "OD2" Residue "B PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 118": "OD1" <-> "OD2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 524": "OE1" <-> "OE2" Residue "E ASP 58": "OD1" <-> "OD2" Residue "E GLU 426": "OE1" <-> "OE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 511": "OE1" <-> "OE2" Residue "H ASP 14": "OD1" <-> "OD2" Residue "H ASP 46": "OD1" <-> "OD2" Residue "H ASP 187": "OD1" <-> "OD2" Residue "H GLU 226": "OE1" <-> "OE2" Residue "H GLU 317": "OE1" <-> "OE2" Residue "H GLU 518": "OE1" <-> "OE2" Residue "Q ASP 299": "OD1" <-> "OD2" Residue "Q ASP 357": "OD1" <-> "OD2" Residue "Q ASP 499": "OD1" <-> "OD2" Residue "Z ASP 342": "OD1" <-> "OD2" Residue "Z GLU 520": "OE1" <-> "OE2" Residue "a GLU 15": "OE1" <-> "OE2" Residue "a ASP 51": "OD1" <-> "OD2" Residue "a GLU 68": "OE1" <-> "OE2" Residue "a ASP 529": "OD1" <-> "OD2" Residue "d ASP 261": "OD1" <-> "OD2" Residue "d PHE 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 212": "OE1" <-> "OE2" Residue "e TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 532": "OD1" <-> "OD2" Residue "g ASP 52": "OD1" <-> "OD2" Residue "g TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 521": "OD1" <-> "OD2" Residue "h GLU 413": "OE1" <-> "OE2" Residue "q ASP 193": "OD1" <-> "OD2" Residue "q ASP 393": "OD1" <-> "OD2" Residue "q GLU 485": "OE1" <-> "OE2" Residue "z GLU 101": "OE1" <-> "OE2" Residue "z TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 357": "OE1" <-> "OE2" Residue "z ASP 480": "OD1" <-> "OD2" Residue "N TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 249": "OE1" <-> "OE2" Residue "N PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 67432 Number of models: 1 Model: "" Number of chains: 49 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: "N" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2298 Classifications: {'peptide': 300} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 293} 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: 29.83, per 1000 atoms: 0.44 Number of scatterers: 67432 At special positions: 0 Unit cell: (179.86, 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 420 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 13046 8.00 N 11736 7.00 C 42118 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 "HETATM67211 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67339 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67083 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67275 O3A ADP e 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66955 O3A ADP B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67243 O3A ADP d 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66987 O3A ADP D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67019 O3A ADP E 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: 21.64 Conformation dependent library (CDL) restraints added in 10.9 seconds 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16322 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 314 helices and 116 sheets defined 49.7% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.57 Creating SS restraints... Processing helix chain 'A' and resid 15 through 35 removed outlier: 3.689A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N SER A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 5.766A 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: 3.603A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.654A 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 156 removed outlier: 6.679A pdb=" N ARG A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ASP A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N CYS A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 178 removed outlier: 4.624A pdb=" N ASP A 166 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 4.686A 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 280 removed outlier: 3.957A pdb=" N ASP A 261 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N ILE A 270 " --> pdb=" O GLU A 267 " (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 429 removed outlier: 4.265A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N SER A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 455 removed outlier: 3.799A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 5.122A 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 478 through 485 removed outlier: 3.724A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 484 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 3.849A 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 119 Processing helix chain 'B' and resid 123 through 143 Processing helix chain 'B' and resid 152 through 169 removed outlier: 4.554A pdb=" N SER B 169 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 190 removed outlier: 3.766A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS B 176 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 5.918A 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: 4.050A pdb=" N HIS B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 307 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: 3.739A 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: 3.700A 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: 4.418A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 5.551A 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 108 through 125 removed outlier: 3.795A 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 192 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: 4.011A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 4.038A 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: 4.442A pdb=" N GLU D 334 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 3.952A 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 441 Processing helix chain 'D' and resid 446 through 468 removed outlier: 3.912A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL D 460 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 5.062A 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 530 Processing helix chain 'E' and resid 30 through 51 removed outlier: 3.552A pdb=" N LEU E 34 " --> pdb=" O GLY E 30 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR E 50 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N SER E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 79 Processing helix chain 'E' and resid 86 through 101 Processing helix chain 'E' and resid 108 through 126 removed outlier: 3.642A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ARG E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 150 Processing helix chain 'E' and resid 163 through 175 removed outlier: 4.738A pdb=" N SER E 175 " --> pdb=" O THR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 180 removed outlier: 4.149A 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: 3.867A 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 439 removed outlier: 3.750A pdb=" N LYS E 439 " --> pdb=" O GLN E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 465 removed outlier: 3.799A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL E 457 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 4.697A 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 510 through 529 Processing helix chain 'G' and resid 19 through 40 removed outlier: 3.648A pdb=" N ARG G 38 " --> pdb=" O ASP G 35 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N THR G 39 " --> 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 115 removed outlier: 3.585A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN G 115 " --> pdb=" O HIS G 111 " (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 164 through 183 removed outlier: 4.207A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N SER G 170 " --> pdb=" O ARG G 167 " (cutoff:3.500A) 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: 4.075A pdb=" N PHE G 264 " --> pdb=" O GLU G 261 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR G 265 " --> pdb=" O GLU G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 307 removed outlier: 3.689A 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: 3.650A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 455 removed outlier: 3.741A pdb=" N TRP G 435 " --> pdb=" O VAL G 432 " (cutoff:3.500A) Proline residue: G 436 - end of helix removed outlier: 3.503A pdb=" N GLN G 442 " --> pdb=" O ALA G 439 " (cutoff:3.500A) removed outlier: 3.993A 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 470 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 34 Processing helix chain 'H' and resid 37 through 39 No H-bonds generated for 'chain 'H' and resid 37 through 39' Processing helix chain 'H' and resid 62 through 68 Processing helix chain 'H' and resid 76 through 89 removed outlier: 3.616A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 113 removed outlier: 4.148A 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 185 removed outlier: 5.267A pdb=" N ALA H 173 " --> pdb=" O GLN H 170 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE H 175 " --> pdb=" O LYS H 172 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL H 183 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET H 184 " --> 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 260 through 284 removed outlier: 3.522A 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: 4.142A pdb=" N THR H 426 " --> pdb=" O ASP H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 453 removed outlier: 3.989A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE H 444 " --> pdb=" O LYS H 440 " (cutoff:3.500A) removed outlier: 5.212A 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: 4.386A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) removed outlier: 5.729A 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 157 through 170 removed outlier: 4.257A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER Q 170 " --> pdb=" O THR Q 166 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 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: 4.854A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) removed outlier: 3.839A 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 341 through 343 No H-bonds generated for 'chain 'Q' and resid 341 through 343' Processing helix chain 'Q' and resid 382 through 404 Processing helix chain 'Q' and resid 414 through 429 removed outlier: 3.893A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 434 through 456 removed outlier: 3.748A pdb=" N PHE Q 445 " --> pdb=" O PHE Q 441 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLU Q 446 " --> pdb=" O ALA Q 442 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA Q 447 " --> pdb=" O GLU Q 443 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE Q 448 " --> pdb=" O ALA Q 444 " (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 501 through 520 Processing helix chain 'Z' and resid 3 through 7 Processing helix chain 'Z' and resid 17 through 37 removed outlier: 4.785A pdb=" N THR Z 36 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N ASN Z 37 " --> 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: 3.671A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) removed outlier: 4.550A 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: 3.962A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 162 through 179 removed outlier: 3.590A 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 262 Processing helix chain 'Z' and resid 265 through 281 removed outlier: 3.612A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 299 through 308 removed outlier: 3.740A pdb=" N GLU Z 308 " --> pdb=" O ALA Z 304 " (cutoff:3.500A) Processing helix chain 'Z' and resid 318 through 328 removed outlier: 4.366A 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: 4.168A pdb=" N GLN Z 434 " --> pdb=" O GLY Z 431 " (cutoff:3.500A) removed outlier: 3.805A 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: 3.665A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N SER a 34 " --> pdb=" O ASN a 30 " (cutoff:3.500A) removed outlier: 5.877A 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 92 through 110 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 144 through 156 Processing helix chain 'a' and resid 163 through 179 removed outlier: 4.384A pdb=" N ASP a 166 " --> pdb=" O ILE a 163 " (cutoff:3.500A) removed outlier: 4.592A 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 280 removed outlier: 4.013A pdb=" N ASP a 261 " --> pdb=" O GLU a 258 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ILE a 270 " --> pdb=" O GLU a 267 " (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: 4.405A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) Processing helix chain 'a' and resid 434 through 455 removed outlier: 3.834A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N VAL a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 5.141A 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 478 through 485 removed outlier: 3.811A pdb=" N LYS a 481 " --> pdb=" O PRO a 478 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ASN a 482 " --> pdb=" O GLU a 479 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS a 484 " --> pdb=" O LYS a 481 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TRP a 485 " --> pdb=" O ASN a 482 " (cutoff:3.500A) 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 119 Processing helix chain 'b' and resid 123 through 143 Processing helix chain 'b' and resid 152 through 169 removed outlier: 4.471A pdb=" N SER b 169 " --> pdb=" O THR b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 171 through 190 removed outlier: 3.648A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS b 176 " --> pdb=" O THR b 173 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ASP b 177 " --> pdb=" O HIS b 174 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE b 179 " --> pdb=" O LYS b 176 " (cutoff:3.500A) 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: 3.985A pdb=" N HIS b 285 " --> pdb=" O ARG b 281 " (cutoff:3.500A) Processing helix chain 'b' and resid 298 through 307 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 Processing helix chain 'b' and resid 431 through 454 Proline residue: b 447 - end of helix removed outlier: 3.913A 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: 3.714A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 4.106A 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 171 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 180 through 194 Proline residue: d 185 - end of helix removed outlier: 3.596A pdb=" N VAL d 194 " --> 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: 3.729A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.911A 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: 4.457A pdb=" N GLU d 334 " --> pdb=" O GLU d 331 " (cutoff:3.500A) removed outlier: 4.085A 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 removed outlier: 3.560A pdb=" N THR d 442 " --> pdb=" O GLU d 438 " (cutoff:3.500A) Processing helix chain 'd' and resid 446 through 466 removed outlier: 3.951A pdb=" N VAL d 460 " --> pdb=" O ASP d 456 " (cutoff:3.500A) removed outlier: 4.812A 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 530 removed outlier: 4.843A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) 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 30 through 51 removed outlier: 3.856A pdb=" N LEU e 34 " --> pdb=" O GLY e 30 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR e 50 " --> pdb=" O ASN e 46 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N SER e 51 " --> pdb=" O THR e 47 " (cutoff:3.500A) Processing helix chain 'e' and resid 74 through 79 Processing helix chain 'e' and resid 86 through 101 Processing helix chain 'e' and resid 106 through 126 removed outlier: 4.302A pdb=" N VAL e 110 " --> pdb=" O THR e 106 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN e 122 " --> pdb=" O GLU e 118 " (cutoff:3.500A) Processing helix chain 'e' and resid 130 through 151 Processing helix chain 'e' and resid 163 through 175 removed outlier: 4.693A pdb=" N SER e 175 " --> pdb=" O THR e 171 " (cutoff:3.500A) Processing helix chain 'e' and resid 177 through 195 removed outlier: 3.950A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) removed outlier: 6.275A 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 295 removed outlier: 3.906A 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 439 removed outlier: 3.961A pdb=" N LYS e 439 " --> pdb=" O GLN e 435 " (cutoff:3.500A) Processing helix chain 'e' and resid 442 through 465 removed outlier: 3.901A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL e 457 " --> pdb=" O ASP e 453 " (cutoff:3.500A) removed outlier: 4.775A 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 528 Processing helix chain 'g' and resid 20 through 37 removed outlier: 3.856A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (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: 3.733A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE g 112 " --> pdb=" O VAL g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 119 through 140 Processing helix chain 'g' and resid 149 through 160 Processing helix chain 'g' and resid 164 through 167 removed outlier: 3.842A 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: 4.235A pdb=" N LEU g 285 " --> pdb=" O ASP g 281 " (cutoff:3.500A) Processing helix chain 'g' and resid 298 through 307 removed outlier: 3.587A 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 340 through 342 No H-bonds generated for 'chain 'g' and resid 340 through 342' Processing helix chain 'g' and resid 381 through 403 Processing helix chain 'g' and resid 413 through 428 removed outlier: 3.805A pdb=" N LYS g 427 " --> pdb=" O THR g 423 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ALA g 428 " --> pdb=" O GLU g 424 " (cutoff:3.500A) Processing helix chain 'g' and resid 434 through 455 removed outlier: 4.011A pdb=" N LEU g 444 " --> pdb=" O VAL g 440 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLU g 445 " --> pdb=" O ALA g 441 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N VAL g 446 " --> pdb=" O GLN g 442 " (cutoff:3.500A) removed outlier: 5.250A 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 470 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 518 Processing helix chain 'h' and resid 19 through 34 Processing helix chain 'h' and resid 62 through 68 Processing helix chain 'h' and resid 76 through 89 removed outlier: 3.524A pdb=" N GLU h 89 " --> pdb=" O GLN h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 113 removed outlier: 4.239A 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: 3.760A 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: 3.532A 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: 4.107A pdb=" N THR h 426 " --> pdb=" O ASP h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 430 through 453 removed outlier: 4.088A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU h 443 " --> pdb=" O ALA h 439 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE h 444 " --> pdb=" O LYS h 440 " (cutoff:3.500A) removed outlier: 5.368A 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: 4.817A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) removed outlier: 5.867A 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 157 through 167 removed outlier: 4.304A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.368A 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: 4.789A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) removed outlier: 3.697A 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 427 Processing helix chain 'q' and resid 433 through 456 removed outlier: 3.519A 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 17 through 37 removed outlier: 4.808A pdb=" N THR z 36 " --> pdb=" O ASP z 32 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N ASN z 37 " --> 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: 3.669A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) removed outlier: 4.733A 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: 4.236A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 162 through 179 removed outlier: 3.619A 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: 4.139A pdb=" N ARG z 264 " --> pdb=" O VAL z 260 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS z 265 " --> pdb=" O LYS z 261 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N PHE z 266 " --> pdb=" O ALA z 262 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ILE z 267 " --> pdb=" O GLU z 263 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 299 through 308 removed outlier: 3.689A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 318 through 328 removed outlier: 4.222A 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: 4.126A pdb=" N GLN z 434 " --> pdb=" O GLY z 431 " (cutoff:3.500A) removed outlier: 3.766A 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 'N' and resid 250 through 252 No H-bonds generated for 'chain 'N' and resid 250 through 252' Processing sheet with id= A, first strand: chain 'A' and resid 9 through 13 Processing sheet with