Starting phenix.real_space_refine on Thu Mar 14 10:38:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh9_40481/03_2024/8sh9_40481_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh9_40481/03_2024/8sh9_40481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh9_40481/03_2024/8sh9_40481.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh9_40481/03_2024/8sh9_40481.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh9_40481/03_2024/8sh9_40481_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sh9_40481/03_2024/8sh9_40481_updated.pdb" } resolution = 2.7 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= 0.051 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 415 5.16 5 C 41982 2.51 5 N 11685 2.21 5 O 13003 1.98 5 F 48 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 51": "OD1" <-> "OD2" Residue "A ASP 529": "OD1" <-> "OD2" Residue "B ASP 77": "OD1" <-> "OD2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "D ASP 63": "OD1" <-> "OD2" Residue "D PHE 251": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 331": "OE1" <-> "OE2" Residue "D TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 467": "OE1" <-> "OE2" Residue "E GLU 32": "OE1" <-> "OE2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "E TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 532": "OD1" <-> "OD2" Residue "H GLU 11": "OE1" <-> "OE2" Residue "H TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 27": "OE1" <-> "OE2" Residue "Q ASP 393": "OD1" <-> "OD2" Residue "Q TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 415": "OE1" <-> "OE2" Residue "a GLU 66": "OE1" <-> "OE2" Residue "a GLU 77": "OE1" <-> "OE2" Residue "a GLU 207": "OE1" <-> "OE2" Residue "a GLU 354": "OE1" <-> "OE2" Residue "a GLU 416": "OE1" <-> "OE2" Residue "b GLU 19": "OE1" <-> "OE2" Residue "b ASP 77": "OD1" <-> "OD2" Residue "d ASP 46": "OD1" <-> "OD2" Residue "d GLU 101": "OE1" <-> "OE2" Residue "d ASP 118": "OD1" <-> "OD2" Residue "d TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 279": "OE1" <-> "OE2" Residue "d GLU 399": "OE1" <-> "OE2" Residue "d GLU 402": "OE1" <-> "OE2" Residue "e TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 242": "OD1" <-> "OD2" Residue "g TYR 303": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 70": "OD1" <-> "OD2" Residue "h GLU 103": "OE1" <-> "OE2" Residue "h TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 451": "OD1" <-> "OD2" Residue "z GLU 112": "OE1" <-> "OE2" Residue "z ASP 496": "OD1" <-> "OD2" Residue "P TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 67197 Number of models: 1 Model: "" Number of chains: 50 Chain: "N" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 322 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain breaks: 3 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: 4102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4102 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 17, 'TRANS': 510} Chain: "h" Number of atoms: 4032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4032 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 16, 'TRANS': 508} Chain: "q" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4053 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 16, 'TRANS': 516} Chain: "z" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4033 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 512} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "P" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1727 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 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: 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: 29.10, per 1000 atoms: 0.43 Number of scatterers: 67197 At special positions: 0 Unit cell: (180.918, 176.686, 179.86, 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 415 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 13003 8.00 N 11685 7.00 C 41982 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 "HETATM66848 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66720 O3A ADP B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66752 O3A ADP D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67104 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66976 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66784 O3A ADP E 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.35 Conformation dependent library (CDL) restraints added in 11.6 seconds 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16252 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 323 helices and 111 sheets defined 50.9% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.57 Creating SS restraints... Processing helix chain 'A' and resid 15 through 35 removed outlier: 3.672A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N SER A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 5.890A 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: 3.710A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 135 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 144 through 156 Processing helix chain 'A' and resid 163 through 178 removed outlier: 4.475A pdb=" N ASP A 166 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 4.769A 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: 4.100A pdb=" N ASP A 261 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 4.681A 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: 4.477A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N SER A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 455 removed outlier: 3.778A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 5.131A 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: 3.817A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (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 removed outlier: 3.565A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 143 Processing helix chain 'B' and resid 152 through 169 removed outlier: 4.511A pdb=" N SER B 169 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 190 removed outlier: 3.623A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS B 176 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ASP B 177 " --> pdb=" O HIS B 174 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE B 179 " --> pdb=" O LYS B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 198 No H-bonds generated for 'chain 'B' and resid 196 through 198' Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 261 through 285 removed outlier: 3.984A 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: 3.854A pdb=" N ARG B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 454 Proline residue: B 447 - end of helix removed outlier: 3.719A 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: 4.461A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 5.495A pdb=" N SER D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 80 Processing helix chain 'D' and resid 86 through 101 Processing helix chain 'D' and resid 106 through 125 removed outlier: 4.213A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.891A 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: 4.107A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 4.014A 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: 4.450A pdb=" N GLU D 334 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 4.004A 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 447 through 468 removed outlier: 3.904A pdb=" N VAL D 460 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 4.828A 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 503 through 506 Processing helix chain 'D' and resid 512 through 530 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: 3.617A pdb=" N LEU E 34 " --> pdb=" O GLY E 30 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR E 50 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N SER E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 80 Processing helix chain 'E' and resid 86 through 101 Processing helix chain 'E' and resid 108 through 126 removed outlier: 3.598A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.521A 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: 4.674A pdb=" N SER E 175 " --> pdb=" O THR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 180 removed outlier: 3.955A 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: 3.890A 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 392 through 414 Processing helix chain 'E' and resid 424 through 437 Processing helix chain 'E' and resid 442 through 465 removed outlier: 3.947A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL E 457 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 4.776A 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 40 removed outlier: 3.814A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N THR G 39 " --> pdb=" O ASP G 35 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N CYS G 40 " --> pdb=" O ILE G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 68 Processing helix chain 'G' and resid 75 through 90 Processing helix chain 'G' and resid 95 through 115 removed outlier: 3.647A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 3.543A 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: 4.185A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) removed outlier: 5.511A 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: 4.101A pdb=" N PHE G 264 " --> pdb=" O GLU G 261 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR G 265 " --> pdb=" O GLU G 262 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLN G 284 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 307 removed outlier: 3.592A 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: 4.161A pdb=" N ALA G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 455 removed outlier: 3.617A pdb=" N TRP G 435 " --> pdb=" O VAL G 432 " (cutoff:3.500A) Proline residue: G 436 - end of helix removed outlier: 3.885A 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: 3.597A pdb=" N GLU H 89 " --> pdb=" O GLN H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 113 removed outlier: 4.169A 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: 5.359A pdb=" N ALA H 173 " --> pdb=" O GLN H 170 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL H 183 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 3.611A 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 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: 3.509A 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: 4.039A pdb=" N THR H 426 " --> pdb=" O ASP H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 453 removed outlier: 4.003A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE H 444 " --> pdb=" O LYS H 440 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ILE H 445 " --> pdb=" O ALA H 441 " (cutoff:3.500A) Proline residue: H 446 - end of helix Processing helix chain 'H' and resid 457 through 469 Processing helix chain 'H' and resid 496 through 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: 4.317A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) removed outlier: 5.767A 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: 4.154A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.219A 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: 4.709A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) removed outlier: 3.890A 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 428 removed outlier: 3.519A pdb=" N GLU Q 428 " --> pdb=" O THR Q 424 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 456 removed outlier: 3.699A 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 'Q' and resid 536 through 538 No H-bonds generated for 'chain 'Q' and resid 536 through 538' Processing helix chain 'Z' and resid 3 through 7 Processing helix chain 'Z' and resid 17 through 37 removed outlier: 4.814A pdb=" N THR Z 36 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 