Starting phenix.real_space_refine on Fri Mar 15 01:00:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shq_40492/03_2024/8shq_40492_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shq_40492/03_2024/8shq_40492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shq_40492/03_2024/8shq_40492.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shq_40492/03_2024/8shq_40492.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shq_40492/03_2024/8shq_40492_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shq_40492/03_2024/8shq_40492_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.044 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 423 5.16 5 C 42490 2.51 5 N 11819 2.21 5 O 13163 1.98 5 F 48 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "P PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 297": "OD1" <-> "OD2" Residue "N TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 105": "OD1" <-> "OD2" Residue "A ASP 293": "OD1" <-> "OD2" Residue "A GLU 519": "OE1" <-> "OE2" Residue "B ASP 37": "OD1" <-> "OD2" Residue "B ASP 77": "OD1" <-> "OD2" Residue "B GLU 197": "OE1" <-> "OE2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 221": "OD1" <-> "OD2" Residue "B ASP 316": "OD1" <-> "OD2" Residue "D TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 23": "OD1" <-> "OD2" Residue "E GLU 207": "OE1" <-> "OE2" Residue "E GLU 426": "OE1" <-> "OE2" Residue "E ASP 532": "OD1" <-> "OD2" Residue "G ASP 52": "OD1" <-> "OD2" Residue "H ASP 14": "OD1" <-> "OD2" Residue "H ASP 70": "OD1" <-> "OD2" Residue "H PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 38": "OE1" <-> "OE2" Residue "Q ASP 200": "OD1" <-> "OD2" Residue "Q ASP 393": "OD1" <-> "OD2" Residue "Z TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 529": "OD1" <-> "OD2" Residue "b ASP 49": "OD1" <-> "OD2" Residue "b GLU 197": "OE1" <-> "OE2" Residue "b TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 509": "OE1" <-> "OE2" Residue "d GLU 93": "OE1" <-> "OE2" Residue "d ASP 261": "OD1" <-> "OD2" Residue "e ASP 23": "OD1" <-> "OD2" Residue "e TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 532": "OD1" <-> "OD2" Residue "g TYR 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 521": "OD1" <-> "OD2" Residue "h ASP 70": "OD1" <-> "OD2" Residue "h ASP 251": "OD1" <-> "OD2" Residue "h PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 116": "OE1" <-> "OE2" Residue "q ASP 357": "OD1" <-> "OD2" Residue "q ASP 393": "OD1" <-> "OD2" Residue "z TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 68007 Number of models: 1 Model: "" Number of chains: 50 Chain: "P" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1507 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 3, 'TRANS': 182} Chain breaks: 9 Chain: "N" Number of atoms: 1366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1366 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 3, 'TRANS': 176} Chain breaks: 1 Chain: "A" Number of atoms: 4069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4069 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 14, 'TRANS': 521} Chain: "B" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3952 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 10, 'TRANS': 515} Chain: "D" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3923 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "E" Number of atoms: 4132 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} Conformer: "C" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} bond proxies already assigned to first conformer: 4158 Chain: "G" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4089 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "H" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4054 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 16, 'TRANS': 511} Chain: "Q" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4086 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 18, 'TRANS': 519} Chain: "Z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "a" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4041 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Chain: "b" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3943 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 10, 'TRANS': 514} Chain: "d" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3917 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 4169 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} Conformer: "B" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} bond proxies already assigned to first conformer: 4195 Chain: "g" Number of atoms: 4088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4088 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "h" Number of atoms: 4032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4032 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 16, 'TRANS': 508} Chain: "q" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4053 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 16, 'TRANS': 516} Chain: "z" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4033 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 512} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N BPHE E 9 " occ=0.38 ... (20 atoms not shown) pdb=" CZ CPHE E 9 " occ=0.62 residue: pdb=" N APHE e 9 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE e 9 " occ=0.50 Time building chain proxies: 28.68, per 1000 atoms: 0.42 Number of scatterers: 68007 At special positions: 0 Unit cell: (179.86, 176.686, 180.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 423 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 13163 8.00 N 11819 7.00 C 42490 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 "HETATM67914 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67658 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67786 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67594 O3A ADP E 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67562 O3A ADP D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67530 O3A ADP B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67850 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: 20.52 Conformation dependent library (CDL) restraints added in 11.3 seconds 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16450 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 320 helices and 112 sheets defined 50.3% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.90 Creating SS restraints... Processing helix chain 'P' and resid 56 through 86 Proline residue: P 59 - end of helix removed outlier: 3.650A pdb=" N ILE P 63 " --> pdb=" O LYS P 60 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ASN P 64 " --> pdb=" O GLY P 61 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TRP P 66 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN P 71 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG P 86 " --> pdb=" O GLU P 83 " (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 150 removed outlier: 3.785A pdb=" N ARG P 144 " --> pdb=" O ARG P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 175 removed outlier: 3.883A pdb=" N LEU P 171 " --> pdb=" O GLY P 167 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE P 174 " --> pdb=" O PHE P 170 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 208 removed outlier: 3.797A pdb=" N ALA P 207 " --> pdb=" O ILE P 203 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU P 208 " --> pdb=" O CYS P 204 " (cutoff:3.500A) Processing helix chain 'P' and resid 261 through 270 Processing helix chain 'N' and resid 186 through 189 Processing helix chain 'A' and resid 15 through 32 removed outlier: 3.674A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (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: 3.663A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.655A 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 145 through 156 Processing helix chain 'A' and resid 163 through 179 removed outlier: 4.442A pdb=" N ASP A 166 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ALA A 169 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 257 through 281 removed outlier: 3.676A pdb=" N LEU A 260 " --> pdb=" O PRO A 257 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP A 261 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 382 through 404 Processing helix chain 'A' and resid 414 through 429 removed outlier: 4.314A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N SER A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 455 removed outlier: 