id= B, first strand: chain 'A' and resid 180 through 182 Processing sheet with id= C, first strand: chain 'A' and resid 196 through 199 Processing sheet with id= D, first strand: chain 'A' and resid 213 through 216 Processing sheet with id= E, first strand: chain 'A' and resid 346 through 348 removed outlier: 6.473A pdb=" N VAL A 285 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N LEU A 237 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU A 287 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N MET A 306 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N THR A 288 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 308 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 408 through 410 Processing sheet with id= G, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.623A pdb=" N ARG A 496 " --> pdb=" O GLY A 487 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 17 through 19 Processing sheet with id= I, first strand: chain 'B' and resid 50 through 53 Processing sheet with id= J, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.185A pdb=" N CYS B 371 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ILE B 202 " --> pdb=" O CYS B 371 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE B 373 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N LYS B 204 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LEU B 375 " --> pdb=" O LYS B 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 218 through 220 Processing sheet with id= L, first strand: chain 'B' and resid 344 through 346 removed outlier: 6.692A pdb=" N CYS B 289 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ALA B 240 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE B 291 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N MET B 310 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N ASN B 292 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE B 312 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 406 through 408 Processing sheet with id= N, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= O, first strand: chain 'D' and resid 59 through 62 Processing sheet with id= P, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.756A pdb=" N VAL D 386 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL D 211 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 6.358A 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: 5.971A pdb=" N VAL D 390 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 227 through 229 Processing sheet with id= R, first strand: chain 'D' and resid 357 through 359 removed outlier: 7.059A pdb=" N VAL D 297 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N ILE D 249 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU D 299 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N MET D 323 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ILE D 300 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE D 325 " --> pdb=" O ILE D 300 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 421 through 423 Processing sheet with id= T, first strand: chain 'D' and resid 491 through 494 Processing sheet with id= U, first strand: chain 'E' and resid 59 through 62 Processing sheet with id= V, first strand: chain 'E' and resid 209 through 215 removed outlier: 6.952A pdb=" N VAL E 383 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N GLU E 212 " --> pdb=" O VAL E 383 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N ILE E 385 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N LYS E 214 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ILE E 387 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 228 through 230 Processing sheet with id= X, first strand: chain 'E' and resid 354 through 356 removed outlier: 7.037A pdb=" N LEU E 299 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N LEU E 251 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ILE E 301 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N CYS E 302 " --> pdb=" O PRO E 320 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N VAL E 322 " --> pdb=" O CYS E 302 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 418 through 420 Processing sheet with id= Z, first strand: chain 'G' and resid 48 through 51 Processing sheet with id= AA, first strand: chain 'G' and resid 185 through 187 Processing sheet with id= AB, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.441A pdb=" N CYS G 372 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N GLU G 202 " --> pdb=" O CYS G 372 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE G 374 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE G 204 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU G 376 " --> pdb=" O ILE G 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'G' and resid 238 through 241 removed outlier: 6.459A pdb=" N VAL G 289 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N LEU G 241 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ILE G 291 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR G 310 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N THR G 292 " --> pdb=" O THR G 310 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE G 312 " --> pdb=" O THR G 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'G' and resid 351 through 355 Processing sheet with id= AE, first strand: chain 'G' and resid 407 through 409 Processing sheet with id= AF, first strand: chain 'G' and resid 478 through 480 Processing sheet with id= AG, first strand: chain 'H' and resid 14 through 17 Processing sheet with id= AH, first strand: chain 'H' and resid 47 through 50 Processing sheet with id= AI, first strand: chain 'H' and resid 195 through 201 removed outlier: 6.221A pdb=" N CYS H 370 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LYS H 198 " --> pdb=" O CYS H 370 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N PHE H 372 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL H 200 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N LEU H 374 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 214 through 217 Processing sheet with id= AK, first strand: chain 'H' and resid 342 through 344 removed outlier: 6.999A pdb=" N VAL H 288 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LEU H 240 " --> pdb=" O VAL H 288 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N LEU H 290 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N PHE H 309 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N SER H 291 " --> pdb=" O PHE H 309 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ALA H 311 " --> pdb=" O SER H 291 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'H' and resid 405 through 407 Processing sheet with id= AM, first strand: chain 'H' and resid 475 through 478 Processing sheet with id= AN, first strand: chain 'Q' and resid 20 through 23 Processing sheet with id= AO, first strand: chain 'Q' and resid 54 through 57 Processing sheet with id= AP, first strand: chain 'Q' and resid 202 through 208 removed outlier: 6.507A pdb=" N SER Q 373 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N CYS Q 205 " --> pdb=" O SER Q 373 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE Q 375 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N ILE Q 207 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LEU Q 377 " --> pdb=" O ILE Q 207 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'Q' and resid 220 through 223 Processing sheet with id= AR, first strand: chain 'Q' and resid 240 through 242 removed outlier: 6.079A pdb=" N MET Q 311 " --> pdb=" O VAL Q 291 " (cutoff:3.500A) removed outlier: 7.575A 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= AS, first strand: chain 'Q' and resid 498 through 500 removed outlier: 3.932A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) removed outlier: 8.559A pdb=" N VAL Q 147 " --> pdb=" O PRO Q 410 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id= AU, first strand: chain 'Z' and resid 12 through 15 removed outlier: 3.549A pdb=" N GLU Z 12 " --> pdb=" O ARG Z 523 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'Z' and resid 45 through 48 Processing sheet with id= AW, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.861A pdb=" N VAL Z 372 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N MET Z 194 " --> pdb=" O VAL Z 372 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU Z 374 " --> pdb=" O MET Z 194 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N MET Z 196 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILE Z 376 " --> pdb=" O MET Z 196 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id= AY, first strand: chain 'Z' and resid 345 through 347 Processing sheet with id= AZ, first strand: chain 'Z' and resid 477 through 479 Processing sheet with id= BA, first strand: chain 'a' and resid 9 through 13 Processing sheet with id= BB, first strand: chain 'a' and resid 43 through 46 Processing sheet with id= BC, first strand: chain 'a' and resid 180 through 182 Processing sheet with id= BD, first strand: chain 'a' and resid 196 through 199 Processing sheet with id= BE, first strand: chain 'a' and resid 213 through 216 Processing sheet with id= BF, first strand: chain 'a' and resid 346 through 348 removed outlier: 6.546A pdb=" N VAL a 285 " --> pdb=" O ALA a 235 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N LEU a 237 " --> pdb=" O VAL a 285 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU a 287 " --> pdb=" O LEU a 237 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N MET a 306 " --> pdb=" O ILE a 286 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N THR a 288 " --> pdb=" O MET a 306 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL a 308 " --> pdb=" O THR a 288 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'a' and resid 408 through 410 Processing sheet with id= BH, first strand: chain 'a' and resid 486 through 489 Processing sheet with id= BI, first strand: chain 'b' and resid 17 through 19 Processing sheet with id= BJ, first strand: chain 'b' and resid 50 through 53 Processing sheet with id= BK, first strand: chain 'b' and resid 199 through 205 removed outlier: 6.231A pdb=" N CYS b 371 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE b 202 " --> pdb=" O CYS b 371 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE b 373 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LYS b 204 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N LEU b 375 " --> pdb=" O LYS b 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= BK Processing sheet with id= BL, first strand: chain 