4.985A 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: 3.614A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) removed outlier: 4.302A 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: 3.662A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 162 through 179 removed outlier: 3.571A 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: 4.087A pdb=" N ARG Z 264 " --> pdb=" O VAL Z 260 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS Z 265 " --> pdb=" O LYS Z 261 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N PHE Z 266 " --> pdb=" O ALA Z 262 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE Z 267 " --> pdb=" O GLU Z 263 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 299 through 308 removed outlier: 3.713A pdb=" N GLU Z 308 " --> pdb=" O ALA Z 304 " (cutoff:3.500A) Processing helix chain 'Z' and resid 318 through 327 removed outlier: 4.272A 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: 4.146A pdb=" N GLN Z 434 " --> pdb=" O GLY Z 431 " (cutoff:3.500A) removed outlier: 3.752A 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: 3.719A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N SER a 34 " --> pdb=" O ASN a 30 " (cutoff:3.500A) removed outlier: 5.682A 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: 3.664A pdb=" N VAL a 94 " --> pdb=" O THR a 90 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN a 110 " --> pdb=" O GLU a 106 " (cutoff:3.500A) Processing helix chain 'a' and resid 114 through 135 Processing helix chain 'a' and resid 140 through 142 No H-bonds generated for 'chain 'a' and resid 140 through 142' Processing helix chain 'a' and resid 144 through 156 Processing helix chain 'a' and resid 163 through 179 removed outlier: 4.410A pdb=" N ASP a 166 " --> pdb=" O ILE a 163 " (cutoff:3.500A) removed outlier: 4.501A 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: 4.443A pdb=" N ASP a 261 " --> pdb=" O GLU a 258 " (cutoff:3.500A) removed outlier: 4.730A 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: 4.386A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) Processing helix chain 'a' and resid 434 through 455 removed outlier: 3.861A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N VAL a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N ILE a 448 " --> pdb=" O SER a 444 " (cutoff:3.500A) Proline residue: a 449 - end of helix Processing helix chain 'a' and resid 460 through 476 Processing helix chain 'a' and resid 481 through 485 removed outlier: 3.800A 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 144 Processing helix chain 'b' and resid 152 through 169 removed outlier: 4.494A pdb=" N SER b 169 " --> pdb=" O THR b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 171 through 190 removed outlier: 3.558A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS b 176 " --> pdb=" O THR b 173 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ASP b 177 " --> pdb=" O HIS b 174 " (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: 3.933A pdb=" N HIS b 285 " --> pdb=" O ARG b 281 " (cutoff:3.500A) Processing helix chain 'b' and resid 298 through 306 Processing helix chain 'b' and resid 317 through 327 Processing helix chain 'b' and resid 338 through 340 No H-bonds generated for 'chain 'b' and resid 338 through 340' Processing helix chain 'b' and resid 380 through 402 Processing helix chain 'b' and resid 412 through 426 Processing helix chain 'b' and resid 431 through 454 Proline residue: b 447 - end of helix removed outlier: 3.660A pdb=" N ALA b 454 " --> pdb=" O ILE b 450 " (cutoff:3.500A) Processing helix chain 'b' and resid 458 through 470 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: 3.644A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 132 through 150 Processing helix chain 'd' and resid 160 through 173 removed outlier: 4.523A pdb=" N SER d 173 " --> pdb=" O THR d 169 " (cutoff:3.500A) 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 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: 4.080A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.937A 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: 4.520A pdb=" N GLU d 334 " --> pdb=" O GLU d 331 " (cutoff:3.500A) removed outlier: 3.731A 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: 3.565A pdb=" N THR d 442 " --> pdb=" O GLU d 438 " (cutoff:3.500A) Processing helix chain 'd' and resid 446 through 466 removed outlier: 3.804A pdb=" N VAL d 460 " --> pdb=" O ASP d 456 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE d 461 " --> pdb=" O ALA d 457 " (cutoff:3.500A) Proline residue: d 462 - end of helix Processing helix chain 'd' and resid 473 through 485 Processing helix chain 'd' and resid 512 through 530 removed outlier: 4.923A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 51 removed outlier: 3.659A pdb=" N ARG e 49 " --> pdb=" O ASN e 46 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N THR e 50 " --> pdb=" O THR e 47 " (cutoff:3.500A) Processing helix chain 'e' and resid 74 through 80 Processing helix chain 'e' and resid 86 through 101 Processing helix chain 'e' and resid 108 through 126 removed outlier: 3.598A pdb=" N GLN e 122 " --> pdb=" O GLU e 118 " (cutoff:3.500A) removed outlier: 3.636A 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: 4.693A pdb=" N SER e 175 " --> pdb=" O THR e 171 " (cutoff:3.500A) Processing helix chain 'e' and resid 177 through 195 removed outlier: 3.978A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) removed outlier: 6.361A 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: 3.829A 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 438 Processing helix chain 'e' and resid 442 through 465 removed outlier: 3.954A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL e 457 " --> pdb=" O ASP e 453 " (cutoff:3.500A) removed outlier: 4.862A 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 528 Processing helix chain 'g' and resid 20 through 40 removed outlier: 3.834A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N THR g 39 " --> pdb=" O ASP g 35 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N CYS g 40 " --> pdb=" O ILE g 36 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 68 Processing helix chain 'g' and resid 75 through 90 Processing helix chain 'g' and resid 95 through 114 removed outlier: 3.795A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.750A 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 183 removed outlier: 3.943A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N SER g 170 " --> pdb=" O ARG g 167 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU g 171 " --> pdb=" O TRP g 168 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL g 183 " --> pdb=" O VAL g 180 " (cutoff:3.500A) 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: 4.315A pdb=" N LEU g 285 " --> pdb=" O ASP g 281 " (cutoff:3.500A) Processing helix chain 'g' and resid 298 through 307 removed outlier: 3.718A 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: 3.674A pdb=" N LYS g 427 " --> pdb=" O THR g 423 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ALA g 428 " --> pdb=" O GLU g 424 " (cutoff:3.500A) Processing helix chain 'g' and resid 434 through 455 removed outlier: 3.963A pdb=" N LEU g 444 " --> pdb=" O VAL g 440 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N GLU g 445 " --> pdb=" O ALA g 441 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N VAL g 446 " --> pdb=" O GLN g 442 " (cutoff:3.500A) removed outlier: 5.317A 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 36 removed outlier: 3.794A pdb=" N VAL h 36 " --> pdb=" O ILE h 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 68 Processing helix chain 'h' and resid 76 through 89 removed outlier: 3.587A pdb=" N GLU h 89 " --> pdb=" O GLN h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 113 removed outlier: 4.155A 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: 3.593A 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: 3.605A 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: 4.155A pdb=" N THR h 426 " --> pdb=" O ASP h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 430 through 453 removed outlier: 4.082A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU h 443 " --> pdb=" O ALA h 439 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE h 444 " --> pdb=" O LYS h 440 " (cutoff:3.500A) removed outlier: 5.234A 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 514 Processing helix chain 'q' and resid 11 through 14 No H-bonds generated for 'chain 'q' and resid 11 through 14' Processing helix chain 'q' and resid 25 through 46 removed outlier: 4.294A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) removed outlier: 5.768A 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: 4.230A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.183A 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 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: 4.851A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR q 286 " --> pdb=" O ALA q 282 " (cutoff:3.500A) Processing helix chain 'q' and resid 299 through 307 Processing helix chain 'q' and resid 318 through 328 Processing helix chain 'q' and resid 382 through 404 Processing helix chain 'q' and resid 414 through 429 removed outlier: 3.725A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 434 through 456 removed outlier: 3.753A pdb=" N PHE q 445 " --> pdb=" O PHE q 441 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU q 446 " --> pdb=" O ALA q 442 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ALA q 447 " --> pdb=" O GLU q 443 " (cutoff:3.500A) removed outlier: 4.871A 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 492 through 495 No H-bonds generated for 'chain 'q' and resid 492 through 495' Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'z' and resid 3 through 7 removed outlier: 3.561A pdb=" N LEU z 7 " --> pdb=" O ALA z 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 3 through 7' Processing helix chain 'z' and resid 17 through 37 removed outlier: 4.865A pdb=" N THR z 36 " --> pdb=" O ASP z 32 " (cutoff:3.500A) removed outlier: 4.952A 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: 3.681A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) removed outlier: 4.504A 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: 4.139A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 162 through 179 removed outlier: 3.617A 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: 4.238A pdb=" N ARG z 264 " --> pdb=" O VAL z 260 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LYS z 265 " --> pdb=" O LYS z 261 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHE z 266 " --> pdb=" O ALA z 262 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ILE z 267 " --> pdb=" O GLU z 263 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 299 through 308 removed outlier: 3.764A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 318 through 327 removed outlier: 4.297A 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 432 through 455 removed outlier: 3.711A pdb=" N ILE z 447 " --> pdb=" O LEU z 444 " (cutoff:3.500A) Proline residue: z 448 - end of helix Processing helix chain 'z' and resid 459 through 473 Processing helix chain 'z' and resid 489 through 492 No H-bonds generated for 'chain 'z' and resid 489 through 492' Processing helix chain 'z' and resid 498 through 516 Processing helix chain 'P' and resid 58 through 84 removed outlier: 4.892A pdb=" N ASN P 64 " --> pdb=" O LYS P 60 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ASP P 65 " --> pdb=" O GLY P 61 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 139 No H-bonds generated for 'chain 'P' and resid 137 through 139' Processing helix chain 'P' and resid 141 through 151 Processing helix chain 'P' and resid 167 through 175 Processing helix chain 'P' and resid 195 through 208 Processing helix chain 