3.748A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 5.082A 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: 3.729A pdb=" N TRP A 485 " --> pdb=" O ASN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 507 through 525 Processing helix chain 'B' and resid 21 through 39 Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 99 through 118 Processing helix chain 'B' and resid 123 through 144 Processing helix chain 'B' and resid 152 through 168 Processing helix chain 'B' and resid 171 through 190 removed outlier: 3.609A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS B 176 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ASP B 177 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 198 No H-bonds generated for 'chain 'B' and resid 196 through 198' Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 261 through 285 removed outlier: 4.045A pdb=" N HIS B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 317 through 327 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 380 through 402 Processing helix chain 'B' and resid 412 through 427 removed outlier: 3.875A pdb=" N ARG B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 454 Proline residue: B 447 - end of helix removed outlier: 3.619A 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: 4.417A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N SER D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 80 Processing helix chain 'D' and resid 86 through 101 Processing helix chain 'D' and resid 108 through 125 removed outlier: 3.899A 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: 4.040A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 4.001A 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: 4.480A pdb=" N GLU D 334 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ILE D 340 " --> pdb=" O CYS D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 350 No H-bonds generated for 'chain 'D' and resid 348 through 350' Processing helix chain 'D' and resid 353 through 355 No H-bonds generated for 'chain 'D' and resid 353 through 355' Processing helix chain 'D' and resid 395 through 417 Processing helix chain 'D' and resid 427 through 442 removed outlier: 3.686A pdb=" N THR D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 468 removed outlier: 3.979A pdb=" N VAL D 460 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) Proline residue: D 462 - end of helix Processing helix chain 'D' and resid 473 through 486 Processing helix chain 'D' and resid 512 through 531 removed outlier: 3.529A pdb=" N LYS D 531 " --> pdb=" O ARG D 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 24 No H-bonds generated for 'chain 'E' and resid 22 through 24' Processing helix chain 'E' and resid 30 through 51 removed outlier: 4.251A pdb=" N THR E 50 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.877A 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: 3.588A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.625A 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 173 Processing helix chain 'E' and resid 177 through 195 removed outlier: 4.020A pdb=" N SER E 180 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ARG E 183 " --> pdb=" O SER E 180 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR E 195 " --> pdb=" O ALA E 192 " (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: 3.851A pdb=" N THR E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 316 Processing helix chain 'E' and resid 327 through 337 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 392 through 414 Processing helix chain 'E' and resid 424 through 439 removed outlier: 3.882A pdb=" N LYS E 439 " --> pdb=" O GLN E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 465 removed outlier: 4.101A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL E 457 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ILE E 458 " --> pdb=" O ALA E 454 " (cutoff:3.500A) Proline residue: E 459 - end of helix Processing helix chain 'E' and resid 470 through 483 Processing helix chain 'E' and resid 501 through 504 No H-bonds generated for 'chain 'E' and resid 501 through 504' Processing helix chain 'E' and resid 510 through 529 Processing helix chain 'G' and resid 19 through 40 removed outlier: 3.671A pdb=" N ARG G 38 " --> pdb=" O ASP G 35 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N THR G 39 " --> pdb=" O ILE G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 69 removed outlier: 3.562A pdb=" N GLU G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 90 Processing helix chain 'G' and resid 95 through 115 removed outlier: 3.624A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 3.553A 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: 4.043A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N SER G 170 " --> pdb=" O ARG G 167 " (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 261 through 285 removed outlier: 4.267A pdb=" N PHE G 264 " --> pdb=" O GLU G 261 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR G 265 " --> pdb=" O GLU G 262 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN G 284 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 307 removed outlier: 3.586A 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 427 removed outlier: 3.616A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 455 removed outlier: 3.842A pdb=" N TRP G 435 " --> pdb=" O VAL G 432 " (cutoff:3.500A) Proline residue: G 436 - end of helix removed outlier: 3.988A pdb=" N ILE G 447 " --> pdb=" O LEU G 444 " (cutoff:3.500A) Proline residue: G 448 - end of helix Processing helix chain 'G' and resid 459 through 471 Processing helix chain 'G' and resid 490 through 493 No H-bonds generated for 'chain 'G' and resid 490 through 493' Processing helix chain 'G' and resid 499 through 517 Processing helix chain 'H' and resid 19 through 39 removed outlier: 3.785A pdb=" N VAL H 36 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N THR H 38 " --> pdb=" O GLU H 34 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 68 Processing helix chain 'H' and resid 76 through 89 removed outlier: 3.689A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 113 removed outlier: 4.056A 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: 5.386A pdb=" N ALA H 173 " --> pdb=" O GLN H 170 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE H 175 " --> pdb=" O LYS H 172 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'H' and resid 205 through 207 No H-bonds generated for 'chain 'H' and resid 205 through 207' Processing helix chain 'H' and resid 225 through 227 No H-bonds generated for 'chain 'H' and resid 225 through 227' Processing helix chain 'H' and resid 260 through 283 Processing helix chain 'H' and resid 297 through 305 Processing helix chain 'H' and resid 316 through 326 Processing helix chain 'H' and resid 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: 4.037A pdb=" N THR H 426 " --> pdb=" O ASP H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 453 removed outlier: 4.074A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLU H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ILE H 444 " --> pdb=" O LYS H 440 " (cutoff:3.500A) removed outlier: 5.304A 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: 4.316A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) removed outlier: 5.695A 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: 4.321A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.538A 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: 4.837A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR Q 286 " --> pdb=" O ALA Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 299 through 307 Processing helix chain 'Q' and resid 318 through 328 Processing helix chain 'Q' and resid 341 through 343 No H-bonds generated for 'chain 'Q' and resid 341 through 343' Processing helix chain 'Q' and resid 382 through 404 Processing helix chain 'Q' and resid 414 through 429 removed outlier: 3.728A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 434 through 456 removed outlier: 3.820A pdb=" N PHE Q 445 " --> pdb=" O PHE Q 441 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLU Q 446 " --> pdb=" O ALA Q 442 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N ALA Q 447 " --> pdb=" O GLU Q 443 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE Q 448 " --> pdb=" O ALA Q 444 " (cutoff:3.500A) Proline residue: Q 449 - end of helix Processing helix chain 'Q' and resid 460 through 473 Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'Z' and resid 3 through 