'b' and resid 218 through 220 Processing sheet with id= BM, first strand: chain 'b' and resid 344 through 346 removed outlier: 6.733A pdb=" N CYS b 289 " --> pdb=" O LEU b 238 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ALA b 240 " --> pdb=" O CYS b 289 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE b 291 " --> pdb=" O ALA b 240 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N MET b 310 " --> pdb=" O PHE b 290 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASN b 292 " --> pdb=" O MET b 310 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE b 312 " --> pdb=" O ASN b 292 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'b' and resid 406 through 408 Processing sheet with id= BO, first strand: chain 'b' and resid 476 through 479 Processing sheet with id= BP, first strand: chain 'd' and resid 59 through 62 Processing sheet with id= BQ, first strand: chain 'd' and resid 208 through 212 removed outlier: 6.718A pdb=" N VAL d 386 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N VAL d 211 " --> pdb=" O VAL d 386 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE d 388 " --> pdb=" O VAL d 211 " (cutoff:3.500A) No H-bonds generated for sheet with id= BQ Processing sheet with id= BR, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.613A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'd' and resid 357 through 359 removed outlier: 6.481A pdb=" N VAL d 297 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ILE d 249 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU d 299 " --> pdb=" O ILE d 249 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N MET d 323 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE d 300 " --> pdb=" O MET d 323 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE d 325 " --> pdb=" O ILE d 300 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'd' and resid 421 through 423 Processing sheet with id= BU, first strand: chain 'd' and resid 491 through 494 Processing sheet with id= BV, first strand: chain 'e' and resid 26 through 29 Processing sheet with id= BW, first strand: chain 'e' and resid 59 through 62 Processing sheet with id= BX, first strand: chain 'e' and resid 209 through 215 removed outlier: 6.960A pdb=" N VAL e 383 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N GLU e 212 " --> pdb=" O VAL e 383 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ILE e 385 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N LYS e 214 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE e 387 " --> pdb=" O LYS e 214 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'e' and resid 228 through 230 Processing sheet with id= BZ, first strand: chain 'e' and resid 354 through 356 removed outlier: 7.047A pdb=" N LEU e 299 " --> pdb=" O ALA e 249 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'e' and resid 418 through 420 Processing sheet with id= CB, first strand: chain 'g' and resid 15 through 18 Processing sheet with id= CC, first strand: chain 'g' and resid 48 through 51 Processing sheet with id= CD, first strand: chain 'g' and resid 185 through 187 Processing sheet with id= CE, first strand: chain 'g' and resid 200 through 205 removed outlier: 3.884A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'g' and resid 218 through 220 Processing sheet with id= CG, first strand: chain 'g' and resid 238 through 241 removed outlier: 6.364A pdb=" N VAL g 289 " --> pdb=" O VAL g 239 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LEU g 241 " --> pdb=" O VAL g 289 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILE g 291 " --> pdb=" O LEU g 241 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR g 310 " --> pdb=" O VAL g 290 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N THR g 292 " --> pdb=" O THR g 310 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE g 312 " --> pdb=" O THR g 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= CG Processing sheet with id= CH, first strand: chain 'g' and resid 407 through 409 Processing sheet with id= CI, first strand: chain 'g' and resid 478 through 481 removed outlier: 3.841A pdb=" N THR g 486 " --> pdb=" O ASN g 481 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'h' and resid 14 through 17 Processing sheet with id= CK, first strand: chain 'h' and resid 47 through 50 Processing sheet with id= CL, first strand: chain 'h' and resid 195 through 201 removed outlier: 6.525A pdb=" N CYS h 370 " --> pdb=" O GLY h 196 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LYS h 198 " --> pdb=" O CYS h 370 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N PHE h 372 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL h 200 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU h 374 " --> pdb=" O VAL h 200 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'h' and resid 214 through 217 Processing sheet with id= CN, first strand: chain 'h' and resid 237 through 240 removed outlier: 7.094A pdb=" N VAL h 288 " --> pdb=" O ALA h 238 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LEU h 240 " --> pdb=" O VAL h 288 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LEU h 290 " --> pdb=" O LEU h 240 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N PHE h 309 " --> pdb=" O VAL h 289 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N SER h 291 " --> pdb=" O PHE h 309 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA h 311 " --> pdb=" O SER h 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= CN Processing sheet with id= CO, first strand: chain 'h' and resid 405 through 407 Processing sheet with id= CP, first strand: chain 'h' and resid 475 through 478 Processing sheet with id= CQ, first strand: chain 'q' and resid 20 through 23 Processing sheet with id= CR, first strand: chain 'q' and resid 54 through 57 Processing sheet with id= CS, first strand: chain 'q' and resid 202 through 208 removed outlier: 6.651A pdb=" N SER q 373 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N CYS q 205 " --> pdb=" O SER q 373 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE q 375 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE q 207 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU q 377 " --> pdb=" O ILE q 207 " (cutoff:3.500A) Processing sheet with id= CT, first strand: chain 'q' and resid 220 through 223 Processing sheet with id= CU, first strand: chain 'q' and resid 240 through 242 removed outlier: 6.088A pdb=" N MET q 311 " --> pdb=" O VAL q 291 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N THR q 293 " --> pdb=" O MET q 311 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL q 313 " --> pdb=" O THR q 293 " (cutoff:3.500A) Processing sheet with id= CV, first strand: chain 'q' and resid 498 through 500 removed outlier: 3.783A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N VAL q 147 " --> pdb=" O PRO q 410 " (cutoff:3.500A) Processing sheet with id= CW, first strand: chain 'q' and resid 478 through 480 Processing sheet with id= CX, first strand: chain 'z' and resid 12 through 15 Processing sheet with id= CY, first strand: chain 'z' and resid 45 through 48 Processing sheet with id= CZ, first strand: chain 'z' and resid 191 through 196 removed outlier: 6.793A pdb=" N VAL z 372 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET z 194 " --> pdb=" O VAL z 372 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU z 374 " --> pdb=" O MET z 194 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N MET z 196 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE z 376 " --> pdb=" O MET z 196 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'z' and resid 210 through 212 Processing sheet with id= DB, first strand: chain 'z' and resid 345 through 347 Processing sheet with id= DC, first strand: chain 'z' and resid 407 through 409 Processing sheet with id= DD, first strand: chain 'z' and resid 477 through 479 Processing sheet with id= DE, first strand: chain 'N' and resid 128 through 130 Processing sheet with id= DF, first strand: chain 'N' and resid 188 through 190 Processing sheet with id= DG, first strand: chain 'N' and resid 198 through 203 removed outlier: 6.720A pdb=" N ALA N 213 " --> pdb=" O SER N 199 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N CYS N 201 " --> pdb=" O LEU N 211 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU N 211 " --> pdb=" O CYS N 201 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N PHE N 203 " --> pdb=" O GLN N 209 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N GLN N 209 " --> pdb=" O PHE N 203 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ASP N 223 " --> pdb=" O LEU N 229 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N LEU N 229 " --> pdb=" O ASP N 223 " (cutoff:3.500A) Processing sheet with id= DH, first strand: chain 'N' and resid 275 through 277 Processing sheet with id= DI, first strand: chain 'N' and resid 284 through 289 removed outlier: 6.645A pdb=" N GLY N 299 " --> pdb=" O ASN N 285 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL N 287 " --> pdb=" O ALA N 297 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA N 297 " --> pdb=" O VAL N 287 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N TYR N 289 " --> pdb=" O ALA N 295 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA N 295 " --> pdb=" O TYR N 289 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA N 317 " --> pdb=" O LEU N 307 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N ASP N 309 " --> pdb=" O GLU N 315 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N GLU N 315 " --> pdb=" O ASP N 309 " (cutoff:3.500A) Processing sheet with id= DJ, first strand: chain 'N' and resid 349 through 351 removed outlier: 3.937A pdb=" N SER N 361 " --> pdb=" O VAL N 351 " (cutoff:3.500A) Processing sheet with id= DK, first strand: chain 'N' and resid 108 through 112 removed outlier: 6.760A pdb=" N SER N 123 " --> pdb=" O LEU N 109 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N MET N 111 " --> pdb=" O VAL N 121 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL N 121 " --> pdb=" O MET N 111 " (cutoff:3.500A) Processing sheet with id= DL, first strand: chain 'N' and resid 328 through 331 removed outlier: 6.364A pdb=" N GLY N 343 " --> pdb=" O SER N 329 " (cutoff:3.500A) 3443 hydrogen bonds defined for protein. 