'P' and resid 219 through 222 No H-bonds generated for 'chain 'P' and resid 219 through 222' Processing helix chain 'P' and resid 226 through 231 Processing helix chain 'P' and resid 251 through 255 Processing helix chain 'P' and resid 261 through 271 removed outlier: 3.925A pdb=" N PHE P 271 " --> pdb=" O PHE P 267 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'N' and resid 242 through 244 removed outlier: 3.693A pdb=" N CYS N 242 " --> pdb=" O GLY N 257 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN N 275 " --> pdb=" O VAL N 265 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASP N 267 " --> pdb=" O CYS N 273 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N CYS N 273 " --> pdb=" O ASP N 267 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'N' and resid 221 through 223 removed outlier: 3.689A pdb=" N GLN N 231 " --> pdb=" O LEU N 221 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASP N 223 " --> pdb=" O LEU N 229 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU N 229 " --> pdb=" O ASP N 223 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 9 through 13 Processing sheet with id= D, first strand: chain 'A' and resid 43 through 46 Processing sheet with id= E, first strand: chain 'A' and resid 137 through 139 Processing sheet with id= F, first strand: chain 'A' and resid 196 through 199 Processing sheet with id= G, first strand: chain 'A' and resid 213 through 216 Processing sheet with id= H, first strand: chain 'A' and resid 346 through 348 removed outlier: 6.535A pdb=" N VAL A 285 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N LEU A 237 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU A 287 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N MET A 306 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N THR A 288 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL A 308 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 486 through 489 Processing sheet with id= J, first strand: chain 'B' and resid 17 through 19 Processing sheet with id= K, first strand: chain 'B' and resid 50 through 53 Processing sheet with id= L, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.373A pdb=" N CYS B 371 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE B 202 " --> pdb=" O CYS B 371 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ILE B 373 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LYS B 204 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LEU B 375 " --> pdb=" O LYS B 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'B' and resid 218 through 220 Processing sheet with id= N, first strand: chain 'B' and resid 344 through 346 removed outlier: 3.504A pdb=" N CYS B 346 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N CYS B 289 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ALA B 240 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ILE B 291 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N MET B 310 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ASN B 292 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE B 312 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 406 through 408 Processing sheet with id= P, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= Q, first strand: chain 'D' and resid 59 through 62 Processing sheet with id= R, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.778A pdb=" N VAL D 386 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N VAL D 211 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE D 388 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N LYS D 213 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N VAL D 390 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 227 through 229 Processing sheet with id= T, first strand: chain 'D' and resid 357 through 359 removed outlier: 6.883A pdb=" N VAL D 297 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N ILE D 249 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU D 299 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N MET D 323 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE D 300 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE D 325 " --> pdb=" O ILE D 300 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 421 through 423 Processing sheet with id= V, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.616A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 59 through 62 Processing sheet with id= X, first strand: chain 'E' and resid 209 through 215 removed outlier: 7.193A pdb=" N VAL E 383 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N GLU E 212 " --> pdb=" O VAL E 383 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ILE E 385 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N LYS E 214 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ILE E 387 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 228 through 230 Processing sheet with id= Z, first strand: chain 'E' and resid 354 through 356 removed outlier: 6.987A pdb=" N LEU E 299 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 418 through 420 Processing sheet with id= AB, first strand: chain 'G' and resid 15 through 17 Processing sheet with id= AC, first strand: chain 'G' and resid 48 through 51 Processing sheet with id= AD, first strand: chain 'G' and resid 185 through 187 Processing sheet with id= AE, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.640A pdb=" N CYS G 372 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N GLU G 202 " --> pdb=" O CYS G 372 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE G 374 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE G 204 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LEU G 376 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR G 373 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'G' and resid 238 through 241 removed outlier: 6.487A pdb=" N VAL G 289 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N LEU G 241 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE G 291 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N THR G 310 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N THR G 292 " --> pdb=" O THR G 310 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE G 312 " --> pdb=" O THR G 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'G' and resid 351 through 355 Processing sheet with id= AH, first strand: chain 'G' and resid 407 through 409 Processing sheet with id= AI, first strand: chain 'G' and resid 478 through 481 removed outlier: 3.718A pdb=" N THR G 486 " --> pdb=" O ASN G 481 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 14 through 17 Processing sheet with id= AK, first strand: chain 'H' and resid 47 through 50 Processing sheet with id= AL, first strand: chain 'H' and resid 195 through 201 removed outlier: 6.403A pdb=" N CYS H 370 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N LYS H 198 " --> pdb=" O CYS H 370 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N PHE H 372 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL H 200 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU H 374 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR H 371 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'H' and resid 214 through 217 Processing sheet with id= AN, first strand: chain 'H' and resid 342 through 344 removed outlier: 6.839A pdb=" N VAL H 288 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N LEU H 240 " --> pdb=" O VAL H 288 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU H 290 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE H 309 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N SER H 291 " --> pdb=" O PHE H 309 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA H 311 " --> pdb=" O SER H 291 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'H' and resid 405 through 407 Processing sheet with id= AP, first strand: chain 'H' and resid 475 through 478 Processing sheet with id= AQ, first strand: chain 'Q' and resid 20 through 23 Processing sheet with id= AR, first strand: chain 'Q' and resid 54 through 57 Processing sheet with id= AS, first strand: chain 'Q' and resid 202 through 208 removed outlier: 6.660A pdb=" N SER Q 373 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N CYS Q 205 " --> pdb=" O SER Q 373 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE Q 375 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N ILE Q 207 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU Q 377 " --> pdb=" O ILE Q 207 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Q' and resid 220 through 223 Processing sheet with id= AU, first strand: chain 'Q' and resid 240 through 242 removed outlier: 6.085A pdb=" N MET Q 311 " --> pdb=" O VAL Q 291 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N THR Q 293 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL Q 313 " --> pdb=" O THR Q 293 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'Q' and resid 498 through 500 removed outlier: 3.935A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N VAL Q 147 " --> pdb=" O PRO Q 410 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id= AX, first strand: chain 'Z' and resid 12 through 15 Processing sheet with id= AY, first strand: chain 'Z' and resid 45 through 48 Processing sheet with id= AZ, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.724A pdb=" N VAL Z 372 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N MET Z 194 " --> pdb=" O VAL Z 372 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N LEU Z 374 " --> pdb=" O MET Z 194 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N MET Z 196 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE Z 376 " --> pdb=" O MET Z 196 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER Z 205 " --> pdb=" O LEU Z 375 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id= BB, first strand: chain 'Z' and resid 345 through 347 Processing sheet with id= BC, first strand: chain 'Z' and resid 477 through 479 Processing sheet with id= BD, first strand: chain 'a' and resid 9 through 13 Processing sheet with id= BE, first strand: chain 'a' and resid 43 through 46 Processing sheet with id= BF, first strand: chain 'a' and resid 137 through 139 Processing sheet with id= BG, first strand: chain 'a' and resid 180 through 182 Processing sheet with id= BH, first strand: chain 'a' and resid 196 through 201 removed outlier: 3.547A pdb=" N GLY a 379 " --> pdb=" O ALA a 200 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'a' and resid 213 through 216 Processing sheet with id= BJ, first strand: chain 'a' and resid 346 through 348 removed outlier: 6.544A pdb=" N VAL a 285 " --> pdb=" O ALA a 235 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N LEU a 237 " --> pdb=" O VAL a 285 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU a 287 " --> pdb=" O LEU a 237 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N MET a 306 " --> pdb=" O ILE a 286 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N THR a 288 " --> pdb=" O MET a 306 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N VAL a 308 " --> pdb=" O THR a 288 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'a' and resid 486 through 489 Processing sheet with id= BL, first strand: chain 'b' and resid 17 through 19 Processing sheet with id= BM, first strand: chain 'b' and resid 50 through 53 Processing sheet with id= BN, first strand: chain 'b' and resid 199 through 205 removed outlier: 6.260A pdb=" N CYS b 371 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE b 202 " --> pdb=" O CYS b 371 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE b 373 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LYS b 204 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LEU b 375 " --> pdb=" O LYS b 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= BN Processing sheet with id= BO, first strand: chain 'b' and resid 218 through 