7 Processing helix chain 'Z' and resid 16 through 37 removed outlier: 3.722A pdb=" N ARG Z 35 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N THR Z 36 " --> pdb=" O VAL Z 33 " (cutoff:3.500A) Processing helix chain 'Z' and resid 60 through 66 Processing helix chain 'Z' and resid 72 through 87 Processing helix chain 'Z' and resid 92 through 112 removed outlier: 3.584A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) removed outlier: 4.505A 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: 3.990A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 162 through 179 removed outlier: 3.661A 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: 4.080A pdb=" N ARG Z 264 " --> pdb=" O VAL Z 260 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LYS Z 265 " --> pdb=" O LYS Z 261 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N PHE Z 266 " --> pdb=" O ALA Z 262 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N ILE Z 267 " --> pdb=" O GLU Z 263 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 299 through 308 removed outlier: 3.772A pdb=" N GLU Z 308 " --> pdb=" O ALA Z 304 " (cutoff:3.500A) Processing helix chain 'Z' and resid 318 through 328 removed outlier: 4.150A pdb=" N GLU Z 322 " --> pdb=" O ARG Z 318 " (cutoff:3.500A) Processing helix chain 'Z' and resid 341 through 343 No H-bonds generated for 'chain 'Z' and resid 341 through 343' Processing helix chain 'Z' and resid 381 through 403 Processing helix chain 'Z' and resid 413 through 428 Proline residue: Z 427 - end of helix Processing helix chain 'Z' and resid 431 through 455 removed outlier: 3.937A pdb=" N GLN Z 434 " --> pdb=" O GLY Z 431 " (cutoff:3.500A) removed outlier: 3.785A 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: 3.612A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N SER a 34 " --> pdb=" O ASN a 30 " (cutoff:3.500A) removed outlier: 5.769A 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: 3.701A pdb=" N VAL a 94 " --> pdb=" O THR a 90 " (cutoff:3.500A) removed outlier: 3.589A 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 144 through 156 Processing helix chain 'a' and resid 163 through 179 removed outlier: 3.979A pdb=" N ASP a 166 " --> pdb=" O ILE a 163 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ALA a 169 " --> pdb=" O ASP a 166 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 186 No H-bonds generated for 'chain 'a' and resid 184 through 186' Processing helix chain 'a' and resid 205 through 207 No H-bonds generated for 'chain 'a' and resid 205 through 207' Processing helix chain 'a' and resid 257 through 281 removed outlier: 4.588A pdb=" N ASP a 261 " --> pdb=" O GLU a 258 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE a 270 " --> pdb=" O GLU a 267 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA a 280 " --> pdb=" O LYS a 277 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR a 281 " --> pdb=" O ILE a 278 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 303 Processing helix chain 'a' and resid 313 through 323 Processing helix chain 'a' and resid 342 through 344 No H-bonds generated for 'chain 'a' and resid 342 through 344' Processing helix chain 'a' and resid 382 through 404 Processing helix chain 'a' and resid 414 through 429 removed outlier: 4.557A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) Processing helix chain 'a' and resid 434 through 455 removed outlier: 3.797A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 5.119A 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: 3.663A pdb=" N LYS a 481 " --> pdb=" O PRO a 478 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ASN a 482 " --> pdb=" O GLU a 479 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TRP a 485 " --> pdb=" O ASN a 482 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 501 No H-bonds generated for 'chain 'a' and resid 498 through 501' Processing helix chain 'a' and resid 507 through 526 Processing helix chain 'b' and resid 21 through 39 Processing helix chain 'b' and resid 67 through 72 Processing helix chain 'b' and resid 79 through 94 Processing helix chain 'b' and resid 99 through 118 Processing helix chain 'b' and resid 123 through 144 Processing helix chain 'b' and resid 152 through 169 removed outlier: 4.427A pdb=" N SER b 169 " --> pdb=" O THR b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 171 through 190 removed outlier: 3.626A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS b 176 " --> pdb=" O THR b 173 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASP b 177 " --> pdb=" O HIS b 174 " (cutoff:3.500A) removed outlier: 3.589A 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: 3.925A pdb=" N HIS b 285 " --> pdb=" O ARG b 281 " (cutoff:3.500A) Processing helix chain 'b' and resid 298 through 306 Processing helix chain 'b' and resid 317 through 327 Processing helix chain 'b' and resid 338 through 340 No H-bonds generated for 'chain 'b' and resid 338 through 340' Processing helix chain 'b' and resid 380 through 402 Processing helix chain 'b' and resid 412 through 427 removed outlier: 3.816A pdb=" N ARG b 427 " --> pdb=" O GLN b 423 " (cutoff:3.500A) Processing helix chain 'b' and resid 431 through 454 Proline residue: b 447 - end of helix removed outlier: 3.851A pdb=" N ALA b 454 " --> pdb=" O ILE b 450 " (cutoff:3.500A) Processing helix chain 'b' and resid 458 through 471 Processing helix chain 'b' and resid 488 through 491 No H-bonds generated for 'chain 'b' and resid 488 through 491' Processing helix chain 'b' and resid 497 through 515 Processing helix chain 'd' and resid 29 through 49 Processing helix chain 'd' and resid 74 through 80 Processing helix chain 'd' and resid 86 through 101 Processing helix chain 'd' and resid 106 through 126 removed outlier: 3.653A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 132 through 151 Processing helix chain 'd' and resid 160 through 173 removed outlier: 4.502A 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: 3.930A 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: 4.445A pdb=" N GLU d 334 " --> pdb=" O GLU d 331 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE d 340 " --> pdb=" O CYS d 337 " (cutoff:3.500A) Processing helix chain 'd' and resid 348 through 350 No H-bonds generated for 'chain 'd' and resid 348 through 350' Processing helix chain 'd' and resid 353 through 355 No H-bonds generated for 'chain 'd' and resid 353 through 355' Processing helix chain 'd' and resid 395 through 416 Processing helix chain 'd' and resid 427 through 442 Processing helix chain 'd' and resid 446 through 466 removed outlier: 3.860A pdb=" N VAL d 460 " --> pdb=" O ASP d 456 " (cutoff:3.500A) removed outlier: 4.802A 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: 5.062A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 51 removed outlier: 3.503A pdb=" N LEU e 34 " --> pdb=" O GLY e 30 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR e 50 " --> pdb=" O ASN e 46 " (cutoff:3.500A) removed outlier: 5.167A 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 125 removed outlier: 3.572A pdb=" N GLN e 122 " --> pdb=" O GLU e 118 " (cutoff:3.500A) Processing helix chain 'e' and resid 130 through 151 Processing helix chain 'e' and resid 163 through 173 Processing helix chain 'e' and resid 177 through 195 removed outlier: 3.870A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ARG e 183 " --> pdb=" O SER e 180 " (cutoff:3.500A) Processing helix chain 'e' and resid 206 through 208 No H-bonds generated for 'chain 'e' and resid 206 through 208' Processing helix chain 'e' and resid 219 through 221 No H-bonds generated for 'chain 'e' and resid 219 through 221' Processing helix chain 'e' and resid 271 through 294 Processing helix chain 'e' and resid 308 through 316 Processing helix chain 'e' and resid 327 through 337 Processing helix chain 'e' and resid 345 through 347 No H-bonds generated for 'chain 'e' and resid 345 through 347' Processing helix chain 'e' and resid 350 through 352 No H-bonds generated for 'chain 'e' and resid 350 through 352' Processing helix chain 'e' and resid 392 through 414 Processing helix chain 'e' and resid 424 through 439 removed outlier: 3.634A pdb=" N LYS e 439 " --> pdb=" O GLN e 435 " (cutoff:3.500A) Processing helix chain 'e' and resid 442 through 465 removed outlier: 3.861A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.668A 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: 4.740A 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: 3.839A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N