9207 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: 29.95 Time building geometry restraints manager: 23.69 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: 22692 1.34 - 1.46: 11924 1.46 - 1.58: 32816 1.58 - 1.70: 48 1.70 - 1.81: 738 Bond restraints: 68218 Sorted by residual: bond pdb=" F2 AF3 z 603 " pdb="AL AF3 z 603 " ideal model delta sigma weight residual 1.637 1.799 -0.162 2.00e-02 2.50e+03 6.53e+01 bond pdb=" F2 AF3 A 603 " pdb="AL AF3 A 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.42e+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 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 6.37e+01 bond pdb=" F2 AF3 Z 603 " pdb="AL AF3 Z 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.34e+01 ... (remaining 68213 not shown) Histogram of bond angle deviations from ideal: 97.73 - 105.56: 1102 105.56 - 113.39: 39899 113.39 - 121.23: 34280 121.23 - 129.06: 16548 129.06 - 136.89: 305 Bond angle restraints: 92134 Sorted by residual: angle pdb=" CA LEU d 513 " pdb=" CB LEU d 513 " pdb=" CG LEU d 513 " ideal model delta sigma weight residual 116.30 130.97 -14.67 3.50e+00 8.16e-02 1.76e+01 angle pdb=" CA MET B 160 " pdb=" CB MET B 160 " pdb=" CG MET B 160 " ideal model delta sigma weight residual 114.10 120.95 -6.85 2.00e+00 2.50e-01 1.17e+01 angle pdb=" C GLN q 472 " pdb=" N GLU q 473 " pdb=" CA GLU q 473 " ideal model delta sigma weight residual 121.58 114.90 6.68 1.95e+00 2.63e-01 1.17e+01 angle pdb=" N GLY q 209 " pdb=" CA GLY q 209 " pdb=" C GLY q 209 " ideal model delta sigma weight residual 113.18 121.06 -7.88 2.37e+00 1.78e-01 1.11e+01 angle pdb=" N GLY Q 209 " pdb=" CA GLY Q 209 " pdb=" C GLY Q 209 " ideal model delta sigma weight residual 113.18 121.02 -7.84 2.37e+00 1.78e-01 1.10e+01 ... (remaining 92129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 41460 35.93 - 71.85: 599 71.85 - 107.78: 58 107.78 - 143.71: 10 143.71 - 179.64: 5 Dihedral angle restraints: 42132 sinusoidal: 16920 harmonic: 25212 Sorted by residual: 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 -60.00 119.64 -179.64 1 2.00e+01 2.50e-03 4.80e+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 -60.00 109.18 -169.18 1 2.00e+01 2.50e-03 4.76e+01 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 300.00 131.76 168.24 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 42129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 8021 0.040 - 0.081: 2057 0.081 - 0.121: 821 0.121 - 0.161: 59 0.161 - 0.202: 5 Chirality restraints: 10963 Sorted by residual: chirality pdb=" CB VAL h 36 " pdb=" CA VAL h 36 " pdb=" CG1 VAL h 36 " pdb=" CG2 VAL h 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB VAL H 36 " pdb=" CA VAL H 36 " pdb=" CG1 VAL H 36 " pdb=" CG2 VAL H 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.05e-01 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 2.60 -0.17 2.00e-01 2.50e+01 7.01e-01 ... (remaining 10960 not shown) Planarity restraints: 11759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS a 73 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.88e+00 pdb=" C LYS a 73 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS a 73 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL a 74 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.47e+00 pdb=" N PRO e 441 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 73 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C LYS A 73 " 0.032 2.00e-02 2.50e+03 pdb=" O LYS A 73 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL A 74 " -0.011 2.00e-02 2.50e+03 ... (remaining 11756 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 571 2.53 - 3.12: 51445 3.12 - 3.71: 106067 3.71 - 4.31: 151191 4.31 - 4.90: 258160 Nonbonded interactions: 567434 Sorted by model distance: nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.932 2.120 nonbonded pdb=" O3B ADP z 601 " pdb="MG MG z 602 " model vdw 1.946 2.170 nonbonded pdb=" O3A ADP B 601 " pdb="MG MG B 602 " model vdw 1.948 2.170 nonbonded pdb=" OD1 ASP b 97 " pdb="MG MG b 602 " model vdw 1.954 2.170 nonbonded pdb="MG MG d 602 " pdb=" F1 AF3 d 603 " model vdw 1.962 2.120 ... (remaining 567429 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: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 8.420 Check model and map are aligned: 0.780 Set scattering table: 0.480 Process input model: 153.730 Find NCS groups from input model: 6.540 Set up NCS constraints: 0.600 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:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 184.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.162 68218 Z= 0.323 Angle : 0.553 14.667 92134 Z= 0.270 Chirality : 0.042 0.202 10963 Planarity : 0.003 0.053 11759 Dihedral : 14.206 179.636 25810 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 1.62 (0.09), residues: 8734 helix: 2.36 (0.08), residues: 4379 sheet: 0.11 (0.15), residues: 1259 loop : -0.35 (0.11), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP N 394 HIS 0.013 0.001 HIS z 161 PHE 0.024 0.001 PHE b 12 TYR 0.015 0.001 TYR N 155 ARG 0.006 0.000 ARG G 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 607 time to evaluate : 6.527 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7420 (t0) cc_final: 0.7027 (t0) REVERT: A 388 MET cc_start: 0.9331 (mtp) cc_final: 0.9033 (mtm) REVERT: G 15 LYS cc_start: 0.8792 (mptt) cc_final: 0.8573 (mmmt) REVERT: G 229 MET cc_start: 0.9437 (mtt) cc_final: 0.9174 (mtt) REVERT: G 521 ASP cc_start: 0.7914 (t70) cc_final: 0.7578 (t70) REVERT: H 440 LYS cc_start: 0.9113 (ttmt) cc_final: 0.8886 (ttpp) REVERT: a 10 ASP cc_start: 0.8403 (m-30) cc_final: 0.8142 (m-30) REVERT: a 473 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7782 (tm-30) REVERT: d 186 MET cc_start: 0.8929 (ttm) cc_final: 0.8705 (ttp) REVERT: e 146 GLU cc_start: 0.8004 (tp30) cc_final: 0.7656 (tp30) REVERT: g 52 ASP cc_start: 0.7363 (t0) cc_final: 0.6915 (t0) REVERT: g 54 MET cc_start: 0.8205 (mpp) cc_final: 0.7995 (mpt) REVERT: g 69 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7892 (mp0) REVERT: g 395 MET cc_start: 0.9314 (mtm) cc_final: 0.9097 (mtm) REVERT: h 324 MET cc_start: 0.8964 (mmm) cc_final: 0.8704 (mmm) REVERT: z 353 TYR cc_start: 0.8619 (t80) cc_final: 0.8341 (t80) REVERT: N 209 GLN cc_start: 0.8547 (mp10) cc_final: 0.8077 (mp10) REVERT: N 326 PHE cc_start: 0.7730 (m-80) cc_final: 0.7346 (m-80) REVERT: N 394 TRP cc_start: 0.7556 (m-90) cc_final: 0.5769 (m-90) outliers start: 0 outliers final: 0 residues processed: 607 average time/residue: 1.5817 time to fit residues: 1234.8233 Evaluate side-chains 472 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 472 time to evaluate : 5.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 733 optimal weight: 0.6980 chunk 658 optimal weight: 0.8980 chunk 365 optimal weight: 2.9990 chunk 224 optimal weight: 10.0000 chunk 444 optimal weight: 9.9990 chunk 351 optimal weight: 5.9990 chunk 681 optimal weight: 2.9990 chunk 263 optimal weight: 6.9990 chunk 414 optimal weight: 0.6980 chunk 506 optimal weight: 9.9990 chunk 789 optimal weight: 10.0000 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN G 61 ASN G 111 HIS H 470 GLN Z 17 GLN ** Z 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 468 ASN g 12 GLN z 161 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.0569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 68218 Z= 0.189 Angle : 0.535 12.612 92134 Z= 0.264 Chirality : 0.041 0.159 10963 Planarity : 0.004 0.052 11759 Dihedral : 7.206 178.724 9484 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.88 % Allowed : 5.89 % Favored : 93.23 % 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: 1.54 (0.09), residues: 8734 helix: 2.24 (0.08), residues: 4379 sheet: 0.16 (0.16), residues: 1234 loop : -0.34 (0.11), residues: 3121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 132 HIS 0.012 0.001 HIS z 161 PHE 0.018 0.001 PHE A 167 TYR 0.013 0.001 TYR G 437 ARG 0.011 0.000 ARG H 425 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 500 time to evaluate : 6.018 Fit side-chains revert: symmetry clash REVERT: A 48 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7719 (p0) REVERT: D 458 MET cc_start: 0.7960 (tpp) cc_final: 0.7134 (mpp) REVERT: G 15 LYS cc_start: 0.8769 (mptt) cc_final: 0.8531 (mmmt) REVERT: G 521 ASP cc_start: 0.7830 (t70) cc_final: 0.7489 (t70) REVERT: H 81 ASP cc_start: 0.8304 (OUTLIER) cc_final: 0.7903 (m-30) REVERT: H 187 ASP cc_start: 0.8169 (p0) cc_final: 0.7956 (p0) REVERT: H 440 LYS cc_start: 0.9104 (ttmt) cc_final: 0.8876 (ttpp) REVERT: a 10 ASP cc_start: 0.8375 (m-30) cc_final: 0.8101 (m-30) REVERT: a 23 MET cc_start: 0.7999 (OUTLIER) cc_final: 0.7784 (tmm) REVERT: a 209 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7592 (mpp) REVERT: a 473 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7792 (tm-30) REVERT: d 186 MET cc_start: 0.8916 (ttm) cc_final: 0.8551 (ttp) REVERT: e 4 MET cc_start: 0.6410 (tmt) cc_final: 0.5406 (mpm) REVERT: e 146 GLU cc_start: 0.7988 (tp30) cc_final: 0.7626 (tp30) REVERT: g 52 ASP cc_start: 0.7375 (t0) cc_final: 0.6768 (t0) REVERT: g 54 MET cc_start: 0.8238 (mpp) cc_final: 0.7896 (mpt) REVERT: g 69 GLU cc_start: 0.8408 (mm-30) cc_final: 0.7950 (mp0) REVERT: h 308 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8673 (mtm) REVERT: h 324 MET cc_start: 0.8939 (mmm) cc_final: 0.8612 (mmm) REVERT: q 116 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8594 (tt0) REVERT: q 368 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7391 (mt-10) REVERT: z 353 TYR cc_start: 0.8885 (t80) cc_final: 0.8600 (t80) REVERT: N 132 TRP cc_start: 0.8079 (OUTLIER) cc_final: 0.7492 (p90) REVERT: N 193 MET cc_start: 0.6860 (OUTLIER) cc_final: 0.6429 (mpm) REVERT: N 209 GLN cc_start: 0.8519 (mp10) cc_final: 0.8052 (mp10) REVERT: N 326 PHE cc_start: 0.7760 (m-80) cc_final: 0.7396 (m-80) REVERT: N 394 TRP cc_start: 0.7640 (m-90) cc_final: 0.7223 (m-90) outliers start: 64 outliers final: 17 residues processed: 522 average time/residue: 1.5484 time to fit residues: 1051.2683 Evaluate side-chains 505 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 479 time to evaluate : 5.