220 Processing sheet with id= BP, first strand: chain 'b' and resid 344 through 346 removed outlier: 3.542A pdb=" N CYS b 346 " --> pdb=" O ALA b 235 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N CYS b 289 " --> pdb=" O LEU b 238 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N ALA b 240 " --> pdb=" O CYS b 289 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE b 291 " --> pdb=" O ALA b 240 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N MET b 310 " --> pdb=" O PHE b 290 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ASN b 292 " --> pdb=" O MET b 310 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ILE b 312 " --> pdb=" O ASN b 292 " (cutoff:3.500A) Processing sheet with id= BQ, first strand: chain 'b' and resid 406 through 408 Processing sheet with id= BR, first strand: chain 'b' and resid 476 through 479 Processing sheet with id= BS, first strand: chain 'd' and resid 59 through 62 Processing sheet with id= BT, first strand: chain 'd' and resid 208 through 214 removed outlier: 6.707A pdb=" N VAL d 386 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL d 211 " --> pdb=" O VAL d 386 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILE d 388 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LYS d 213 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL d 390 " --> pdb=" O LYS d 213 " (cutoff:3.500A) No H-bonds generated for sheet with id= BT Processing sheet with id= BU, first strand: chain 'd' and resid 227 through 229 Processing sheet with id= BV, first strand: chain 'd' and resid 357 through 359 removed outlier: 6.585A pdb=" N VAL d 297 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N ILE d 249 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU d 299 " --> pdb=" O ILE d 249 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N MET d 323 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE d 300 " --> pdb=" O MET d 323 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE d 325 " --> pdb=" O ILE d 300 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'd' and resid 421 through 423 Processing sheet with id= BX, first strand: chain 'd' and resid 491 through 494 Processing sheet with id= BY, first strand: chain 'e' and resid 26 through 29 Processing sheet with id= BZ, first strand: chain 'e' and resid 59 through 62 Processing sheet with id= CA, first strand: chain 'e' and resid 209 through 215 removed outlier: 6.987A pdb=" N VAL e 383 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N GLU e 212 " --> pdb=" O VAL e 383 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILE e 385 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N LYS e 214 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE e 387 " --> pdb=" O LYS e 214 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'e' and resid 228 through 230 Processing sheet with id= CC, first strand: chain 'e' and resid 354 through 356 removed outlier: 7.077A pdb=" N LEU e 299 " --> pdb=" O ALA e 249 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU e 251 " --> pdb=" O LEU e 299 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ILE e 301 " --> pdb=" O LEU e 251 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N CYS e 302 " --> pdb=" O PRO e 320 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL e 322 " --> pdb=" O CYS e 302 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'e' and resid 418 through 420 Processing sheet with id= CE, first strand: chain 'g' and resid 15 through 18 Processing sheet with id= CF, first strand: chain 'g' and resid 48 through 51 Processing sheet with id= CG, first strand: chain 'g' and resid 185 through 187 Processing sheet with id= CH, first strand: chain 'g' and resid 200 through 205 removed outlier: 3.968A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'g' and resid 218 through 220 Processing sheet with id= CJ, first strand: chain 'g' and resid 238 through 241 removed outlier: 6.506A pdb=" N VAL g 289 " --> pdb=" O VAL g 239 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LEU g 241 " --> pdb=" O VAL g 289 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE g 291 " --> pdb=" O LEU g 241 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N THR g 310 " --> pdb=" O VAL g 290 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N THR g 292 " --> pdb=" O THR g 310 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE g 312 " --> pdb=" O THR g 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= CJ Processing sheet with id= CK, first strand: chain 'g' and resid 407 through 409 Processing sheet with id= CL, first strand: chain 'g' and resid 478 through 481 removed outlier: 3.713A pdb=" N THR g 486 " --> pdb=" O ASN g 481 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'h' and resid 14 through 17 Processing sheet with id= CN, first strand: chain 'h' and resid 47 through 50 Processing sheet with id= CO, first strand: chain 'h' and resid 195 through 201 removed outlier: 6.615A pdb=" N CYS h 370 " --> pdb=" O GLY h 196 " (cutoff:3.500A) removed outlier: 7.973A pdb=" N LYS h 198 " --> pdb=" O CYS h 370 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE h 372 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL h 200 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU h 374 " --> pdb=" O VAL h 200 " (cutoff:3.500A) Processing sheet with id= CP, first strand: chain 'h' and resid 214 through 217 Processing sheet with id= CQ, first strand: chain 'h' and resid 237 through 240 removed outlier: 6.992A pdb=" N VAL h 288 " --> pdb=" O ALA h 238 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU h 240 " --> pdb=" O VAL h 288 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LEU h 290 " --> pdb=" O LEU h 240 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N PHE h 309 " --> pdb=" O VAL h 289 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N SER h 291 " --> pdb=" O PHE h 309 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA h 311 " --> pdb=" O SER h 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= CQ Processing sheet with id= CR, first strand: chain 'h' and resid 405 through 407 Processing sheet with id= CS, first strand: chain 'h' and resid 475 through 478 Processing sheet with id= CT, first strand: chain 'q' and resid 20 through 23 Processing sheet with id= CU, first strand: chain 'q' and resid 54 through 57 Processing sheet with id= CV, first strand: chain 'q' and resid 202 through 208 removed outlier: 6.557A pdb=" N SER q 373 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N CYS q 205 " --> pdb=" O SER q 373 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE q 375 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N ILE q 207 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N LEU q 377 " --> pdb=" O ILE q 207 " (cutoff:3.500A) Processing sheet with id= CW, first strand: chain 'q' and resid 220 through 223 Processing sheet with id= CX, first strand: chain 'q' and resid 240 through 242 removed outlier: 6.070A pdb=" N MET q 311 " --> pdb=" O VAL q 291 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N THR q 293 " --> pdb=" O MET q 311 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL q 313 " --> pdb=" O THR q 293 " (cutoff:3.500A) Processing sheet with id= CY, first strand: chain 'q' and resid 498 through 500 removed outlier: 3.812A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) removed outlier: 8.470A pdb=" N VAL q 147 " --> pdb=" O PRO q 410 " (cutoff:3.500A) Processing sheet with id= CZ, first strand: chain 'q' and resid 478 through 480 Processing sheet with id= DA, first strand: chain 'z' and resid 12 through 15 Processing sheet with id= DB, first strand: chain 'z' and resid 45 through 48 Processing sheet with id= DC, first strand: chain 'z' and resid 191 through 196 removed outlier: 6.872A pdb=" N VAL z 372 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N MET z 194 " --> pdb=" O VAL z 372 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N LEU z 374 " --> pdb=" O MET z 194 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N MET z 196 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ILE z 376 " --> pdb=" O MET z 196 " (cutoff:3.500A) Processing sheet with id= DD, first strand: chain 'z' and resid 210 through 212 Processing sheet with id= DE, first strand: chain 'z' and resid 345 through 347 Processing sheet with id= DF, first strand: chain 'z' and resid 477 through 479 Processing sheet with id= DG, first strand: chain 'P' and resid 162 through 164 removed outlier: 4.611A pdb=" N LYS P 218 " --> pdb=" O ILE P 164 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA P 235 " --> pdb=" O ILE P 187 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LYS P 240 " --> pdb=" O LEU P 244 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU P 244 " --> pdb=" O LYS P 240 " (cutoff:3.500A) 3480 hydrogen bonds defined for protein. 9180 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 28.85 Time building geometry restraints manager: 23.41 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: 22621 1.34 - 1.46: 11837 1.46 - 1.58: 32719 1.58 - 1.70: 48 1.70 - 1.81: 735 Bond restraints: 67960 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 6.54e+01 bond pdb=" F2 AF3 Z 603 " pdb="AL AF3 Z 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.42e+01 bond pdb=" F2 AF3 D 603 " pdb="AL AF3 D 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.39e+01 bond pdb=" F2 AF3 d 603 " pdb="AL AF3 d 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.39e+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 ... (remaining 67955 not shown) Histogram of bond angle deviations from ideal: 98.26 - 105.89: 1222 105.89 - 113.51: 39718 113.51 - 121.14: 33495 121.14 - 128.76: 17025 128.76 - 136.39: 295 Bond angle restraints: 91755 Sorted by residual: angle pdb=" CA ARG P 149 " pdb=" CB ARG P 149 " pdb=" CG ARG P 149 " ideal model delta sigma weight residual 114.10 123.76 -9.66 2.00e+00 2.50e-01 2.33e+01 angle pdb=" C MET P 148 " pdb=" N ARG P 149 " pdb=" CA ARG P 149 " ideal model delta sigma weight residual 121.14 115.09 6.05 1.75e+00 3.27e-01 1.20e+01 angle pdb=" N GLY Q 209 " pdb=" CA GLY Q 209 " pdb=" C GLY Q 209 " ideal model delta sigma weight residual 113.18 120.95 -7.77 2.37e+00 1.78e-01 1.07e+01 angle pdb=" N GLY q 209 " pdb=" CA GLY q 209 " pdb=" C GLY q 209 " ideal model delta sigma weight residual 113.18 120.80 -7.62 2.37e+00 1.78e-01 1.03e+01 angle pdb=" C CYS E 181 " pdb=" N HIS E 182 " pdb=" CA HIS E 182 " ideal model delta sigma weight residual 121.54 127.28 -5.74 1.91e+00 2.74e-01 9.02e+00 ... (remaining 91750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 41312 35.66 - 71.32: 624 71.32 - 106.98: 63 106.98 - 142.63: 11 142.63 - 178.29: 8 Dihedral angle restraints: 42018 sinusoidal: 16924 harmonic: 25094 Sorted by residual: 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 -60.00 118.29 -178.29 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP Q 601 " pdb=" O3A ADP Q 601 " pdb=" PA ADP Q 601 " pdb=" PB ADP Q 601 " ideal model delta sinusoidal sigma weight residual 300.00 123.46 176.54 1 2.00e+01 2.50e-03 4.80e+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 300.00 127.50 172.50 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 42015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 8475 0.045 - 0.090: 1758 0.090 - 0.135: 679 0.135 - 0.179: 10 0.179 - 0.224: 1 Chirality restraints: 10923 Sorted by residual: chirality pdb=" CA ARG P 149 " pdb=" N ARG P 149 " pdb=" C ARG P 149 " pdb=" CB ARG P 149 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ILE g 363 " pdb=" N ILE g 363 " pdb=" C ILE g 363 " pdb=" CB ILE g 363 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CB ILE G 460 " pdb=" CA ILE G 460 " pdb=" CG1 ILE G 460 " pdb=" CG2 ILE G 460 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.47e-01 ... (remaining 10920 not shown) Planarity restraints: 11716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.033 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO e 441 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET H 2 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO H 3 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO H 3 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 3 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU P 274 " 0.024 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO P 275 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO P 275 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO P 275 " 0.021 5.00e-02 4.00e+02 ... (remaining 11713 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 567 2.54 - 3.13: 52285 3.13 - 3.72: 106746 3.72 - 4.31: 151359 4.31 - 4.90: 256039 Nonbonded interactions: 566996 Sorted by model distance: nonbonded pdb="MG MG D 602 " pdb=" F2 AF3 D 603 " model vdw 1.955 2.120 nonbonded pdb="MG MG H 602 " pdb=" F2 AF3 H 603 " model vdw 1.957 2.120 nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.971 2.120 nonbonded pdb="MG MG d 602 " pdb=" F1 AF3 d 603 " model vdw 1.971 2.120 nonbonded pdb="MG MG e 602 " pdb=" F1 AF3 e 603 " model vdw 1.987 2.120 ... (remaining 566991 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' selection = (chain 'g' and (resid 3 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: 1.180 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: 0.060 Extract box with map and model: 8.300 Check model and map are aligned: 0.790 Set scattering table: 0.470 Process input model: 150.910 Find NCS groups from input model: 6.770 Set up NCS constraints: 0.700 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: 0.010 Load rotamer database and sin/cos tables:10.