THR g 39 " --> pdb=" O ASP g 35 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N CYS g 40 " --> pdb=" O ILE g 36 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 69 removed outlier: 3.659A pdb=" N GLU g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 75 through 90 Processing helix chain 'g' and resid 95 through 114 removed outlier: 3.566A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N PHE g 112 " --> pdb=" O VAL g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 119 through 139 Processing helix chain 'g' and resid 149 through 160 Processing helix chain 'g' and resid 164 through 183 removed outlier: 3.970A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N SER g 170 " --> pdb=" O ARG g 167 " (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 261 through 285 removed outlier: 4.107A pdb=" N PHE g 264 " --> pdb=" O GLU g 261 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR g 265 " --> pdb=" O GLU g 262 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN g 284 " --> pdb=" O ASP g 281 " (cutoff:3.500A) Processing helix chain 'g' and resid 298 through 307 removed outlier: 3.771A 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: 4.461A pdb=" N ALA g 428 " --> pdb=" O GLU g 424 " (cutoff:3.500A) Processing helix chain 'g' and resid 434 through 455 removed outlier: 3.982A pdb=" N LEU g 444 " --> pdb=" O VAL g 440 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLU g 445 " --> pdb=" O ALA g 441 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N VAL g 446 " --> pdb=" O GLN g 442 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ILE g 447 " --> pdb=" O ALA g 443 " (cutoff:3.500A) Proline residue: g 448 - end of helix Processing helix chain 'g' and resid 459 through 471 Processing helix chain 'g' and resid 490 through 493 No H-bonds generated for 'chain 'g' and resid 490 through 493' Processing helix chain 'g' and resid 499 through 517 Processing helix chain 'h' and resid 19 through 36 removed outlier: 3.593A pdb=" N ALA h 35 " --> pdb=" O VAL h 31 " (cutoff:3.500A) removed outlier: 4.146A 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: 3.659A pdb=" N VAL h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 113 removed outlier: 4.261A 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: 5.513A pdb=" N ALA h 173 " --> pdb=" O GLN h 170 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE h 175 " --> pdb=" O LYS h 172 " (cutoff:3.500A) Processing helix chain 'h' and resid 192 through 194 No H-bonds generated for 'chain 'h' and resid 192 through 194' Processing helix chain 'h' and resid 205 through 207 No H-bonds generated for 'chain 'h' and resid 205 through 207' Processing helix chain 'h' and resid 225 through 227 No H-bonds generated for 'chain 'h' and resid 225 through 227' Processing helix chain 'h' and resid 260 through 283 Processing helix chain 'h' and resid 297 through 305 Processing helix chain 'h' and resid 316 through 326 Processing helix chain 'h' and resid 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: 4.171A pdb=" N THR h 426 " --> pdb=" O ASP h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 430 through 453 removed outlier: 4.124A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLU h 443 " --> pdb=" O ALA h 439 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE h 444 " --> pdb=" O LYS h 440 " (cutoff:3.500A) removed outlier: 5.263A 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: 4.676A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) removed outlier: 5.669A 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: 4.328A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.491A 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: 4.756A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N THR q 286 " --> pdb=" O ALA q 282 " (cutoff:3.500A) Processing helix chain 'q' and resid 299 through 307 Processing helix chain 'q' and resid 318 through 328 Processing helix chain 'q' and resid 341 through 343 No H-bonds generated for 'chain 'q' and resid 341 through 343' Processing helix chain 'q' and resid 382 through 404 Processing helix chain 'q' and resid 414 through 429 removed outlier: 3.798A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 456 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: 3.715A pdb=" N LEU z 7 " --> pdb=" O ALA z 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 3 through 7' Processing helix chain 'z' and resid 16 through 37 removed outlier: 3.724A pdb=" N ARG z 35 " --> pdb=" O ASP z 32 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR z 36 " --> pdb=" O VAL z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 60 through 66 Processing helix chain 'z' and resid 72 through 87 Processing helix chain 'z' and resid 92 through 112 removed outlier: 3.585A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) removed outlier: 4.369A 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: 3.768A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 162 through 179 removed outlier: 3.535A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) Processing helix chain 'z' and resid 188 through 190 No H-bonds generated for 'chain 'z' and resid 188 through 190' Processing helix chain 'z' and resid 201 through 203 No H-bonds generated for 'chain 'z' and resid 201 through 203' Processing helix chain 'z' and resid 253 through 262 Processing helix chain 'z' and resid 265 through 281 removed outlier: 3.657A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 299 through 308 removed outlier: 3.789A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 318 through 328 removed outlier: 4.178A 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: 4.173A pdb=" N GLN z 434 " --> pdb=" O GLY z 431 " (cutoff:3.500A) removed outlier: 3.772A 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 sheet with id= A, first strand: chain 'P' and resid 162 through 164 removed outlier: 4.508A pdb=" N LYS P 218 " --> pdb=" O ILE P 164 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR P 188 " --> pdb=" O VAL P 217 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N LYS P 240 " --> pdb=" O LEU P 244 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N LEU P 244 " --> pdb=" O LYS P 240 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'N' and resid 200 through 203 removed outlier: 4.187A pdb=" N ALA N 200 " --> pdb=" O ALA N 213 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA N 213 " --> pdb=" O ALA N 200 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ASP N 223 " --> pdb=" O LEU N 229 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU N 229 " --> pdb=" O ASP N 223 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'N' and resid 242 through 244 removed outlier: 7.051A pdb=" N ASP N 267 " --> pdb=" O CYS N 273 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N CYS N 273 " --> pdb=" O ASP N 267 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'N' and resid 284 through 289 removed outlier: 6.623A pdb=" N GLY N 299 " --> pdb=" O ASN N 285 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL N 287 " --> pdb=" O ALA N 297 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA N 297 " --> pdb=" O VAL N 287 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TYR N 289 " --> pdb=" O ALA N 295 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ALA N 295 " --> pdb=" O TYR N 289 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER N 298 " --> pdb=" O ARG N 306 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG N 306 " --> pdb=" O SER N 298 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR N 304 " --> pdb=" O SER N 300 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA N 317 " --> pdb=" O LEU N 307 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ASP N 309 " --> pdb=" O GLU N 315 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLU N 315 " --> pdb=" O ASP N 309 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 9 through 13 Processing sheet with id= F, first strand: chain 'A' and resid 43 through 46 Processing sheet with id= G, first strand: chain 'A' and resid 196 through 199 Processing sheet with id= H, first strand: chain 'A' and resid 213 through 216 Processing sheet with id= I, first strand: chain 'A' and resid 346 through 348 removed outlier: 6.486A pdb=" N VAL A 285 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LEU A 237 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LEU A 287 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N MET A 306 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N