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain a residue 209 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain d residue 272 MET Chi-restraints excluded: chain e residue 96 LYS Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain h residue 308 MET Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 116 GLU Chi-restraints excluded: chain q residue 250 ILE Chi-restraints excluded: chain q residue 368 GLU Chi-restraints excluded: chain z residue 53 ASP Chi-restraints excluded: chain N residue 132 TRP Chi-restraints excluded: chain N residue 193 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 438 optimal weight: 8.9990 chunk 244 optimal weight: 9.9990 chunk 656 optimal weight: 1.9990 chunk 537 optimal weight: 9.9990 chunk 217 optimal weight: 0.9990 chunk 790 optimal weight: 9.9990 chunk 854 optimal weight: 8.9990 chunk 704 optimal weight: 6.9990 chunk 783 optimal weight: 9.9990 chunk 269 optimal weight: 4.9990 chunk 634 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 361 HIS D 82 GLN G 61 ASN G 111 HIS Z 161 HIS Z 453 GLN ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 12 GLN q 41 GLN N 231 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 68218 Z= 0.430 Angle : 0.616 9.919 92134 Z= 0.305 Chirality : 0.044 0.169 10963 Planarity : 0.004 0.054 11759 Dihedral : 7.178 174.761 9484 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.29 % Allowed : 8.05 % Favored : 90.66 % 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: 1.24 (0.09), residues: 8734 helix: 1.96 (0.08), residues: 4385 sheet: 0.05 (0.15), residues: 1224 loop : -0.45 (0.11), residues: 3125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 132 HIS 0.014 0.001 HIS Z 161 PHE 0.021 0.002 PHE a 167 TYR 0.014 0.001 TYR q 304 ARG 0.013 0.000 ARG h 425 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 472 time to evaluate : 6.072 Fit side-chains revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8213 (mt-10) REVERT: E 288 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8531 (ptm) REVERT: G 15 LYS cc_start: 0.8824 (mptt) cc_final: 0.8551 (mmmt) REVERT: G 521 ASP cc_start: 0.7912 (t70) cc_final: 0.7613 (t70) REVERT: H 81 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.7971 (m-30) REVERT: H 440 LYS cc_start: 0.9113 (ttmt) cc_final: 0.8872 (ttpp) REVERT: a 10 ASP cc_start: 0.8361 (m-30) cc_final: 0.8128 (m-30) REVERT: a 473 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7909 (tm-30) REVERT: d 48 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8499 (pp) REVERT: d 186 MET cc_start: 0.8942 (ttm) cc_final: 0.8721 (ttp) REVERT: e 146 GLU cc_start: 0.7995 (tp30) cc_final: 0.7607 (tp30) REVERT: g 52 ASP cc_start: 0.7571 (t0) cc_final: 0.6908 (t0) REVERT: g 54 MET cc_start: 0.8355 (mpp) cc_final: 0.7937 (mpt) REVERT: h 227 MET cc_start: 0.9266 (mtp) cc_final: 0.8921 (mtp) REVERT: h 324 MET cc_start: 0.8977 (mmm) cc_final: 0.8722 (mmm) REVERT: h 524 ARG cc_start: 0.7176 (tmm160) cc_final: 0.6941 (tmm160) REVERT: q 368 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7529 (mt-10) REVERT: q 430 CYS cc_start: 0.8752 (m) cc_final: 0.8341 (m) REVERT: z 244 VAL cc_start: 0.8515 (OUTLIER) cc_final: 0.8248 (t) REVERT: z 353 TYR cc_start: 0.8905 (t80) cc_final: 0.8685 (t80) REVERT: z 389 ASP cc_start: 0.8632 (m-30) cc_final: 0.8419 (m-30) REVERT: N 209 GLN cc_start: 0.8691 (mp10) cc_final: 0.8193 (mp10) REVERT: N 326 PHE cc_start: 0.7791 (m-80) cc_final: 0.7406 (m-80) REVERT: N 391 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9075 (tm) REVERT: N 394 TRP cc_start: 0.7705 (m-90) cc_final: 0.6628 (m-90) outliers start: 94 outliers final: 22 residues processed: 519 average time/residue: 1.5714 time to fit residues: 1060.0862 Evaluate side-chains 482 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 453 time to evaluate : 5.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 272 MET Chi-restraints excluded: chain e residue 96 LYS Chi-restraints excluded: chain e residue 448 MET Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 82 GLU Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 249 MET Chi-restraints excluded: chain q residue 368 GLU Chi-restraints excluded: chain z residue 53 ASP Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 415 GLU Chi-restraints excluded: chain N residue 391 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 781 optimal weight: 10.0000 chunk 594 optimal weight: 0.8980 chunk 410 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 377 optimal weight: 4.9990 chunk 530 optimal weight: 3.9990 chunk 793 optimal weight: 0.8980 chunk 839 optimal weight: 40.0000 chunk 414 optimal weight: 9.9990 chunk 751 optimal weight: 3.9990 chunk 226 optimal weight: 2.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN G 61 ASN G 111 HIS Z 161 HIS a 205 GLN g 12 GLN h 151 GLN q 41 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 68218 Z= 0.246 Angle : 0.544 8.719 92134 Z= 0.268 Chirality : 0.042 0.153 10963 Planarity : 0.003 0.051 11759 Dihedral : 7.074 179.358 9484 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.19 % Allowed : 9.56 % Favored : 89.25 % 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: 1.29 (0.09), residues: 8734 helix: 2.02 (0.08), residues: 4378 sheet: 0.03 (0.15), residues: 1222 loop : -0.44 (0.11), residues: 3134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 222 HIS 0.013 0.001 HIS Z 161 PHE 0.014 0.001 PHE a 167 TYR 0.013 0.001 TYR b 456 ARG 0.013 0.000 ARG h 425 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 472 time to evaluate : 6.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7348 (t0) cc_final: 0.7112 (t0) REVERT: G 15 LYS cc_start: 0.8753 (mptt) cc_final: 0.8466 (mmmt) REVERT: G 521 ASP cc_start: 0.7816 (t70) cc_final: 0.7504 (t70) REVERT: H 81 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.7975 (m-30) REVERT: H 227 MET cc_start: 0.9077 (OUTLIER) cc_final: 0.8091 (mpt) REVERT: H 440 LYS cc_start: 0.9126 (ttmt) cc_final: 0.8891 (ttpp) REVERT: a 10 ASP cc_start: 0.8225 (m-30) cc_final: 0.8003 (m-30) REVERT: a 473 GLU cc_start: 0.8212 (tm-30) cc_final: 0.7855 (tm-30) REVERT: b 353 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.7792 (tmm) REVERT: d 186 MET cc_start: 0.8936 (ttm) cc_final: 0.8716 (ttp) REVERT: e 146 GLU cc_start: 0.7987 (tp30) cc_final: 0.7638 (tp30) REVERT: g 52 ASP cc_start: 0.7608 (t0) cc_final: 0.6920 (t0) REVERT: g 54 MET cc_start: 0.8361 (mpp) cc_final: 0.7900 (mpt) REVERT: h 324 MET cc_start: 0.8980 (mmm) cc_final: 0.8732 (mmm) REVERT: q 116 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8636 (tt0) REVERT: q 368 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7505 (mt-10) REVERT: z 244 VAL cc_start: 0.8518 (OUTLIER) cc_final: 0.8318 (t) REVERT: z 353 TYR cc_start: 0.8918 (t80) cc_final: 0.8702 (t80) REVERT: N 209 GLN cc_start: 0.8666 (mp10) cc_final: 0.8173 (mp10) REVERT: N 326 PHE cc_start: 0.7769 (m-80) cc_final: 0.7427 (m-80) REVERT: N 394 TRP cc_start: 0.7725 (m-90) cc_final: 0.6718 (m-90) outliers start: 87 outliers final: 26 residues processed: 522 average time/residue: 1.5539 time to fit residues: 1060.2959 Evaluate side-chains 488 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 456 time to evaluate : 6.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 366 THR Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain e residue 96 LYS Chi-restraints excluded: chain e residue 448 MET Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 82 GLU Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 116 GLU Chi-restraints excluded: chain q residue 249 MET Chi-restraints excluded: chain q residue 250 ILE Chi-restraints excluded: chain q residue 316 ASN Chi-restraints excluded: chain q residue 368 GLU Chi-restraints excluded: chain z residue 53 ASP Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 699 optimal weight: 5.9990 chunk 476 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 625 optimal weight: 9.9990 chunk 346 optimal weight: 0.9980 chunk 716 optimal weight: 7.9990 chunk 580 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 428 optimal weight: 4.9990 chunk 753 optimal weight: 4.9990 chunk 211 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 61 ASN G 111 HIS Z 161 HIS g 12 GLN h 151 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.0967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 68218 Z= 0.326 Angle : 0.567 9.415 92134 Z= 0.279 Chirality : 0.042 0.165 10963 Planarity : 0.004 0.052 11759 Dihedral : 7.016 179.667 9484 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.27 % Allowed : 10.39 % Favored : 88.33 % 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: 1.23 (0.09), residues: 8734 helix: 1.96 (0.08), residues: 4387 sheet: -0.02 (0.15), residues: 1219 loop : -0.45 (0.11), residues: 3128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 132 HIS 0.013 0.001 HIS Z 161 PHE 0.015 0.001 PHE a 167 TYR 0.014 0.001 TYR b 456 ARG 0.014 0.000 ARG h 425 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 470 time to evaluate : 6.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7431 (t0) cc_final: 0.6918 (t0) REVERT: A 48 ASP cc_start: 0.8743 (OUTLIER) cc_final: 0.8443 (p0) REVERT: A 358 ASP cc_start: 0.8489 (t70) cc_final: 0.8034 (t0) REVERT: D 57 MET cc_start: 0.9017 (mmm) cc_final: 0.8797 (mmm) REVERT: G 15 LYS cc_start: 0.8767 (mptt) cc_final: 0.8472 (mmmt) REVERT: G 521 ASP cc_start: 0.7841 (t70) cc_final: 0.7541 (t70) REVERT: H 81 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.7961 (m-30) REVERT: H 440 LYS cc_start: 0.9111 (ttmt) cc_final: 0.8869 (ttpp) REVERT: a 10 ASP cc_start: 0.8228 (m-30) cc_final: 0.8008 (m-30) REVERT: a 480 ARG cc_start: 0.8118 (mtp180) cc_final: 0.7524 (mtp85) REVERT: b 353 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.7785 (tmm) REVERT: b 415 MET cc_start: 0.9402 (mmm) cc_final: 0.8972 (mmp) REVERT: d 186 MET cc_start: 0.8942 (ttm) cc_final: 0.8730 (ttp) REVERT: e 146 GLU cc_start: 0.7992 (tp30) cc_final: 0.7637 (tp30) REVERT: g 52 ASP cc_start: 0.7680 (t0) cc_final: 0.7011 (t0) REVERT: g 54 MET cc_start: 0.8392 (mpp) cc_final: 0.7919 (mpt) REVERT: h 14 ASP cc_start: 0.8369 (m-30) cc_final: 0.8148 (m-30) REVERT: h 324 MET cc_start: 0.8969 (mmm) cc_final: 0.8747 (mmm) REVERT: q 368 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7516 (mt-10) REVERT: z 244 VAL cc_start: 0.8486 (OUTLIER) cc_final: 0.8259 (t) REVERT: N 209 GLN cc_start: 0.8701 (mp10) cc_final: 0.8161 (mp10) REVERT: N 326 PHE cc_start: 0.7760 (m-80) cc_final: 0.7415 (m-80) REVERT: N 364 PHE cc_start: 0.7214 (p90) cc_final: 0.6990 (p90) REVERT: N 391 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.9108 (tm) REVERT: N 394 TRP cc_start: 0.7732 (m-90) cc_final: 0.6699 (m-90) outliers start: 93 outliers final: 40 residues processed: 532 average time/residue: 1.5366 time to fit residues: 1063.1588 Evaluate side-chains 497 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 451 time to evaluate : 5.