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 179.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 67960 Z= 0.276 Angle : 0.521 9.658 91755 Z= 0.254 Chirality : 0.041 0.224 10923 Planarity : 0.003 0.051 11716 Dihedral : 14.495 178.292 25766 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: 1.77 (0.09), residues: 8685 helix: 2.33 (0.08), residues: 4481 sheet: 0.55 (0.16), residues: 1109 loop : -0.28 (0.11), residues: 3095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g 168 HIS 0.007 0.001 HIS z 161 PHE 0.019 0.001 PHE e 386 TYR 0.015 0.001 TYR b 297 ARG 0.007 0.000 ARG e 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 606 time to evaluate : 6.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLN cc_start: 0.8734 (mm110) cc_final: 0.8301 (pm20) REVERT: G 15 LYS cc_start: 0.8634 (mmtm) cc_final: 0.8393 (mmtt) REVERT: G 52 ASP cc_start: 0.8311 (t70) cc_final: 0.7583 (t0) REVERT: G 54 MET cc_start: 0.8158 (mpp) cc_final: 0.7777 (mpt) REVERT: G 497 GLU cc_start: 0.8370 (pt0) cc_final: 0.8128 (pt0) REVERT: H 14 ASP cc_start: 0.8445 (t0) cc_final: 0.8200 (t0) REVERT: H 81 ASP cc_start: 0.8430 (m-30) cc_final: 0.8065 (m-30) REVERT: H 185 MET cc_start: 0.8635 (mtp) cc_final: 0.8417 (mtp) REVERT: H 316 GLU cc_start: 0.8142 (tt0) cc_final: 0.7831 (tp30) REVERT: H 324 MET cc_start: 0.9172 (mmm) cc_final: 0.8905 (mmm) REVERT: Q 34 GLN cc_start: 0.7921 (tp-100) cc_final: 0.7506 (tp-100) REVERT: Z 10 LYS cc_start: 0.8899 (mtmm) cc_final: 0.8688 (mtmm) REVERT: Z 108 LEU cc_start: 0.9113 (tp) cc_final: 0.8907 (tp) REVERT: e 20 LYS cc_start: 0.8769 (ttmt) cc_final: 0.8567 (ttmm) REVERT: h 401 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7723 (tmmt) REVERT: h 440 LYS cc_start: 0.9049 (ttmt) cc_final: 0.8849 (ttmm) REVERT: z 53 ASP cc_start: 0.8614 (m-30) cc_final: 0.8338 (m-30) REVERT: z 472 GLU cc_start: 0.8334 (tm-30) cc_final: 0.8127 (tp30) REVERT: P 80 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8336 (mm-40) REVERT: P 231 ASN cc_start: 0.8140 (p0) cc_final: 0.7475 (p0) outliers start: 0 outliers final: 0 residues processed: 606 average time/residue: 1.6742 time to fit residues: 1289.5007 Evaluate side-chains 499 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 499 time to evaluate : 7.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 729 optimal weight: 10.0000 chunk 654 optimal weight: 0.4980 chunk 363 optimal weight: 0.0970 chunk 223 optimal weight: 6.9990 chunk 441 optimal weight: 8.9990 chunk 349 optimal weight: 9.9990 chunk 677 optimal weight: 2.9990 chunk 262 optimal weight: 2.9990 chunk 411 optimal weight: 1.9990 chunk 504 optimal weight: 0.8980 chunk 784 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 231 GLN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 366 ASN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 394 ASN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.0560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 67960 Z= 0.156 Angle : 0.519 8.512 91755 Z= 0.257 Chirality : 0.040 0.165 10923 Planarity : 0.004 0.051 11716 Dihedral : 7.728 179.167 9433 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.65 % Allowed : 5.91 % Favored : 93.45 % 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: 1.61 (0.09), residues: 8685 helix: 2.15 (0.08), residues: 4482 sheet: 0.53 (0.16), residues: 1082 loop : -0.29 (0.11), residues: 3121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP P 66 HIS 0.008 0.001 HIS z 161 PHE 0.021 0.001 PHE P 69 TYR 0.025 0.001 TYR A 181 ARG 0.009 0.000 ARG P 250 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 530 time to evaluate : 6.233 Fit side-chains REVERT: N 267 ASP cc_start: 0.7516 (t70) cc_final: 0.7115 (t0) REVERT: A 187 GLN cc_start: 0.8759 (mm110) cc_final: 0.8342 (pm20) REVERT: D 458 MET cc_start: 0.8384 (mmm) cc_final: 0.8163 (mmm) REVERT: G 52 ASP cc_start: 0.8342 (t70) cc_final: 0.7622 (t0) REVERT: G 54 MET cc_start: 0.8199 (mpp) cc_final: 0.7915 (mpt) REVERT: G 151 MET cc_start: 0.8583 (mmm) cc_final: 0.8117 (mmm) REVERT: G 497 GLU cc_start: 0.8316 (pt0) cc_final: 0.8096 (pt0) REVERT: H 14 ASP cc_start: 0.8377 (t0) cc_final: 0.8084 (t0) REVERT: H 81 ASP cc_start: 0.8342 (m-30) cc_final: 0.8073 (m-30) REVERT: H 185 MET cc_start: 0.8648 (mtp) cc_final: 0.8330 (mtp) REVERT: H 316 GLU cc_start: 0.8210 (tt0) cc_final: 0.7708 (tp30) REVERT: H 324 MET cc_start: 0.9168 (mmm) cc_final: 0.8885 (mmm) REVERT: Q 34 GLN cc_start: 0.7902 (tp-100) cc_final: 0.7496 (tp-100) REVERT: Z 353 TYR cc_start: 0.9003 (t80) cc_final: 0.8768 (t80) REVERT: a 66 GLU cc_start: 0.8570 (tt0) cc_final: 0.8355 (pt0) REVERT: a 246 MET cc_start: 0.9118 (mmm) cc_final: 0.8832 (mmt) REVERT: e 20 LYS cc_start: 0.8791 (ttmt) cc_final: 0.8582 (ttmm) REVERT: e 32 GLU cc_start: 0.7545 (mm-30) cc_final: 0.7338 (mm-30) REVERT: e 160 LYS cc_start: 0.9284 (OUTLIER) cc_final: 0.9026 (mtmm) REVERT: g 306 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7521 (mtm-85) REVERT: g 521 ASP cc_start: 0.8374 (t0) cc_final: 0.8132 (t0) REVERT: g 528 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8455 (tmmt) REVERT: h 221 SER cc_start: 0.9087 (m) cc_final: 0.8806 (p) REVERT: h 401 LYS cc_start: 0.8050 (mmtt) cc_final: 0.7683 (tmmt) REVERT: h 440 LYS cc_start: 0.9045 (ttmt) cc_final: 0.8838 (ttmm) REVERT: q 61 GLU cc_start: 0.8610 (mp0) cc_final: 0.8022 (mp0) REVERT: z 46 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8359 (ttt) REVERT: z 53 ASP cc_start: 0.8604 (m-30) cc_final: 0.8344 (m-30) REVERT: z 352 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8201 (tt0) REVERT: P 145 MET cc_start: 0.8712 (ppp) cc_final: 0.8398 (ppp) outliers start: 47 outliers final: 11 residues processed: 549 average time/residue: 1.6483 time to fit residues: 1156.3771 Evaluate side-chains 512 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 496 time to evaluate : 6.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 266 MET Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain e residue 23 ASP Chi-restraints excluded: chain e residue 160 LYS Chi-restraints excluded: chain e residue 212 GLU Chi-restraints excluded: chain g residue 255 ASP Chi-restraints excluded: chain g residue 306 ARG Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain z residue 46 MET Chi-restraints excluded: chain z residue 352 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 436 optimal weight: 0.9980 chunk 243 optimal weight: 5.9990 chunk 653 optimal weight: 0.8980 chunk 534 optimal weight: 0.9980 chunk 216 optimal weight: 10.0000 chunk 786 optimal weight: 0.8980 chunk 849 optimal weight: 6.9990 chunk 700 optimal weight: 5.9990 chunk 779 optimal weight: 9.9990 chunk 267 optimal weight: 8.9990 chunk 630 optimal weight: 10.0000 overall best weight: 1.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS D 366 ASN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 501 ASN Z 84 GLN Z 161 HIS e 515 GLN z 84 GLN z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.0662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 67960 Z= 0.211 Angle : 0.521 9.605 91755 Z= 0.256 Chirality : 0.041 0.168 10923 Planarity : 0.004 0.067 11716 Dihedral : 7.523 178.737 9433 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.76 % Allowed : 7.52 % Favored : 91.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.09), residues: 8685 helix: 2.04 (0.08), residues: 4478 sheet: 0.45 (0.16), residues: 1090 loop : -0.30 (0.11), residues: 3117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g 168 HIS 0.010 0.001 HIS z 161 PHE 0.016 0.001 PHE e 386 TYR 0.027 0.001 TYR A 181 ARG 0.009 0.000 ARG e 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 519 time to evaluate : 6.348 Fit side-chains revert: symmetry clash REVERT: N 267 ASP cc_start: 0.7466 (t70) cc_final: 0.7130 (t0) REVERT: A 187 GLN cc_start: 0.8762 (mm110) cc_final: 0.8309 (pm20) REVERT: B 77 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7948 (p0) REVERT: E 393 MET cc_start: 0.8734 (mpt) cc_final: 0.8388 (mpt) REVERT: G 15 LYS cc_start: 0.8441 (mmmt) cc_final: 0.8179 (mmmt) REVERT: G 52 ASP cc_start: 0.8349 (t70) cc_final: 0.7676 (t0) REVERT: G 54 MET cc_start: 0.8201 (mpp) cc_final: 0.7933 (mpt) REVERT: G 151 MET cc_start: 0.8677 (mmm) cc_final: 0.8191 (mmm) REVERT: G 497 GLU cc_start: 0.8360 (pt0) cc_final: 0.8120 (pt0) REVERT: H 14 ASP cc_start: 0.8367 (t0) cc_final: 0.8052 (t0) REVERT: H 17 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8266 (pp30) REVERT: H 81 ASP cc_start: 0.8330 (m-30) cc_final: 0.8061 (m-30) REVERT: H 185 MET cc_start: 0.8733 (mtp) cc_final: 0.8356 (mtp) REVERT: H 316 GLU cc_start: 0.8133 (tt0) cc_final: 0.7828 (tp30) REVERT: H 324 MET cc_start: 0.9170 (mmm) cc_final: 0.8880 (mmm) REVERT: Q 34 GLN cc_start: 0.7934 (tp-100) cc_final: 0.7540 (tp-100) REVERT: Q 55 MET cc_start: 0.8764 (mtt) cc_final: 0.8521 (mtt) REVERT: a 246 MET cc_start: 0.9163 (mmm) cc_final: 0.8870 (mmt) REVERT: e 20 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8574 (ttmm) REVERT: e 32 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7335 (mm-30) REVERT: e 160 LYS cc_start: 0.9267 (OUTLIER) cc_final: 0.9017 (mtmm) REVERT: g 229 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8488 (mtt) REVERT: g 306 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7585 (mtm-85) REVERT: g 521 ASP cc_start: 0.8365 (t0) cc_final: 0.8122 (t0) REVERT: g 528 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8358 (tmmt) REVERT: h 221 SER cc_start: 0.9123 (m) cc_final: 0.8867 (p) REVERT: h 401 LYS cc_start: 0.8025 (mmtt) cc_final: 0.7692 (tmmt) REVERT: h 440 LYS cc_start: 0.9053 (ttmt) cc_final: 0.8841 (ttmm) REVERT: q 61 GLU cc_start: 0.8510 (mp0) cc_final: 0.8038 (mp0) REVERT: z 53 ASP cc_start: 0.8616 (m-30) cc_final: 0.8341 (m-30) REVERT: P 77 ARG cc_start: 0.8090 (tmm160) cc_final: 0.7828 (tmm160) REVERT: P 141 ARG cc_start: 0.8995 (mmt-90) cc_final: 0.8739 (mpp-170) REVERT: P 250 ARG cc_start: 0.7450 (mmm-85) cc_final: 0.7147 (tpp80) outliers start: 55 outliers final: 17 residues processed: 543 average time/residue: 1.6308 time to fit residues: 1137.3851 Evaluate side-chains 519 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 496 time to evaluate : 6.