THR A 288 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL A 308 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 408 through 410 Processing sheet with id= K, first strand: chain 'A' and resid 486 through 489 Processing sheet with id= L, first strand: chain 'B' and resid 17 through 19 Processing sheet with id= M, first strand: chain 'B' and resid 50 through 53 Processing sheet with id= N, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.361A pdb=" N CYS B 371 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE B 202 " --> pdb=" O CYS B 371 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE B 373 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LYS B 204 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LEU B 375 " --> pdb=" O LYS B 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'B' and resid 218 through 220 Processing sheet with id= P, first strand: chain 'B' and resid 344 through 346 removed outlier: 3.638A pdb=" N CYS B 346 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N CYS B 289 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ALA B 240 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE B 291 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N MET B 310 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ASN B 292 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE B 312 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 406 through 408 Processing sheet with id= R, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= S, first strand: chain 'D' and resid 59 through 62 Processing sheet with id= T, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.766A pdb=" N VAL D 386 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N VAL D 211 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE D 388 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LYS D 213 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N VAL D 390 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 227 through 229 Processing sheet with id= V, first strand: chain 'D' and resid 246 through 249 removed outlier: 6.761A pdb=" N VAL D 297 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ILE D 249 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU D 299 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N MET D 323 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ILE D 300 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE D 325 " --> pdb=" O ILE D 300 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'D' and resid 421 through 423 Processing sheet with id= X, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.651A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 59 through 62 Processing sheet with id= Z, first strand: chain 'E' and resid 209 through 215 removed outlier: 6.964A pdb=" N VAL E 383 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N GLU E 212 " --> pdb=" O VAL E 383 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ILE E 385 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LYS E 214 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE E 387 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 228 through 230 removed outlier: 3.526A pdb=" N LEU E 358 " --> pdb=" O GLU E 375 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 248 through 250 removed outlier: 7.222A pdb=" N LEU E 299 " --> pdb=" O ALA E 249 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'E' and resid 418 through 420 Processing sheet with id= AD, first strand: chain 'G' and resid 48 through 51 Processing sheet with id= AE, first strand: chain 'G' and resid 185 through 187 Processing sheet with id= AF, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.538A pdb=" N CYS G 372 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLU G 202 " --> pdb=" O CYS G 372 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ILE G 374 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ILE G 204 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N LEU G 376 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR G 373 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'G' and resid 238 through 241 removed outlier: 6.627A pdb=" N VAL G 289 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N LEU G 241 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE G 291 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR G 310 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N THR G 292 " --> pdb=" O THR G 310 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE G 312 " --> pdb=" O THR G 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'G' and resid 351 through 355 Processing sheet with id= AI, first strand: chain 'G' and resid 407 through 409 Processing sheet with id= AJ, first strand: chain 'G' and resid 478 through 481 removed outlier: 3.815A pdb=" N THR G 486 " --> pdb=" O ASN G 481 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'H' and resid 14 through 17 Processing sheet with id= AL, first strand: chain 'H' and resid 47 through 50 Processing sheet with id= AM, first strand: chain 'H' and resid 195 through 201 removed outlier: 6.474A pdb=" N CYS H 370 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N LYS H 198 " --> pdb=" O CYS H 370 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N PHE H 372 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL H 200 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N LEU H 374 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'H' and resid 214 through 217 Processing sheet with id= AO, first strand: chain 'H' and resid 237 through 240 removed outlier: 6.803A pdb=" N VAL H 288 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU H 240 " --> pdb=" O VAL H 288 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU H 290 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N PHE H 309 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N SER H 291 " --> pdb=" O PHE H 309 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA H 311 " --> pdb=" O SER H 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'H' and resid 405 through 407 Processing sheet with id= AQ, first strand: chain 'H' and resid 475 through 478 Processing sheet with id= AR, first strand: chain 'Q' and resid 20 through 22 Processing sheet with id= AS, first strand: chain 'Q' and resid 54 through 57 Processing sheet with id= AT, first strand: chain 'Q' and resid 202 through 208 removed outlier: 6.592A pdb=" N SER Q 373 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N CYS Q 205 " --> pdb=" O SER Q 373 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE Q 375 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N ILE Q 207 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LEU Q 377 " --> pdb=" O ILE Q 207 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'Q' and resid 220 through 223 removed outlier: 3.507A pdb=" N THR Q 358 " --> pdb=" O VAL Q 355 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'Q' and resid 240 through 242 removed outlier: 6.012A pdb=" N MET Q 311 " --> pdb=" O VAL Q 291 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N THR Q 293 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL Q 313 " --> pdb=" O THR Q 293 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'Q' and resid 498 through 500 removed outlier: 3.932A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) removed outlier: 8.556A pdb=" N VAL Q 147 " --> pdb=" O PRO Q 410 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id= AY, first strand: chain 'Z' and resid 12 through 15 removed outlier: 3.556A pdb=" N GLU Z 12 " --> pdb=" O ARG Z 523 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'Z' and resid 45 through 48 Processing sheet with id= BA, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.824A pdb=" N VAL Z 372 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N MET Z 194 " --> pdb=" O VAL Z 372 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N LEU Z 374 " --> pdb=" O MET Z 194 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N MET Z 196 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ILE Z 376 " --> pdb=" O MET Z 196 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER Z 205 " --> pdb=" O LEU Z 375 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id= BC, first strand: chain 'Z' and resid 345 through 347 Processing sheet with id= BD, first strand: chain 'Z' and resid 407 through 409 Processing sheet with id= BE, first strand: chain 'Z' and resid 477 through 479 removed outlier: 3.694A pdb=" N MET Z 487 " --> pdb=" O GLY Z 478 