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain G residue 61 ASN Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 246 SER Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain e residue 96 LYS Chi-restraints excluded: chain e residue 448 MET Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 82 GLU Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 249 MET Chi-restraints excluded: chain q residue 250 ILE Chi-restraints excluded: chain q residue 316 ASN Chi-restraints excluded: chain q residue 368 GLU Chi-restraints excluded: chain z residue 53 ASP Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain N residue 279 THR Chi-restraints excluded: chain N residue 391 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 282 optimal weight: 4.9990 chunk 756 optimal weight: 4.9990 chunk 166 optimal weight: 7.9990 chunk 493 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 840 optimal weight: 20.0000 chunk 697 optimal weight: 0.9990 chunk 389 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 278 optimal weight: 6.9990 chunk 441 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 111 HIS Z 161 HIS g 12 GLN h 151 GLN q 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 68218 Z= 0.308 Angle : 0.564 9.320 92134 Z= 0.277 Chirality : 0.042 0.160 10963 Planarity : 0.004 0.061 11759 Dihedral : 6.976 177.639 9484 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.29 % Allowed : 11.02 % Favored : 87.69 % 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: 1.24 (0.09), residues: 8734 helix: 1.97 (0.08), residues: 4388 sheet: 0.00 (0.15), residues: 1207 loop : -0.45 (0.11), residues: 3139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 222 HIS 0.013 0.001 HIS Z 161 PHE 0.018 0.001 PHE a 167 TYR 0.017 0.001 TYR z 353 ARG 0.016 0.000 ARG h 425 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 461 time to evaluate : 6.074 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7402 (t0) cc_final: 0.6876 (t0) REVERT: A 48 ASP cc_start: 0.8810 (OUTLIER) cc_final: 0.8482 (p0) REVERT: A 358 ASP cc_start: 0.8495 (t70) cc_final: 0.8018 (t0) REVERT: B 471 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: E 448 MET cc_start: 0.9146 (OUTLIER) cc_final: 0.8710 (mmt) REVERT: G 15 LYS cc_start: 0.8756 (mptt) cc_final: 0.8460 (mmmt) REVERT: H 81 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.7982 (m-30) REVERT: H 227 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.7992 (mpp) REVERT: H 440 LYS cc_start: 0.9108 (ttmt) cc_final: 0.8860 (ttpp) REVERT: Q 492 MET cc_start: 0.8187 (mmm) cc_final: 0.7536 (mtm) REVERT: a 10 ASP cc_start: 0.8249 (m-30) cc_final: 0.8037 (m-30) REVERT: a 480 ARG cc_start: 0.7964 (mtp180) cc_final: 0.7460 (mtp85) REVERT: b 353 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.7813 (tmm) REVERT: b 415 MET cc_start: 0.9438 (mmm) cc_final: 0.9021 (mmp) REVERT: d 186 MET cc_start: 0.8938 (ttm) cc_final: 0.8731 (ttp) REVERT: d 261 ASP cc_start: 0.8608 (OUTLIER) cc_final: 0.8268 (p0) REVERT: e 146 GLU cc_start: 0.8074 (tp30) cc_final: 0.7663 (tp30) REVERT: g 52 ASP cc_start: 0.7695 (t0) cc_final: 0.7089 (t0) REVERT: g 54 MET cc_start: 0.8400 (mpp) cc_final: 0.7983 (mpt) REVERT: h 227 MET cc_start: 0.9240 (mtp) cc_final: 0.8872 (mtp) REVERT: h 324 MET cc_start: 0.8963 (mmm) cc_final: 0.8747 (mmm) REVERT: q 368 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7514 (mt-10) REVERT: z 244 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8291 (t) REVERT: N 141 HIS cc_start: 0.7595 (OUTLIER) cc_final: 0.7244 (p90) REVERT: N 209 GLN cc_start: 0.8721 (mp10) cc_final: 0.8179 (mp10) REVERT: N 326 PHE cc_start: 0.7779 (m-80) cc_final: 0.7368 (m-80) REVERT: N 364 PHE cc_start: 0.7259 (p90) cc_final: 0.7041 (p90) REVERT: N 391 LEU cc_start: 0.9509 (OUTLIER) cc_final: 0.9181 (tm) REVERT: N 394 TRP cc_start: 0.7724 (m-90) cc_final: 0.6674 (m-90) outliers start: 94 outliers final: 40 residues processed: 525 average time/residue: 1.5015 time to fit residues: 1032.6827 Evaluate side-chains 504 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 453 time to evaluate : 5.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 448 MET Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 246 SER Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain d residue 261 ASP Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 96 LYS Chi-restraints excluded: chain e residue 448 MET Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 82 GLU Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 249 MET Chi-restraints excluded: chain q residue 250 ILE Chi-restraints excluded: chain q residue 316 ASN Chi-restraints excluded: chain q residue 368 GLU Chi-restraints excluded: chain z residue 53 ASP Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain N residue 141 HIS Chi-restraints excluded: chain N residue 279 THR Chi-restraints excluded: chain N residue 391 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 810 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 479 optimal weight: 0.9980 chunk 614 optimal weight: 4.9990 chunk 475 optimal weight: 0.9990 chunk 707 optimal weight: 10.0000 chunk 469 optimal weight: 4.9990 chunk 837 optimal weight: 1.9990 chunk 524 optimal weight: 0.0020 chunk 510 optimal weight: 3.9990 chunk 386 optimal weight: 3.9990 overall best weight: 1.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 172 ASN G 61 ASN G 111 HIS Z 161 HIS ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 12 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 68218 Z= 0.170 Angle : 0.522 10.487 92134 Z= 0.255 Chirality : 0.041 0.160 10963 Planarity : 0.003 0.052 11759 Dihedral : 6.729 168.713 9484 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.08 % Allowed : 11.79 % Favored : 87.13 % 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: 8734 helix: 2.13 (0.08), residues: 4365 sheet: 0.06 (0.15), residues: 1211 loop : -0.39 (0.11), residues: 3158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 132 HIS 0.014 0.001 HIS Z 161 PHE 0.014 0.001 PHE N 382 TYR 0.013 0.001 TYR b 456 ARG 0.008 0.000 ARG H 425 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 491 time to evaluate : 6.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7257 (t0) cc_final: 0.6881 (t0) REVERT: A 48 ASP cc_start: 0.8895 (OUTLIER) cc_final: 0.8546 (p0) REVERT: A 68 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8197 (mt-10) REVERT: A 358 ASP cc_start: 0.8439 (t70) cc_final: 0.7968 (t0) REVERT: D 355 MET cc_start: 0.9151 (mmm) cc_final: 0.8850 (mtp) REVERT: G 15 LYS cc_start: 0.8740 (mptt) cc_final: 0.8452 (mmmt) REVERT: G 463 LEU cc_start: 0.9554 (OUTLIER) cc_final: 0.9340 (tp) REVERT: H 81 ASP cc_start: 0.8321 (OUTLIER) cc_final: 0.7952 (m-30) REVERT: H 440 LYS cc_start: 0.9109 (ttmt) cc_final: 0.8882 (ttpp) REVERT: Z 522 MET cc_start: 0.8530 (mtt) cc_final: 0.8210 (mtt) REVERT: a 473 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7729 (tm-30) REVERT: b 353 MET cc_start: 0.8875 (OUTLIER) cc_final: 0.7762 (tmm) REVERT: b 415 MET cc_start: 0.9434 (mmm) cc_final: 0.9043 (mmp) REVERT: d 186 MET cc_start: 0.8913 (ttm) cc_final: 0.8593 (ttp) REVERT: e 146 GLU cc_start: 0.8067 (tp30) cc_final: 0.7708 (tp30) REVERT: g 52 ASP cc_start: 0.7638 (t0) cc_final: 0.7035 (t0) REVERT: g 54 MET cc_start: 0.8376 (mpp) cc_final: 0.7950 (mpt) REVERT: h 1 MET cc_start: 0.5506 (tmt) cc_final: 0.5254 (tmm) REVERT: h 324 MET cc_start: 0.8914 (mmm) cc_final: 0.8702 (mmm) REVERT: N 141 HIS cc_start: 0.7591 (OUTLIER) cc_final: 0.7255 (p90) REVERT: N 209 GLN cc_start: 0.8678 (mp10) cc_final: 0.8158 (mp10) REVERT: N 326 PHE cc_start: 0.7781 (m-80) cc_final: 0.7360 (m-80) REVERT: N 391 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9288 (tm) REVERT: N 394 TRP cc_start: 0.7781 (m-90) cc_final: 0.6710 (m-90) outliers start: 79 outliers final: 33 residues processed: 544 average time/residue: 1.4699 time to fit residues: 1055.9373 Evaluate side-chains 509 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 468 time to evaluate : 6.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain a residue 68 GLU Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 473 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain b residue 485 ILE Chi-restraints excluded: chain e residue 96 LYS Chi-restraints excluded: chain e residue 448 MET Chi-restraints excluded: chain g residue 82 GLU Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain h residue 482 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 249 MET Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 415 GLU Chi-restraints excluded: chain N residue 141 HIS Chi-restraints excluded: chain N residue 279 THR Chi-restraints excluded: chain N residue 340 LEU Chi-restraints excluded: chain N residue 391 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 518 optimal weight: 7.9990 chunk 334 optimal weight: 7.9990 chunk 500 optimal weight: 1.9990 chunk 252 optimal weight: 5.9990 chunk 164 optimal weight: 7.9990 chunk 162 optimal weight: 0.9980 chunk 532 optimal weight: 8.9990 chunk 570 optimal weight: 7.9990 chunk 414 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 658 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 GLN D 172 ASN G 61 ASN G 111 HIS ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 12 GLN q 41 GLN N 104 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 68218 Z= 0.328 Angle : 0.574 10.872 92134 Z= 0.281 Chirality : 0.042 0.200 10963 Planarity : 0.004 0.051 11759 Dihedral : 6.800 170.577 9484 Min Nonbonded Distance : 1.649 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.16 % Allowed : 12.12 % Favored : 86.72 % 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: 1.29 (0.09), residues: 8734 helix: 2.02 (0.08), residues: 4390 sheet: 0.03 (0.15), residues: 1230 loop : -0.44 (0.11), residues: 3114 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 132 HIS 0.013 0.001 HIS Z 161 PHE 0.016 0.001 PHE a 167 TYR 0.023 0.001 TYR b 456 ARG 0.012 0.000 ARG h 425 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 463 time to evaluate : 6.