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 264 MET Chi-restraints excluded: chain N residue 270 SER 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 H residue 17 GLN Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain e residue 23 ASP Chi-restraints excluded: chain e residue 160 LYS Chi-restraints excluded: chain e residue 212 GLU Chi-restraints excluded: chain g residue 229 MET Chi-restraints excluded: chain g residue 306 ARG Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 21 GLN Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 499 ASP Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain z residue 311 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 776 optimal weight: 7.9990 chunk 590 optimal weight: 5.9990 chunk 407 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 375 optimal weight: 0.0970 chunk 527 optimal weight: 6.9990 chunk 788 optimal weight: 8.9990 chunk 835 optimal weight: 0.9980 chunk 412 optimal weight: 0.9990 chunk 747 optimal weight: 3.9990 chunk 225 optimal weight: 6.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 366 ASN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 501 ASN Z 161 HIS z 84 GLN z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 67960 Z= 0.170 Angle : 0.508 10.063 91755 Z= 0.249 Chirality : 0.040 0.168 10923 Planarity : 0.003 0.052 11716 Dihedral : 7.311 179.641 9433 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.81 % Allowed : 8.51 % Favored : 90.68 % 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: 8685 helix: 2.04 (0.08), residues: 4482 sheet: 0.40 (0.16), residues: 1094 loop : -0.30 (0.11), residues: 3109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g 168 HIS 0.012 0.001 HIS Z 161 PHE 0.012 0.001 PHE P 69 TYR 0.011 0.001 TYR z 351 ARG 0.009 0.000 ARG e 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 520 time to evaluate : 6.421 Fit side-chains revert: symmetry clash REVERT: N 267 ASP cc_start: 0.7364 (t70) cc_final: 0.7060 (t0) REVERT: A 187 GLN cc_start: 0.8758 (mm110) cc_final: 0.8315 (pm20) REVERT: A 306 MET cc_start: 0.8234 (mtt) cc_final: 0.7936 (mtt) REVERT: A 360 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7942 (mt-10) REVERT: B 77 ASP cc_start: 0.8147 (OUTLIER) cc_final: 0.7945 (p0) REVERT: D 145 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8869 (mm) REVERT: E 393 MET cc_start: 0.8722 (mpt) cc_final: 0.8388 (mpt) REVERT: G 15 LYS cc_start: 0.8412 (mmmt) cc_final: 0.8195 (mmmt) REVERT: G 47 MET cc_start: 0.8803 (OUTLIER) cc_final: 0.8296 (mtm) REVERT: G 52 ASP cc_start: 0.8317 (t70) cc_final: 0.7653 (t0) REVERT: G 54 MET cc_start: 0.8209 (mpp) cc_final: 0.7933 (mpt) REVERT: G 151 MET cc_start: 0.8673 (mmm) cc_final: 0.8157 (mmm) REVERT: G 497 GLU cc_start: 0.8332 (pt0) cc_final: 0.8112 (pt0) REVERT: H 14 ASP cc_start: 0.8366 (t0) cc_final: 0.8045 (t0) REVERT: H 81 ASP cc_start: 0.8314 (m-30) cc_final: 0.8078 (m-30) REVERT: H 185 MET cc_start: 0.8704 (mtp) cc_final: 0.8388 (mtp) REVERT: H 316 GLU cc_start: 0.8207 (tt0) cc_final: 0.7691 (tp30) REVERT: H 324 MET cc_start: 0.9155 (mmm) cc_final: 0.8861 (mmm) REVERT: Q 34 GLN cc_start: 0.7918 (tp-100) cc_final: 0.7533 (tp-100) REVERT: Q 55 MET cc_start: 0.8739 (mtt) cc_final: 0.8535 (mtt) REVERT: e 20 LYS cc_start: 0.8787 (ttmt) cc_final: 0.8567 (ttmm) REVERT: e 32 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7271 (mm-30) REVERT: e 160 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.9042 (mtmm) REVERT: g 229 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8654 (mtt) REVERT: g 306 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7528 (mtm-85) REVERT: g 521 ASP cc_start: 0.8333 (t0) cc_final: 0.8114 (t0) REVERT: g 528 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8377 (tmmt) REVERT: h 221 SER cc_start: 0.9123 (m) cc_final: 0.8883 (p) REVERT: h 401 LYS cc_start: 0.8060 (mmtt) cc_final: 0.7736 (tmmt) REVERT: h 440 LYS cc_start: 0.9046 (ttmt) cc_final: 0.8834 (ttmm) REVERT: q 61 GLU cc_start: 0.8486 (mp0) cc_final: 0.8049 (mp0) REVERT: q 318 LYS cc_start: 0.8711 (pptt) cc_final: 0.8233 (pptt) REVERT: z 53 ASP cc_start: 0.8603 (m-30) cc_final: 0.8335 (m-30) REVERT: P 80 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8096 (mm-40) REVERT: P 141 ARG cc_start: 0.8976 (mmt-90) cc_final: 0.8709 (mtm-85) REVERT: P 231 ASN cc_start: 0.8425 (OUTLIER) cc_final: 0.7846 (p0) outliers start: 59 outliers final: 21 residues processed: 550 average time/residue: 1.6191 time to fit residues: 1150.2038 Evaluate side-chains 526 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 497 time to evaluate : 6.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 145 ILE Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 266 MET Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain e residue 23 ASP Chi-restraints excluded: chain e residue 160 LYS Chi-restraints excluded: chain e residue 212 GLU Chi-restraints excluded: chain g residue 229 MET Chi-restraints excluded: chain g residue 255 ASP Chi-restraints excluded: chain g residue 306 ARG Chi-restraints excluded: chain g residue 350 LEU Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 21 GLN Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 366 LYS Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 499 ASP Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain P residue 184 MET Chi-restraints excluded: chain P residue 231 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 695 optimal weight: 7.9990 chunk 474 optimal weight: 8.9990 chunk 12 optimal weight: 4.9990 chunk 621 optimal weight: 7.9990 chunk 344 optimal weight: 8.9990 chunk 712 optimal weight: 0.9990 chunk 577 optimal weight: 0.9980 chunk 0 optimal weight: 30.0000 chunk 426 optimal weight: 8.9990 chunk 749 optimal weight: 3.9990 chunk 210 optimal weight: 10.0000 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN H 501 ASN Z 161 HIS ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 390 ASN z 84 GLN z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 67960 Z= 0.362 Angle : 0.581 10.449 91755 Z= 0.286 Chirality : 0.043 0.167 10923 Planarity : 0.004 0.052 11716 Dihedral : 7.401 179.291 9433 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.09 % Allowed : 9.08 % Favored : 89.83 % 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: 8685 helix: 1.86 (0.08), residues: 4511 sheet: 0.35 (0.16), residues: 1115 loop : -0.37 (0.11), residues: 3059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g 168 HIS 0.016 0.001 HIS Z 161 PHE 0.018 0.002 PHE H 220 TYR 0.031 0.001 TYR A 181 ARG 0.008 0.000 ARG P 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 497 time to evaluate : 6.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 267 ASP cc_start: 0.7586 (t0) cc_final: 0.7298 (t0) REVERT: A 187 GLN cc_start: 0.8812 (mm110) cc_final: 0.8299 (pm20) REVERT: B 77 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7984 (p0) REVERT: G 15 LYS cc_start: 0.8450 (mmmt) cc_final: 0.8220 (mmmt) REVERT: G 52 ASP cc_start: 0.8330 (t70) cc_final: 0.7718 (t0) REVERT: G 54 MET cc_start: 0.8164 (mpp) cc_final: 0.7735 (mpt) REVERT: G 151 MET cc_start: 0.8768 (mmm) cc_final: 0.8437 (mmm) REVERT: G 497 GLU cc_start: 0.8452 (pt0) cc_final: 0.8183 (pt0) REVERT: H 14 ASP cc_start: 0.8414 (t0) cc_final: 0.8054 (t0) REVERT: H 17 GLN cc_start: 0.8536 (OUTLIER) cc_final: 0.8291 (pp30) REVERT: H 81 ASP cc_start: 0.8292 (m-30) cc_final: 0.8068 (m-30) REVERT: H 185 MET cc_start: 0.8796 (mtp) cc_final: 0.8438 (mtp) REVERT: H 316 GLU cc_start: 0.8178 (tt0) cc_final: 0.7873 (tp30) REVERT: H 324 MET cc_start: 0.9175 (mmm) cc_final: 0.8902 (mmm) REVERT: Q 27 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8258 (mt-10) REVERT: Q 34 GLN cc_start: 0.7987 (tp-100) cc_final: 0.7652 (tp-100) REVERT: Q 55 MET cc_start: 0.8790 (mtt) cc_final: 0.8564 (mtt) REVERT: Z 364 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8418 (mt-10) REVERT: a 156 MET cc_start: 0.9095 (mtp) cc_final: 0.8772 (mtm) REVERT: d 340 ILE cc_start: 0.9261 (mt) cc_final: 0.9023 (mm) REVERT: e 20 LYS cc_start: 0.8787 (ttmt) cc_final: 0.8576 (ttmm) REVERT: e 160 LYS cc_start: 0.9265 (OUTLIER) cc_final: 0.9021 (mtmm) REVERT: g 59 MET cc_start: 0.9186 (ttp) cc_final: 0.8948 (ttp) REVERT: g 306 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.7624 (mtm-85) REVERT: g 521 ASP cc_start: 0.8376 (t0) cc_final: 0.8132 (t0) REVERT: g 528 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8330 (tmmt) REVERT: h 356 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: h 401 LYS cc_start: 0.8210 (mmtt) cc_final: 0.7838 (tmmt) REVERT: h 440 LYS cc_start: 0.9064 (ttmt) cc_final: 0.8864 (ttmm) REVERT: q 61 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: q 152 LYS cc_start: 0.9352 (OUTLIER) cc_final: 0.9114 (ptmm) REVERT: z 53 ASP cc_start: 0.8575 (m-30) cc_final: 0.8353 (m-30) REVERT: P 77 ARG cc_start: 0.8269 (tmm160) cc_final: 0.8040 (tmm160) REVERT: P 80 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8163 (mm-40) REVERT: P 202 MET cc_start: 0.9353 (mtp) cc_final: 0.9108 (mtm) REVERT: P 231 ASN cc_start: 0.8283 (OUTLIER) cc_final: 0.7818 (p0) outliers start: 79 outliers final: 30 residues processed: 543 average time/residue: 1.6167 time to fit residues: 1124.7632 Evaluate side-chains 531 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 491 time to evaluate : 6.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 264 MET Chi-restraints excluded: chain N residue 270 SER Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain B residue 6 LEU 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 D residue 69 THR Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 266 MET Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Q residue 526 MET Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 354 THR Chi-restraints excluded: chain Z residue 364 GLU Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 485 ILE Chi-restraints excluded: chain e residue 23 ASP Chi-restraints excluded: chain e residue 160 LYS Chi-restraints excluded: chain e residue 212 GLU Chi-restraints excluded: chain g residue 306 ARG Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 21 GLN Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 356 GLU Chi-restraints excluded: chain q residue 61 GLU Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain q residue 318 LYS Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 499 ASP 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 P residue 149 ARG Chi-restraints excluded: chain P residue 231 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 280 optimal weight: 9.9990 chunk 752 optimal weight: 0.4980 chunk 165 optimal weight: 4.9990 chunk 490 optimal weight: 2.9990 chunk 206 optimal weight: 0.5980 chunk 835 optimal weight: 8.9990 chunk 693 optimal weight: 4.9990 chunk 387 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 276 optimal weight: 0.6980 chunk 438 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 501 ASN Z 161 HIS g 390 ASN z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 67960 Z= 0.153 Angle : 0.513 11.080 91755 Z= 0.251 Chirality : 0.040 0.172 10923 Planarity : 0.003 0.051 11716 Dihedral : 7.038 171.768 9433 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.98 % Allowed : 9.76 % Favored : 89.27 % 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: 1.44 (0.09), residues: 8685 helix: 2.01 (0.08), residues: 4478 sheet: 0.34 (0.16), residues: 1092 loop : -0.32 (0.11), residues: 3115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g 168 HIS 0.012 0.001 HIS Z 161 PHE 0.014 0.001 PHE P 69 TYR 0.030 0.001 TYR A 181 ARG 0.011 0.000 ARG P 141 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 517 time to evaluate : 6.473 Fit side-chains revert: symmetry clash REVERT: N 267 ASP cc_start: 0.7419 (t0) cc_final: 0.7177 (t0) REVERT: A 187 GLN