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'a' and resid 9 through 13 Processing sheet with id= BG, first strand: chain 'a' and resid 43 through 46 Processing sheet with id= BH, first strand: chain 'a' and resid 180 through 182 Processing sheet with id= BI, first strand: chain 'a' and resid 196 through 201 removed outlier: 3.517A pdb=" N GLY a 379 " --> pdb=" O ALA a 200 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'a' and resid 213 through 216 Processing sheet with id= BK, first strand: chain 'a' and resid 346 through 348 removed outlier: 6.653A pdb=" N VAL a 285 " --> pdb=" O ALA a 235 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N LEU a 237 " --> pdb=" O VAL a 285 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU a 287 " --> pdb=" O LEU a 237 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N MET a 306 " --> pdb=" O ILE a 286 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N THR a 288 " --> pdb=" O MET a 306 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL a 308 " --> pdb=" O THR a 288 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'a' and resid 408 through 410 Processing sheet with id= BM, first strand: chain 'a' and resid 486 through 489 Processing sheet with id= BN, first strand: chain 'b' and resid 17 through 19 Processing sheet with id= BO, first strand: chain 'b' and resid 50 through 53 Processing sheet with id= BP, first strand: chain 'b' and resid 199 through 205 removed outlier: 6.405A pdb=" N CYS b 371 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ILE b 202 " --> pdb=" O CYS b 371 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE b 373 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N LYS b 204 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N LEU b 375 " --> pdb=" O LYS b 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= BP Processing sheet with id= BQ, first strand: chain 'b' and resid 218 through 220 Processing sheet with id= BR, first strand: chain 'b' and resid 344 through 346 removed outlier: 6.829A pdb=" N CYS b 289 " --> pdb=" O LEU b 238 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA b 240 " --> pdb=" O CYS b 289 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE b 291 " --> pdb=" O ALA b 240 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N MET b 310 " --> pdb=" O PHE b 290 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ASN b 292 " --> pdb=" O MET b 310 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE b 312 " --> pdb=" O ASN b 292 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'b' and resid 406 through 408 Processing sheet with id= BT, first strand: chain 'b' and resid 476 through 479 Processing sheet with id= BU, first strand: chain 'd' and resid 59 through 62 Processing sheet with id= BV, first strand: chain 'd' and resid 208 through 214 removed outlier: 6.682A pdb=" N VAL d 386 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N VAL d 211 " --> pdb=" O VAL d 386 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE d 388 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N LYS d 213 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL d 390 " --> pdb=" O LYS d 213 " (cutoff:3.500A) No H-bonds generated for sheet with id= BV Processing sheet with id= BW, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.591A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'd' and resid 357 through 359 removed outlier: 6.569A pdb=" N VAL d 297 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N ILE d 249 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU d 299 " --> pdb=" O ILE d 249 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N MET d 323 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N ILE d 300 " --> pdb=" O MET d 323 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE d 325 " --> pdb=" O ILE d 300 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'd' and resid 421 through 423 Processing sheet with id= BZ, first strand: chain 'd' and resid 491 through 494 Processing sheet with id= CA, first strand: chain 'e' and resid 26 through 29 Processing sheet with id= CB, first strand: chain 'e' and resid 59 through 62 Processing sheet with id= CC, first strand: chain 'e' and resid 209 through 215 removed outlier: 7.084A pdb=" N VAL e 383 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N GLU e 212 " --> pdb=" O VAL e 383 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N ILE e 385 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N LYS e 214 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE e 387 " --> pdb=" O LYS e 214 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'e' and resid 228 through 230 Processing sheet with id= CE, first strand: chain 'e' and resid 354 through 356 removed outlier: 7.101A pdb=" N LEU e 299 " --> pdb=" O ALA e 249 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'e' and resid 418 through 420 Processing sheet with id= CG, first strand: chain 'g' and resid 15 through 18 Processing sheet with id= CH, first strand: chain 'g' and resid 48 through 51 Processing sheet with id= CI, first strand: chain 'g' and resid 185 through 187 Processing sheet with id= CJ, first strand: chain 'g' and resid 200 through 205 removed outlier: 3.732A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) Processing sheet with id= CK, first strand: chain 'g' and resid 218 through 220 Processing sheet with id= CL, first strand: chain 'g' and resid 238 through 241 removed outlier: 6.466A pdb=" N VAL g 289 " --> pdb=" O VAL g 239 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N LEU g 241 " --> pdb=" O VAL g 289 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE g 291 " --> pdb=" O LEU g 241 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR g 310 " --> pdb=" O VAL g 290 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N THR g 292 " --> pdb=" O THR g 310 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE g 312 " --> pdb=" O THR g 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= CL Processing sheet with id= CM, first strand: chain 'g' and resid 407 through 409 Processing sheet with id= CN, first strand: chain 'g' and resid 478 through 480 Processing sheet with id= CO, first strand: chain 'h' and resid 14 through 17 Processing sheet with id= CP, first strand: chain 'h' and resid 47 through 50 Processing sheet with id= CQ, first strand: chain 'h' and resid 195 through 201 removed outlier: 6.573A pdb=" N CYS h 370 " --> pdb=" O GLY h 196 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LYS h 198 " --> pdb=" O CYS h 370 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N PHE h 372 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N VAL h 200 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LEU h 374 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR h 371 " --> pdb=" O VAL h 211 " (cutoff:3.500A) Processing sheet with id= CR, first strand: chain 'h' and resid 214 through 217 Processing sheet with id= CS, first strand: chain 'h' and resid 237 through 240 removed outlier: 7.138A pdb=" N VAL h 288 " --> pdb=" O ALA h 238 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU h 240 " --> pdb=" O VAL h 288 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU h 290 " --> pdb=" O LEU h 240 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N PHE h 309 " --> pdb=" O VAL h 289 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N SER h 291 " --> pdb=" O PHE h 309 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ALA h 311 " --> pdb=" O SER h 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= CS Processing sheet with id= CT, first strand: chain 'h' and resid 405 through 407 Processing sheet with id= CU, first strand: chain 'h' and resid 475 through 478 Processing sheet with id= CV, first strand: chain 'q' and resid 20 through 23 Processing sheet with id= CW, first strand: chain 'q' and resid 54 through 57 Processing sheet with id= CX, first strand: chain 'q' and resid 202 through 208 removed outlier: 6.658A pdb=" N SER q 373 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N CYS q 205 " --> pdb=" O SER q 373 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE q 375 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N ILE q 207 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU q 377 " --> pdb=" O ILE q 207 " (cutoff:3.500A) Processing sheet with id= CY, first strand: chain 'q' and resid 220 through 223 Processing sheet with id= CZ, first strand: chain 'q' and resid 240 through 242 removed outlier: 6.107A pdb=" N MET q 311 " --> pdb=" O VAL