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7298 (t0) cc_final: 0.6898 (t0) REVERT: A 48 ASP cc_start: 0.8946 (OUTLIER) cc_final: 0.8594 (p0) REVERT: A 358 ASP cc_start: 0.8474 (t70) cc_final: 0.7989 (t0) REVERT: G 15 LYS cc_start: 0.8758 (mptt) cc_final: 0.8459 (mmmt) REVERT: G 117 MET cc_start: 0.8971 (ttm) cc_final: 0.8755 (ttt) REVERT: H 81 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.7980 (m-30) REVERT: H 440 LYS cc_start: 0.9103 (ttmt) cc_final: 0.8869 (ttpp) REVERT: a 433 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.8178 (mtt-85) REVERT: a 473 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7753 (tm-30) REVERT: b 353 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.7818 (tmm) REVERT: d 186 MET cc_start: 0.8938 (ttm) cc_final: 0.8626 (ttp) REVERT: d 261 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8196 (p0) REVERT: e 146 GLU cc_start: 0.8080 (tp30) cc_final: 0.7726 (tp30) REVERT: g 52 ASP cc_start: 0.7702 (t0) cc_final: 0.7063 (t0) REVERT: g 54 MET cc_start: 0.8425 (mpp) cc_final: 0.7968 (mpt) REVERT: h 1 MET cc_start: 0.5495 (tmt) cc_final: 0.5068 (ttp) REVERT: h 324 MET cc_start: 0.8954 (mmm) cc_final: 0.8735 (mmm) REVERT: q 344 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8738 (tpp) REVERT: N 141 HIS cc_start: 0.7689 (OUTLIER) cc_final: 0.7380 (p90) REVERT: N 209 GLN cc_start: 0.8724 (mp10) cc_final: 0.8171 (mp10) REVERT: N 326 PHE cc_start: 0.7789 (m-80) cc_final: 0.7392 (m-80) REVERT: N 391 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9251 (tm) REVERT: N 394 TRP cc_start: 0.7749 (m-90) cc_final: 0.6666 (m-90) outliers start: 85 outliers final: 44 residues processed: 519 average time/residue: 1.5579 time to fit residues: 1055.1562 Evaluate side-chains 506 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 453 time to evaluate : 6.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 80 MET Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 433 ARG Chi-restraints excluded: chain a residue 473 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain d residue 261 ASP Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 96 LYS Chi-restraints excluded: chain e residue 448 MET Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 82 GLU Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain h residue 482 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 249 MET Chi-restraints excluded: chain q residue 250 ILE Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 316 ASN Chi-restraints excluded: chain q residue 344 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain N residue 141 HIS Chi-restraints excluded: chain N residue 279 THR Chi-restraints excluded: chain N residue 391 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 761 optimal weight: 6.9990 chunk 802 optimal weight: 1.9990 chunk 732 optimal weight: 3.9990 chunk 780 optimal weight: 4.9990 chunk 469 optimal weight: 0.9990 chunk 340 optimal weight: 1.9990 chunk 612 optimal weight: 6.9990 chunk 239 optimal weight: 6.9990 chunk 705 optimal weight: 3.9990 chunk 738 optimal weight: 0.2980 chunk 777 optimal weight: 0.8980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 172 ASN G 111 HIS Z 161 HIS ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 12 GLN q 41 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 68218 Z= 0.159 Angle : 0.525 11.321 92134 Z= 0.256 Chirality : 0.041 0.182 10963 Planarity : 0.003 0.052 11759 Dihedral : 6.630 161.315 9484 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.88 % Allowed : 12.57 % Favored : 86.55 % 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: 1.43 (0.09), residues: 8734 helix: 2.14 (0.08), residues: 4373 sheet: 0.12 (0.15), residues: 1210 loop : -0.38 (0.11), residues: 3151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP N 132 HIS 0.016 0.001 HIS Z 161 PHE 0.019 0.001 PHE N 233 TYR 0.017 0.001 TYR d 179 ARG 0.010 0.000 ARG H 425 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 477 time to evaluate : 6.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 ASP cc_start: 0.8399 (t70) cc_final: 0.7953 (t0) REVERT: D 355 MET cc_start: 0.9124 (mmm) cc_final: 0.8838 (mtp) REVERT: D 458 MET cc_start: 0.7652 (tpp) cc_final: 0.7127 (mpp) REVERT: E 48 MET cc_start: 0.9018 (tpp) cc_final: 0.8719 (mmm) REVERT: G 15 LYS cc_start: 0.8738 (mptt) cc_final: 0.8450 (mmmt) REVERT: G 463 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9326 (tp) REVERT: H 81 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.7949 (m-30) REVERT: H 440 LYS cc_start: 0.9105 (ttmt) cc_final: 0.8876 (ttpp) REVERT: b 353 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.7758 (tmm) REVERT: d 186 MET cc_start: 0.8905 (ttm) cc_final: 0.8592 (ttp) REVERT: e 146 GLU cc_start: 0.8064 (tp30) cc_final: 0.7701 (tp30) REVERT: g 52 ASP cc_start: 0.7645 (t0) cc_final: 0.7005 (t0) REVERT: g 54 MET cc_start: 0.8396 (mpp) cc_final: 0.7950 (mpt) REVERT: h 1 MET cc_start: 0.5497 (tmt) cc_final: 0.5243 (tmm) REVERT: h 324 MET cc_start: 0.8904 (mmm) cc_final: 0.8700 (mmm) REVERT: N 141 HIS cc_start: 0.7546 (OUTLIER) cc_final: 0.7222 (p90) REVERT: N 209 GLN cc_start: 0.8677 (mp10) cc_final: 0.8203 (mp10) REVERT: N 326 PHE cc_start: 0.7836 (m-80) cc_final: 0.7389 (m-80) REVERT: N 391 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9234 (tm) REVERT: N 394 TRP cc_start: 0.7761 (m-90) cc_final: 0.6664 (m-90) outliers start: 64 outliers final: 35 residues processed: 520 average time/residue: 1.5942 time to fit residues: 1082.1567 Evaluate side-chains 505 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 465 time to evaluate : 5.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 521 ASP Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain e residue 96 LYS Chi-restraints excluded: chain e residue 448 MET Chi-restraints excluded: chain g residue 82 GLU Chi-restraints excluded: chain g residue 242 ASP Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain h residue 482 GLU Chi-restraints excluded: chain q residue 222 VAL Chi-restraints excluded: chain q residue 249 MET Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain N residue 141 HIS Chi-restraints excluded: chain N residue 279 THR Chi-restraints excluded: chain N residue 340 LEU Chi-restraints excluded: chain N residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 512 optimal weight: 0.2980 chunk 825 optimal weight: 3.9990 chunk 503 optimal weight: 1.9990 chunk 391 optimal weight: 0.9980 chunk 573 optimal weight: 4.9990 chunk 865 optimal weight: 9.9990 chunk 796 optimal weight: 0.8980 chunk 689 optimal weight: 0.0980 chunk 71 optimal weight: 2.9990 chunk 532 optimal weight: 8.9990 chunk 422 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN G 111 HIS Q 32 ASN Z 161 HIS ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 12 GLN N 104 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 68218 Z= 0.143 Angle : 0.526 15.877 92134 Z= 0.256 Chirality : 0.040 0.201 10963 Planarity : 0.003 0.068 11759 Dihedral : 6.506 156.936 9484 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.66 % Allowed : 12.86 % Favored : 86.48 % 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: 1.49 (0.09), residues: 8734 helix: 2.17 (0.08), residues: 4372 sheet: 0.17 (0.15), residues: 1212 loop : -0.34 (0.11), residues: 3150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP N 132 HIS 0.016 0.001 HIS Z 161 PHE 0.018 0.001 PHE N 233 TYR 0.019 0.001 TYR z 353 ARG 0.015 0.000 ARG h 425 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 483 time to evaluate : 6.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 ASP cc_start: 0.8354 (t70) cc_final: 0.7920 (t0) REVERT: D 355 MET cc_start: 0.9120 (mmm) cc_final: 0.8835 (mtp) REVERT: D 458 MET cc_start: 0.7648 (tpp) cc_final: 0.7021 (mpp) REVERT: E 48 MET cc_start: 0.9019 (tpp) cc_final: 0.8775 (mmm) REVERT: G 15 LYS cc_start: 0.8724 (mptt) cc_final: 0.8434 (mmmt) REVERT: G 463 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9280 (tp) REVERT: H 81 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7936 (m-30) REVERT: H 440 LYS cc_start: 0.9103 (ttmt) cc_final: 0.8872 (ttpp) REVERT: a 480 ARG cc_start: 0.8214 (mtp180) cc_final: 0.7705 (mtp85) REVERT: b 353 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.7728 (tmm) REVERT: d 186 MET cc_start: 0.8898 (ttm) cc_final: 0.8574 (ttp) REVERT: d 261 ASP cc_start: 0.8514 (OUTLIER) cc_final: 0.8175 (p0) REVERT: e 146 GLU cc_start: 0.8059 (tp30) cc_final: 0.7693 (tp30) REVERT: g 52 ASP cc_start: 0.7621 (t0) cc_final: 0.6975 (t0) REVERT: g 54 MET cc_start: 0.8358 (mpp) cc_final: 0.7910 (mpt) REVERT: h 1 MET cc_start: 0.5470 (tmt) cc_final: 0.5128 (ttp) REVERT: h 324 MET cc_start: 0.8901 (mmm) cc_final: 0.8697 (mmm) REVERT: N 141 HIS cc_start: 0.7556 (OUTLIER) cc_final: 0.7271 (p90) REVERT: N 209 GLN cc_start: 0.8669 (mp10) cc_final: 0.8196 (mp10) REVERT: N 326 PHE cc_start: 0.7866 (m-80) cc_final: 0.7417 (m-80) REVERT: N 391 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9230 (tm) REVERT: N 394 TRP cc_start: 0.7756 (m-90) cc_final: 0.6668 (m-90) outliers start: 48 outliers final: 29 residues processed: 516 average time/residue: 1.5614 time to fit residues: 1054.8969 Evaluate side-chains 508 residues out of total 7300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 473 time to evaluate : 5.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 521 ASP Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain d residue 261 ASP Chi-restraints excluded: chain e residue 96 LYS Chi-restraints excluded: chain e residue 448 MET Chi-restraints excluded: chain g residue 82 GLU Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 222 VAL Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain N residue 141 HIS Chi-restraints excluded: chain N residue 279 THR Chi-restraints excluded: chain N residue 340 LEU Chi-restraints excluded: chain N residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 547 optimal weight: 8.9990 chunk 734 optimal weight: 5.9990 chunk 211 optimal weight: 9.9990 chunk 635 optimal weight: 5.9990 chunk 101 optimal weight: 8.9990 chunk 191 optimal weight: 0.9980 chunk 690 optimal weight: 1.9990 chunk 288 optimal weight: 6.9990 chunk 709 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 111 HIS ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 12 GLN ** h 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.072723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.059024 restraints weight = 173142.774| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 2.78 r_work: 0.2579 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 68218 Z= 0.361 Angle : 0.591 14.896 92134 Z= 0.289 Chirality : 0.043 0.219 10963 Planarity : 0.004 0.052 11759 Dihedral : 6.663 159.611 9484 Min Nonbonded Distance : 1.605 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.79 % Allowed : 12.98 % Favored : 86.22 % 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: 1.31 (0.09), residues: 8734 helix: 2.04 (0.08), residues: 4379 sheet: 0.09 (0.15), residues: 1244 loop : -0.45 (0.11), residues: 3111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP N 132 HIS 0.013 0.001 HIS Z 161 PHE 0.017 0.001 PHE D 454 TYR 0.015 0.001 TYR z 353 ARG 0.010 0.000 ARG H 425 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17224.56 seconds wall clock time: 303 minutes 16.39 seconds (18196.39 seconds total)