cc_start: 0.8806 (mm110) cc_final: 0.8338 (pm20) REVERT: A 360 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7989 (mt-10) REVERT: D 25 GLN cc_start: 0.8605 (tp-100) cc_final: 0.8385 (tp-100) REVERT: D 145 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8829 (mm) REVERT: G 52 ASP cc_start: 0.8318 (t70) cc_final: 0.7765 (t0) REVERT: G 54 MET cc_start: 0.8169 (mpp) cc_final: 0.7961 (mpp) REVERT: G 151 MET cc_start: 0.8690 (mmm) cc_final: 0.8334 (mmm) REVERT: G 497 GLU cc_start: 0.8344 (pt0) cc_final: 0.8105 (pt0) REVERT: H 14 ASP cc_start: 0.8373 (t0) cc_final: 0.8062 (t0) REVERT: H 81 ASP cc_start: 0.8274 (m-30) cc_final: 0.8035 (m-30) REVERT: H 185 MET cc_start: 0.8738 (mtp) cc_final: 0.8424 (mtp) REVERT: H 316 GLU cc_start: 0.8249 (tt0) cc_final: 0.7709 (tp30) REVERT: H 324 MET cc_start: 0.9137 (mmm) cc_final: 0.8833 (mmm) REVERT: Q 27 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8243 (mt-10) REVERT: Q 34 GLN cc_start: 0.7941 (tp-100) cc_final: 0.7584 (tp-100) REVERT: Z 353 TYR cc_start: 0.9021 (t80) cc_final: 0.8772 (t80) REVERT: Z 458 ASP cc_start: 0.8284 (OUTLIER) cc_final: 0.7813 (p0) REVERT: d 340 ILE cc_start: 0.9246 (mt) cc_final: 0.8995 (mm) REVERT: e 160 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.9042 (mtmm) REVERT: g 306 ARG cc_start: 0.7953 (OUTLIER) cc_final: 0.7526 (mtm-85) REVERT: g 528 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8338 (tmmt) REVERT: h 401 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7727 (tmmt) REVERT: h 440 LYS cc_start: 0.9049 (ttmt) cc_final: 0.8845 (ttmm) REVERT: q 61 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8024 (mp0) REVERT: q 152 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.9073 (ptmm) REVERT: q 318 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8335 (pptt) REVERT: z 53 ASP cc_start: 0.8555 (m-30) cc_final: 0.8317 (m-30) REVERT: P 80 GLN cc_start: 0.8762 (mm-40) cc_final: 0.8155 (mm-40) REVERT: P 202 MET cc_start: 0.9355 (mtp) cc_final: 0.9126 (mtm) REVERT: P 231 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.7903 (p0) outliers start: 71 outliers final: 25 residues processed: 558 average time/residue: 1.5940 time to fit residues: 1147.6106 Evaluate side-chains 525 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 491 time to evaluate : 6.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 270 SER Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain H residue 32 ILE Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 266 MET Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Q residue 526 MET Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 354 THR Chi-restraints excluded: chain Z residue 458 ASP Chi-restraints excluded: chain b residue 11 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain e residue 23 ASP Chi-restraints excluded: chain e residue 160 LYS Chi-restraints excluded: chain g residue 255 ASP Chi-restraints excluded: chain g residue 306 ARG Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 21 GLN Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain q residue 61 GLU Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain q residue 318 LYS Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 499 ASP Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 149 ARG Chi-restraints excluded: chain P residue 231 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 805 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 476 optimal weight: 5.9990 chunk 610 optimal weight: 8.9990 chunk 472 optimal weight: 2.9990 chunk 703 optimal weight: 7.9990 chunk 466 optimal weight: 7.9990 chunk 832 optimal weight: 6.9990 chunk 521 optimal weight: 10.0000 chunk 507 optimal weight: 9.9990 chunk 384 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS B 288 ASN B 302 GLN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 501 ASN Z 161 HIS ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 390 ASN z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 67960 Z= 0.455 Angle : 0.618 13.309 91755 Z= 0.305 Chirality : 0.045 0.168 10923 Planarity : 0.004 0.052 11716 Dihedral : 7.273 172.192 9433 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.98 % Allowed : 10.21 % Favored : 88.82 % 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: 1.20 (0.09), residues: 8685 helix: 1.78 (0.08), residues: 4509 sheet: 0.28 (0.16), residues: 1115 loop : -0.42 (0.11), residues: 3061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP g 168 HIS 0.012 0.001 HIS z 161 PHE 0.022 0.002 PHE H 220 TYR 0.017 0.002 TYR Q 304 ARG 0.009 0.000 ARG P 230 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 493 time to evaluate : 6.148 Fit side-chains REVERT: N 267 ASP cc_start: 0.7565 (t0) cc_final: 0.7225 (t0) REVERT: N 272 GLN cc_start: 0.7886 (mt0) cc_final: 0.7674 (mt0) REVERT: G 52 ASP cc_start: 0.8344 (t70) cc_final: 0.7785 (t0) REVERT: G 54 MET cc_start: 0.8175 (mpp) cc_final: 0.7802 (mpt) REVERT: G 151 MET cc_start: 0.8776 (mmm) cc_final: 0.8418 (mmm) REVERT: G 497 GLU cc_start: 0.8496 (pt0) cc_final: 0.8221 (pt0) REVERT: H 14 ASP cc_start: 0.8424 (t0) cc_final: 0.8080 (t0) REVERT: H 17 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8308 (pp30) REVERT: H 81 ASP cc_start: 0.8279 (m-30) cc_final: 0.8060 (m-30) REVERT: H 185 MET cc_start: 0.8841 (mtp) cc_final: 0.8586 (mtp) REVERT: H 316 GLU cc_start: 0.8196 (tt0) cc_final: 0.7876 (tp30) REVERT: H 324 MET cc_start: 0.9156 (mmm) cc_final: 0.8883 (mmm) REVERT: Q 27 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8275 (mt-10) REVERT: Q 34 GLN cc_start: 0.8040 (tp-100) cc_final: 0.7703 (tp-100) REVERT: Z 458 ASP cc_start: 0.8424 (OUTLIER) cc_final: 0.7896 (p0) REVERT: a 5 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8462 (tt) REVERT: a 156 MET cc_start: 0.9114 (mtm) cc_final: 0.8868 (mtm) REVERT: e 160 LYS cc_start: 0.9262 (OUTLIER) cc_final: 0.9020 (mtmm) REVERT: g 306 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7673 (mtm-85) REVERT: g 528 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8310 (tmmt) REVERT: h 221 SER cc_start: 0.9195 (m) cc_final: 0.8953 (p) REVERT: h 356 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7633 (mt-10) REVERT: h 401 LYS cc_start: 0.8277 (mmtt) cc_final: 0.7891 (tmmt) REVERT: q 61 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7864 (mp0) REVERT: q 152 LYS cc_start: 0.9373 (OUTLIER) cc_final: 0.9137 (ptmm) REVERT: q 318 LYS cc_start: 0.8742 (OUTLIER) cc_final: 0.8339 (pptt) REVERT: z 53 ASP cc_start: 0.8527 (m-30) cc_final: 0.8293 (m-30) REVERT: P 77 ARG cc_start: 0.8156 (tmm160) cc_final: 0.7946 (tmm160) REVERT: P 80 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8169 (mm-40) REVERT: P 86 ARG cc_start: 0.8550 (tmm160) cc_final: 0.8230 (tmm160) REVERT: P 141 ARG cc_start: 0.8671 (mpp-170) cc_final: 0.8312 (mpp-170) REVERT: P 202 MET cc_start: 0.9338 (mtp) cc_final: 0.9133 (mtm) REVERT: P 231 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7733 (p0) outliers start: 71 outliers final: 30 residues processed: 534 average time/residue: 1.6211 time to fit residues: 1112.4416 Evaluate side-chains 523 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 482 time to evaluate : 6.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 264 MET Chi-restraints excluded: chain N residue 270 SER Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain G residue 49 MET Chi-restraints excluded: chain G residue 292 THR Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 266 MET Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Q residue 526 MET Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 354 THR Chi-restraints excluded: chain Z residue 458 ASP Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 49 ILE Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 485 ILE Chi-restraints excluded: chain e residue 23 ASP Chi-restraints excluded: chain e residue 160 LYS Chi-restraints excluded: chain g residue 306 ARG Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 21 GLN Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 356 GLU Chi-restraints excluded: chain q residue 61 GLU Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain q residue 318 LYS Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 499 ASP Chi-restraints excluded: chain q residue 526 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 P residue 231 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 515 optimal weight: 4.9990 chunk 332 optimal weight: 0.2980 chunk 497 optimal weight: 0.9980 chunk 250 optimal weight: 0.9980 chunk 163 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 529 optimal weight: 0.9980 chunk 567 optimal weight: 3.9990 chunk 411 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 654 optimal weight: 4.9990 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 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 501 ASN Z 161 HIS a 450 ASN ** a 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 227 ASN g 390 ASN z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 67960 Z= 0.146 Angle : 0.529 13.031 91755 Z= 0.259 Chirality : 0.040 0.207 10923 Planarity : 0.003 0.056 11716 Dihedral : 6.887 162.553 9433 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.65 % Allowed : 10.79 % Favored : 88.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.09), residues: 8685 helix: 1.96 (0.08), residues: 4477 sheet: 0.30 (0.16), residues: 1099 loop : -0.33 (0.11), residues: 3109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP g 168 HIS 0.015 0.001 HIS Z 161 PHE 0.012 0.001 PHE P 69 TYR 0.012 0.001 TYR q 505 ARG 0.010 0.000 ARG P 144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 510 time to evaluate : 6.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 267 ASP cc_start: 0.7367 (t0) cc_final: 0.7136 (t0) REVERT: N 272 GLN cc_start: 0.7997 (mt0) cc_final: 0.7703 (mt0) REVERT: A 360 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7967 (mt-10) REVERT: B 77 ASP cc_start: 0.8167 (OUTLIER) cc_final: 0.7941 (p0) REVERT: B 302 GLN cc_start: 0.9491 (OUTLIER) cc_final: 0.9221 (tt0) REVERT: B 415 MET cc_start: 0.9187 (mmm) cc_final: 0.8892 (mmp) REVERT: D 25 GLN cc_start: 0.8616 (tp-100) cc_final: 0.8393 (tp-100) REVERT: D 145 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8832 (mm) REVERT: G 49 MET cc_start: 0.8796 (ttp) cc_final: 0.8429 (mtp) REVERT: G 52 ASP cc_start: 0.8310 (t70) cc_final: 0.7700 (t0) REVERT: G 54 MET cc_start: 0.8204 (mpp) cc_final: 0.7981 (mpp) REVERT: G 151 MET cc_start: 0.8690 (mmm) cc_final: 0.8319 (mmm) REVERT: G 497 GLU cc_start: 0.8351 (pt0) cc_final: 0.8096 (pt0) REVERT: H 14 ASP cc_start: 0.8398 (t0) cc_final: 0.8044 (t0) REVERT: H 17 GLN cc_start: 0.8541 (pp30) cc_final: 0.8293 (pp30) REVERT: H 81 ASP cc_start: 0.8260 (m-30) cc_final: 0.8058 (m-30) REVERT: H 316 GLU cc_start: 0.8257 (tt0) cc_final: 0.7710 (tp30) REVERT: H 324 MET cc_start: 0.9121 (mmm) cc_final: 0.8846 (mmm) REVERT: Q 27 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8241 (mt-10) REVERT: Q 34 GLN cc_start: 0.7914 (tp-100) cc_final: 0.7587 (tp-100) REVERT: Q 55 MET cc_start: 0.8673 (mtm) cc_final: 0.8397 (ttm) REVERT: b 495 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7794 (mt-10) REVERT: e 160 LYS cc_start: 0.9255 (OUTLIER) cc_final: 0.9042 (mtmm) REVERT: g 306 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7495 (mtm-85) REVERT: g 528 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8301 (tmmt) REVERT: h 221 SER cc_start: 0.9150 (m) cc_final: 0.8832 (p) REVERT: h 401 LYS cc_start: 0.8131 (mmtt) cc_final: 0.7783 (tmmt) REVERT: q 61 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8001 (mp0) REVERT: q 152 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.9094 (ptmm) REVERT: q 318 LYS cc_start: 0.8757 (OUTLIER) cc_final: 0.8457 (pttp) REVERT: z 53 ASP cc_start: 0.8512 (m-30) cc_final: 0.8269 (m-30) REVERT: P 77 ARG cc_start: 0.8123 (tmm160) cc_final: 0.7860 (tmm160) REVERT: P 86 ARG cc_start: 0.8497 (tmm160) cc_final: 0.8237 (tmm160) REVERT: P 202 MET cc_start: 0.9347 (mtp) cc_final: 0.9137 (mtm) REVERT: P 231 ASN cc_start: 0.8214 (OUTLIER) cc_final: 0.7787 (p0) outliers start: 47 outliers final: 22 residues processed: 539 average time/residue: 1.5936 time to fit residues: 1116.9272 Evaluate side-chains 518 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 486 time to evaluate : 6.