q 291 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N THR q 293 " --> pdb=" O MET q 311 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL q 313 " --> pdb=" O THR q 293 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'q' and resid 498 through 500 removed outlier: 3.831A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N VAL q 147 " --> pdb=" O PRO q 410 " (cutoff:3.500A) Processing sheet with id= DB, first strand: chain 'q' and resid 478 through 480 Processing sheet with id= DC, first strand: chain 'z' and resid 12 through 15 Processing sheet with id= DD, first strand: chain 'z' and resid 45 through 48 Processing sheet with id= DE, first strand: chain 'z' and resid 191 through 196 removed outlier: 6.880A pdb=" N VAL z 372 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N MET z 194 " --> pdb=" O VAL z 372 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU z 374 " --> pdb=" O MET z 194 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N MET z 196 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ILE z 376 " --> pdb=" O MET z 196 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N SER z 205 " --> pdb=" O LEU z 375 " (cutoff:3.500A) Processing sheet with id= DF, first strand: chain 'z' and resid 210 through 212 Processing sheet with id= DG, first strand: chain 'z' and resid 345 through 347 Processing sheet with id= DH, first strand: chain 'z' and resid 477 through 479 3483 hydrogen bonds defined for protein. 9009 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: 30.89 Time building geometry restraints manager: 22.45 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: 22830 1.34 - 1.46: 9480 1.46 - 1.58: 35680 1.58 - 1.70: 48 1.70 - 1.82: 745 Bond restraints: 68783 Sorted by residual: bond pdb=" F2 AF3 z 603 " pdb="AL AF3 z 603 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" F2 AF3 a 603 " pdb="AL AF3 a 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.43e+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 6.38e+01 bond pdb=" F2 AF3 A 603 " pdb="AL AF3 A 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.38e+01 bond pdb=" F2 AF3 g 603 " pdb="AL AF3 g 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.37e+01 ... (remaining 68778 not shown) Histogram of bond angle deviations from ideal: 97.59 - 105.32: 1071 105.32 - 113.06: 39627 113.06 - 120.80: 31370 120.80 - 128.54: 20497 128.54 - 136.28: 297 Bond angle restraints: 92862 Sorted by residual: angle pdb=" C ASP a 47 " pdb=" N ASP a 48 " pdb=" CA ASP a 48 " ideal model delta sigma weight residual 122.61 127.92 -5.31 1.56e+00 4.11e-01 1.16e+01 angle pdb=" C GLU P 147 " pdb=" N MET P 148 " pdb=" CA MET P 148 " ideal model delta sigma weight residual 122.38 116.35 6.03 1.81e+00 3.05e-01 1.11e+01 angle pdb=" C VAL d 275 " pdb=" N LEU d 276 " pdb=" CA LEU d 276 " ideal model delta sigma weight residual 120.31 115.36 4.95 1.52e+00 4.33e-01 1.06e+01 angle pdb=" N GLY q 209 " pdb=" CA GLY q 209 " pdb=" C GLY q 209 " ideal model delta sigma weight residual 113.18 120.46 -7.28 2.37e+00 1.78e-01 9.43e+00 angle pdb=" C ALA Q 151 " pdb=" N LYS Q 152 " pdb=" CA LYS Q 152 " ideal model delta sigma weight residual 121.54 127.34 -5.80 1.91e+00 2.74e-01 9.21e+00 ... (remaining 92857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 41838 35.91 - 71.83: 585 71.83 - 107.74: 61 107.74 - 143.66: 7 143.66 - 179.57: 6 Dihedral angle restraints: 42497 sinusoidal: 17100 harmonic: 25397 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 -60.00 119.57 -179.57 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 -60.00 116.13 -176.13 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP q 601 " pdb=" O3A ADP q 601 " pdb=" PA ADP q 601 " pdb=" PB ADP q 601 " ideal model delta sinusoidal sigma weight residual 300.00 127.11 172.89 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 42494 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 7582 0.033 - 0.067: 2299 0.067 - 0.100: 717 0.100 - 0.133: 433 0.133 - 0.167: 16 Chirality restraints: 11047 Sorted by residual: chirality pdb=" CA ASP a 48 " pdb=" N ASP a 48 " pdb=" C ASP a 48 " pdb=" CB ASP a 48 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CB ILE G 363 " pdb=" CA ILE G 363 " pdb=" CG1 ILE G 363 " pdb=" CG2 ILE G 363 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CA GLN e 522 " pdb=" N GLN e 522 " pdb=" C GLN e 522 " pdb=" CB GLN e 522 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.88e-01 ... (remaining 11044 not shown) Planarity restraints: 11854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG G 5 " 0.056 5.00e-02 4.00e+02 8.27e-02 1.09e+01 pdb=" N PRO G 6 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO G 6 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO G 6 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP a 47 " -0.011 2.00e-02 2.50e+03 2.26e-02 5.12e+00 pdb=" C ASP a 47 " 0.039 2.00e-02 2.50e+03 pdb=" O ASP a 47 " -0.015 2.00e-02 2.50e+03 pdb=" N ASP a 48 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO e 441 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.031 5.00e-02 4.00e+02 ... (remaining 11851 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 553 2.53 - 3.12: 52123 3.12 - 3.72: 107587 3.72 - 4.31: 151206 4.31 - 4.90: 257641 Nonbonded interactions: 569110 Sorted by model distance: nonbonded pdb="MG MG e 602 " pdb=" F1 AF3 e 603 " model vdw 1.938 2.120 nonbonded pdb=" O1A ADP z 601 " pdb="MG MG z 602 " model vdw 1.982 2.170 nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.983 2.120 nonbonded pdb="MG MG g 602 " pdb=" F1 AF3 g 603 " model vdw 1.984 2.120 nonbonded pdb=" OD1 ASP b 97 " pdb="MG MG b 602 " model vdw 1.985 2.170 ... (remaining 569105 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 535 or resid 601 through 603)) selection = chain 'a' } ncs_group { reference = (chain 'B' and (resid 2 through 526 or resid 601 through 603)) selection = chain 'b' } ncs_group { reference = (chain 'D' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 538 or resid 601 through 603)) selection = chain 'd' } ncs_group { reference = (chain 'E' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) selection = (chain 'e' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) } ncs_group { reference = (chain 'G' and (resid 5 through 528 or resid 601 through 603)) selection = (chain 'g' and (resid 5 through 528 or resid 601 through 603)) } ncs_group { reference = (chain 'H' and (resid 1 through 525 or resid 601 through 603)) selection = chain 'h' } ncs_group { reference = (chain 'Q' and (resid 2 through 534 or resid 601 through 603)) selection = chain 'q' } ncs_group { reference = chain 'Z' selection = (chain 'z' and (resid 2 through 526 or resid 601 through 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 8.260 Check model and map are aligned: 0.740 Set scattering table: 0.450 Process input model: 152.670 Find NCS groups from input model: 6.270 Set up NCS constraints: 0.560 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:11.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 182.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 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 0.161 68783 Z= 0.260 Angle : 0.514 10.599 92862 Z= 0.251 Chirality : 0.040 0.167 11047 Planarity : 0.003 0.083 11854 Dihedral : 14.165 179.570 26047 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.32 % Favored : 96.66 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 1.83 (0.09), residues: 8778 helix: 2.52 (0.08), residues: 4439 sheet: 0.32 (0.16), residues: 1163 loop : -0.32 (0.11), residues: 3176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g 168 HIS 0.009 0.001 HIS z 161 PHE 0.019 0.001 PHE h 455 TYR 0.015 0.001 TYR z 351 ARG 0.004 0.000 ARG Z 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 604 time to evaluate : 6.086 Fit side-chains revert: symmetry clash REVERT: P 84 MET cc_start: 0.6265 (ttp) cc_final: 0.5745 (mtm) REVERT: N 184 MET cc_start: 0.8670 (tmm) cc_final: 0.8406 (tmm) REVERT: N 288 ARG cc_start: 0.8120 (ttm110) cc_final: 0.7539 (ttp-110) REVERT: N 308 TYR cc_start: 0.8225 (m-80) cc_final: 0.7684 (m-80) REVERT: A 47 ASP cc_start: 0.8067 (m-30) cc_final: 0.7651 (m-30) REVERT: G 152 MET cc_start: 0.9095 (mmm) cc_final: 0.8886 (mmm) REVERT: H 14 ASP cc_start: 0.8373 (t0) cc_final: 0.8078 (t0) REVERT: Z 86 ASP cc_start: 0.8144 (m-30) cc_final: 0.7908 (m-30) REVERT: a 473 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7805 (OUTLIER) REVERT: d 513 LEU cc_start: 0.9074 (tp) cc_final: 0.8834 (tm) REVERT: e 21 ASP cc_start: 0.8635 (m-30) cc_final: 0.8413 (m-30) REVERT: e 67 ASP cc_start: 0.8552 (m-30) cc_final: 0.8325 (m-30) REVERT: g 415 GLU cc_start: 0.8241 (mp0) cc_final: 0.8026 (mp0) REVERT: h 324 MET cc_start: 0.9219 (mmm) cc_final: 0.8837 (mmm) REVERT: h 440 LYS cc_start: 0.9130 (tttt) cc_final: 0.8925 (mtpp) REVERT: q 121 ILE cc_start: 0.8925 (pt) cc_final: 0.8718 (pt) REVERT: z 10 LYS cc_start: 0.9009 (pttm) cc_final: 0.8735 (pmtt) REVERT: z 17 GLN cc_start: 0.8769 (mp10) cc_final: 0.8550 (mp10) REVERT: z 389 ASP cc_start: 0.8496 (m-30) cc_final: 0.8155 (m-30) outliers start: 0 outliers final: 3 residues processed: 604 average time/residue: 1.6064 time to fit residues: 1247.0389 Evaluate side-chains 480 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 478 time to evaluate : 6.