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 270 SER 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 302 GLN Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 354 THR Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain e residue 23 ASP Chi-restraints excluded: chain e residue 160 LYS Chi-restraints excluded: chain g residue 255 ASP Chi-restraints excluded: chain g residue 306 ARG Chi-restraints excluded: chain g residue 350 LEU Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 21 GLN Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain q residue 61 GLU Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain q residue 318 LYS Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 499 ASP Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 231 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 757 optimal weight: 3.9990 chunk 797 optimal weight: 5.9990 chunk 727 optimal weight: 0.9980 chunk 776 optimal weight: 10.0000 chunk 467 optimal weight: 0.9990 chunk 338 optimal weight: 10.0000 chunk 609 optimal weight: 9.9990 chunk 238 optimal weight: 10.0000 chunk 701 optimal weight: 7.9990 chunk 733 optimal weight: 3.9990 chunk 773 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 501 ASN a 450 ASN z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 153 HIS P 199 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 67960 Z= 0.310 Angle : 0.574 13.255 91755 Z= 0.280 Chirality : 0.042 0.168 10923 Planarity : 0.004 0.084 11716 Dihedral : 6.935 164.280 9433 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.67 % Allowed : 10.94 % Favored : 88.39 % 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: 1.33 (0.09), residues: 8685 helix: 1.90 (0.08), residues: 4498 sheet: 0.25 (0.16), residues: 1132 loop : -0.35 (0.11), residues: 3055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP g 168 HIS 0.013 0.001 HIS z 161 PHE 0.015 0.001 PHE H 455 TYR 0.032 0.001 TYR A 181 ARG 0.016 0.000 ARG P 149 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 490 time to evaluate : 6.222 Fit side-chains REVERT: N 267 ASP cc_start: 0.7538 (t0) cc_final: 0.7275 (t0) REVERT: N 272 GLN cc_start: 0.7883 (mt0) cc_final: 0.7621 (mt0) REVERT: A 187 GLN cc_start: 0.9064 (tp40) cc_final: 0.8388 (pm20) REVERT: A 360 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8024 (mt-10) REVERT: B 77 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.8010 (p0) REVERT: G 52 ASP cc_start: 0.8321 (t70) cc_final: 0.7699 (t0) REVERT: G 54 MET cc_start: 0.8221 (mpp) cc_final: 0.7909 (mpt) REVERT: G 151 MET cc_start: 0.8745 (mmm) cc_final: 0.8371 (mmm) REVERT: G 497 GLU cc_start: 0.8425 (pt0) cc_final: 0.8163 (pt0) REVERT: H 14 ASP cc_start: 0.8417 (t0) cc_final: 0.8066 (t0) REVERT: H 316 GLU cc_start: 0.8155 (tt0) cc_final: 0.7843 (tp30) REVERT: H 324 MET cc_start: 0.9120 (mmm) cc_final: 0.8840 (mmm) REVERT: H 401 LYS cc_start: 0.8604 (mmpt) cc_final: 0.8404 (mmmt) REVERT: Q 27 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8244 (mt-10) REVERT: Q 34 GLN cc_start: 0.7956 (tp-100) cc_final: 0.7638 (tp-100) REVERT: Z 458 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.7895 (p0) REVERT: b 495 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7869 (mt-10) REVERT: e 160 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.9037 (mtmm) REVERT: g 306 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7566 (mtm-85) REVERT: g 528 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8401 (tptp) REVERT: h 221 SER cc_start: 0.9171 (m) cc_final: 0.8916 (p) REVERT: h 401 LYS cc_start: 0.8237 (mmtt) cc_final: 0.7832 (tmmt) REVERT: q 61 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: q 152 LYS cc_start: 0.9357 (OUTLIER) cc_final: 0.9124 (ptmm) REVERT: q 318 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8543 (pptt) REVERT: z 53 ASP cc_start: 0.8500 (m-30) cc_final: 0.8251 (m-30) REVERT: P 77 ARG cc_start: 0.8104 (tmm160) cc_final: 0.7826 (tmm160) REVERT: P 86 ARG cc_start: 0.8563 (tmm160) cc_final: 0.8299 (tmm160) REVERT: P 171 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8904 (mp) REVERT: P 202 MET cc_start: 0.9337 (mtp) cc_final: 0.9132 (mtm) REVERT: P 231 ASN cc_start: 0.8075 (OUTLIER) cc_final: 0.7656 (p0) outliers start: 49 outliers final: 24 residues processed: 519 average time/residue: 1.6410 time to fit residues: 1097.5663 Evaluate side-chains 520 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 486 time to evaluate : 6.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 264 MET Chi-restraints excluded: chain N residue 270 SER Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 430 MET 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 D residue 69 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 266 MET Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 354 THR Chi-restraints excluded: chain Z residue 458 ASP Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain e residue 23 ASP Chi-restraints excluded: chain e residue 160 LYS Chi-restraints excluded: chain g residue 306 ARG Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 21 GLN Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain q residue 61 GLU Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain q residue 318 LYS Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 171 LEU Chi-restraints excluded: chain P residue 231 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 509 optimal weight: 0.8980 chunk 820 optimal weight: 0.0670 chunk 500 optimal weight: 0.0270 chunk 389 optimal weight: 4.9990 chunk 570 optimal weight: 4.9990 chunk 860 optimal weight: 0.5980 chunk 792 optimal weight: 5.9990 chunk 685 optimal weight: 3.9990 chunk 71 optimal weight: 10.0000 chunk 529 optimal weight: 3.9990 chunk 420 optimal weight: 8.9990 overall best weight: 1.1178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 501 ASN Z 161 HIS z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 67960 Z= 0.158 Angle : 0.536 12.158 91755 Z= 0.259 Chirality : 0.040 0.167 10923 Planarity : 0.003 0.068 11716 Dihedral : 6.724 158.679 9433 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.60 % Allowed : 11.16 % Favored : 88.24 % 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: 1.45 (0.09), residues: 8685 helix: 2.01 (0.08), residues: 4470 sheet: 0.30 (0.16), residues: 1105 loop : -0.30 (0.11), residues: 3110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g 168 HIS 0.020 0.001 HIS Z 161 PHE 0.013 0.001 PHE P 69 TYR 0.011 0.001 TYR q 505 ARG 0.019 0.000 ARG P 149 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 497 time to evaluate : 6.135 Fit side-chains revert: symmetry clash REVERT: N 267 ASP cc_start: 0.7362 (t0) cc_final: 0.7145 (t0) REVERT: N 272 GLN cc_start: 0.7992 (mt0) cc_final: 0.7696 (mt0) REVERT: A 187 GLN cc_start: 0.9045 (tp40) cc_final: 0.8431 (pm20) REVERT: A 360 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7971 (mt-10) REVERT: B 77 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7958 (p0) REVERT: D 25 GLN cc_start: 0.8614 (tp-100) cc_final: 0.8397 (tp-100) REVERT: D 145 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8830 (mm) REVERT: G 49 MET cc_start: 0.8810 (ttp) cc_final: 0.8470 (mtp) REVERT: G 52 ASP cc_start: 0.8306 (t70) cc_final: 0.7712 (t0) REVERT: G 151 MET cc_start: 0.8697 (mmm) cc_final: 0.8316 (mmm) REVERT: G 497 GLU cc_start: 0.8320 (pt0) cc_final: 0.8088 (pt0) REVERT: H 14 ASP cc_start: 0.8396 (t0) cc_final: 0.8052 (t0) REVERT: H 17 GLN cc_start: 0.8516 (pp30) cc_final: 0.8274 (pp30) REVERT: H 316 GLU cc_start: 0.8254 (tt0) cc_final: 0.7693 (tp30) REVERT: H 324 MET cc_start: 0.9096 (mmm) cc_final: 0.8816 (mmm) REVERT: Q 27 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8227 (mt-10) REVERT: Q 34 GLN cc_start: 0.7922 (tp-100) cc_final: 0.7592 (tp-100) REVERT: Q 55 MET cc_start: 0.8662 (ttm) cc_final: 0.8417 (ttm) REVERT: Z 458 ASP cc_start: 0.8271 (OUTLIER) cc_final: 0.7799 (p0) REVERT: b 495 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7785 (mt-10) REVERT: e 160 LYS cc_start: 0.9273 (OUTLIER) cc_final: 0.9026 (mtmm) REVERT: g 306 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7490 (mtm-85) REVERT: g 528 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8409 (tptp) REVERT: h 221 SER cc_start: 0.9149 (m) cc_final: 0.8851 (p) REVERT: h 401 LYS cc_start: 0.8141 (mmtt) cc_final: 0.7783 (tmmt) REVERT: q 61 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7936 (mp0) REVERT: q 152 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.9083 (ptmm) REVERT: z 53 ASP cc_start: 0.8505 (m-30) cc_final: 0.8265 (m-30) REVERT: z 337 ASP cc_start: 0.8224 (m-30) cc_final: 0.7928 (m-30) REVERT: P 80 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8141 (mp10) REVERT: P 202 MET cc_start: 0.9346 (mtp) cc_final: 0.9135 (mtm) outliers start: 44 outliers final: 22 residues processed: 523 average time/residue: 1.6467 time to fit residues: 1110.7493 Evaluate side-chains 509 residues out of total 7276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 479 time to evaluate : 6.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 264 MET Chi-restraints excluded: chain N residue 270 SER Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 430 MET 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 D residue 69 THR Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain Q residue 316 ASN Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 354 THR Chi-restraints excluded: chain Z residue 458 ASP Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain e residue 23 ASP Chi-restraints excluded: chain e residue 160 LYS Chi-restraints excluded: chain g residue 306 ARG Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 21 GLN Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain q residue 61 GLU Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 499 ASP Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 231 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 544 optimal weight: 7.9990 chunk 730 optimal weight: 0.9980 chunk 209 optimal weight: 0.9980 chunk 632 optimal weight: 8.9990 chunk 101 optimal weight: 0.5980 chunk 190 optimal weight: 10.0000 chunk 686 optimal weight: 10.0000 chunk 287 optimal weight: 6.9990 chunk 704 optimal weight: 4.9990 chunk 86 optimal weight: 0.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 501 ASN Z 161 HIS q 359 GLN z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.072796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.058697 restraints weight = 181132.025| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 3.05 r_work: 0.2558 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 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 = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 67960 Z= 0.183 Angle : 0.539 12.916 91755 Z= 0.261 Chirality : 0.041 0.164 10923 Planarity : 0.003 0.065 11716 Dihedral : 6.667 158.403 9433 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.56 % Allowed : 11.36 % Favored : 88.07 % 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: 1.45 (0.09), residues: 8685 helix: 2.02 (0.08), residues: 4475 sheet: 0.30 (0.16), residues: 1123 loop : -0.31 (0.11), residues: 3087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g 168 HIS 0.017 0.001 HIS Z 161 PHE 0.016 0.001 PHE P 271 TYR 0.029 0.001 TYR A 181 ARG 0.017 0.000 ARG P 149 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17897.37 seconds wall clock time: 314 minutes 19.55 seconds (18859.55 seconds total)