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain G residue 519 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 738 optimal weight: 10.0000 chunk 663 optimal weight: 0.9980 chunk 368 optimal weight: 0.6980 chunk 226 optimal weight: 0.0870 chunk 447 optimal weight: 1.9990 chunk 354 optimal weight: 0.9990 chunk 685 optimal weight: 10.0000 chunk 265 optimal weight: 0.9980 chunk 417 optimal weight: 10.0000 chunk 510 optimal weight: 0.9980 chunk 794 optimal weight: 7.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN E 522 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 217 ASN b 91 GLN d 25 GLN d 468 ASN ** d 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 41 GLN ** z 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS z 380 ASN z 382 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.0566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 68783 Z= 0.141 Angle : 0.513 8.886 92862 Z= 0.256 Chirality : 0.040 0.151 11047 Planarity : 0.004 0.057 11854 Dihedral : 7.312 176.626 9546 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.17 % Favored : 96.81 % Rotamer: Outliers : 0.53 % Allowed : 5.93 % Favored : 93.54 % 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: 1.64 (0.09), residues: 8778 helix: 2.28 (0.08), residues: 4443 sheet: 0.37 (0.16), residues: 1126 loop : -0.33 (0.11), residues: 3209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 222 HIS 0.009 0.001 HIS z 161 PHE 0.021 0.001 PHE P 158 TYR 0.012 0.001 TYR E 420 ARG 0.007 0.000 ARG H 425 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 513 time to evaluate : 6.134 Fit side-chains revert: symmetry clash REVERT: P 84 MET cc_start: 0.6186 (ttp) cc_final: 0.5811 (mpp) REVERT: N 184 MET cc_start: 0.8680 (tmm) cc_final: 0.8441 (tmm) REVERT: N 280 HIS cc_start: 0.7887 (m90) cc_final: 0.7567 (m-70) REVERT: N 290 TYR cc_start: 0.8570 (t80) cc_final: 0.8325 (t80) REVERT: N 296 PHE cc_start: 0.9229 (p90) cc_final: 0.9002 (p90) REVERT: N 308 TYR cc_start: 0.8066 (m-80) cc_final: 0.7608 (m-10) REVERT: A 47 ASP cc_start: 0.7851 (m-30) cc_final: 0.7394 (m-30) REVERT: A 106 GLU cc_start: 0.8432 (tp30) cc_final: 0.8170 (tp30) REVERT: B 415 MET cc_start: 0.9307 (mmm) cc_final: 0.9088 (mmp) REVERT: E 4 MET cc_start: 0.6123 (tmm) cc_final: 0.5341 (mpp) REVERT: E 48 MET cc_start: 0.9229 (tpp) cc_final: 0.9011 (mmp) REVERT: G 47 MET cc_start: 0.8703 (mtp) cc_final: 0.8356 (mtp) REVERT: G 152 MET cc_start: 0.9082 (mmm) cc_final: 0.8833 (mmm) REVERT: G 527 LYS cc_start: 0.9023 (tppt) cc_final: 0.8621 (tppt) REVERT: H 14 ASP cc_start: 0.8394 (t0) cc_final: 0.8107 (t0) REVERT: H 53 ARG cc_start: 0.8420 (mtt180) cc_final: 0.8196 (mtt180) REVERT: H 317 GLU cc_start: 0.7925 (tt0) cc_final: 0.7710 (tt0) REVERT: Z 86 ASP cc_start: 0.8119 (m-30) cc_final: 0.7885 (m-30) REVERT: a 47 ASP cc_start: 0.8257 (p0) cc_final: 0.8055 (p0) REVERT: a 156 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8643 (mtp) REVERT: a 473 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7730 (mp0) REVERT: b 452 ASP cc_start: 0.8149 (m-30) cc_final: 0.7811 (m-30) REVERT: e 4 MET cc_start: 0.6123 (mpp) cc_final: 0.5673 (mpp) REVERT: e 21 ASP cc_start: 0.8622 (m-30) cc_final: 0.8389 (m-30) REVERT: g 152 MET cc_start: 0.9317 (mmp) cc_final: 0.9024 (mmp) REVERT: g 415 GLU cc_start: 0.8262 (mp0) cc_final: 0.8047 (mp0) REVERT: g 527 LYS cc_start: 0.8645 (mmmm) cc_final: 0.8330 (mmmm) REVERT: h 324 MET cc_start: 0.9219 (mmm) cc_final: 0.8893 (mmm) REVERT: h 440 LYS cc_start: 0.9119 (tttt) cc_final: 0.8916 (mtpp) REVERT: z 10 LYS cc_start: 0.9083 (pttm) cc_final: 0.8764 (pmtt) REVERT: z 244 VAL cc_start: 0.8391 (OUTLIER) cc_final: 0.8018 (t) REVERT: z 389 ASP cc_start: 0.8491 (m-30) cc_final: 0.8159 (m-30) REVERT: z 520 GLU cc_start: 0.8509 (tt0) cc_final: 0.8304 (tt0) outliers start: 39 outliers final: 11 residues processed: 524 average time/residue: 1.5400 time to fit residues: 1051.5809 Evaluate side-chains 495 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 482 time to evaluate : 5.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 234 HIS Chi-restraints excluded: chain N residue 307 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Z residue 404 ASP Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain g residue 364 THR Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 415 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 441 optimal weight: 3.9990 chunk 246 optimal weight: 5.9990 chunk 661 optimal weight: 1.9990 chunk 541 optimal weight: 0.9990 chunk 219 optimal weight: 5.9990 chunk 796 optimal weight: 5.9990 chunk 859 optimal weight: 10.0000 chunk 708 optimal weight: 0.1980 chunk 789 optimal weight: 3.9990 chunk 271 optimal weight: 4.9990 chunk 638 optimal weight: 10.0000 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 231 GLN A 164 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 470 GLN ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN Z 161 HIS ** d 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.0694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 68783 Z= 0.214 Angle : 0.522 11.589 92862 Z= 0.256 Chirality : 0.041 0.161 11047 Planarity : 0.004 0.057 11854 Dihedral : 6.949 176.765 9542 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.49 % Favored : 96.49 % Rotamer: Outliers : 0.67 % Allowed : 7.44 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.09), residues: 8778 helix: 2.13 (0.08), residues: 4451 sheet: 0.23 (0.16), residues: 1155 loop : -0.36 (0.11), residues: 3172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 222 HIS 0.011 0.001 HIS z 161 PHE 0.017 0.001 PHE P 158 TYR 0.028 0.001 TYR A 181 ARG 0.009 0.000 ARG H 425 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 494 time to evaluate : 6.107 Fit side-chains revert: symmetry clash REVERT: P 84 MET cc_start: 0.6163 (ttp) cc_final: 0.5664 (mpp) REVERT: P 198 MET cc_start: 0.8762 (ppp) cc_final: 0.8526 (ppp) REVERT: N 182 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7424 (tm-30) REVERT: N 290 TYR cc_start: 0.8559 (t80) cc_final: 0.8340 (t80) REVERT: N 306 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.7305 (pmm-80) REVERT: N 308 TYR cc_start: 0.8076 (m-80) cc_final: 0.7631 (m-10) REVERT: B 4 LEU cc_start: 0.8813 (tt) cc_final: 0.8587 (tt) REVERT: B 245 ASP cc_start: 0.8795 (p0) cc_final: 0.8586 (p0) REVERT: E 4 MET cc_start: 0.6092 (tmm) cc_final: 0.5553 (ptp) REVERT: G 47 MET cc_start: 0.8783 (mtp) cc_final: 0.8495 (mtp) REVERT: G 152 MET cc_start: 0.9111 (mmm) cc_final: 0.8908 (mmm) REVERT: H 14 ASP cc_start: 0.8322 (t0) cc_final: 0.8084 (t0) REVERT: H 53 ARG cc_start: 0.8435 (mtt180) cc_final: 0.8148 (mtt180) REVERT: H 317 GLU cc_start: 0.7913 (tt0) cc_final: 0.7680 (tt0) REVERT: Z 86 ASP cc_start: 0.8180 (m-30) cc_final: 0.7922 (m-30) REVERT: a 47 ASP cc_start: 0.8418 (p0) cc_final: 0.8112 (p0) REVERT: a 156 MET cc_start: 0.8880 (OUTLIER) cc_final: 0.8605 (mtp) REVERT: a 473 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7776 (OUTLIER) REVERT: b 452 ASP cc_start: 0.8223 (m-30) cc_final: 0.7983 (m-30) REVERT: e 4 MET cc_start: 0.6172 (mpp) cc_final: 0.5623 (mpp) REVERT: e 21 ASP cc_start: 0.8656 (m-30) cc_final: 0.8424 (m-30) REVERT: e 526 MET cc_start: 0.9207 (ttt) cc_final: 0.8883 (ttt) REVERT: g 152 MET cc_start: 0.9335 (mmp) cc_final: 0.9023 (mmp) REVERT: g 415 GLU cc_start: 0.8251 (mp0) cc_final: 0.8013 (mp0) REVERT: h 324 MET cc_start: 0.9220 (mmm) cc_final: 0.8814 (mmm) REVERT: q 61 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8002 (mm-30) REVERT: z 10 LYS cc_start: 0.9127 (pttm) cc_final: 0.8745 (pmtt) REVERT: z 389 ASP cc_start: 0.8511 (m-30) cc_final: 0.8204 (m-30) outliers start: 49 outliers final: 23 residues processed: 517 average time/residue: 1.5468 time to fit residues: 1038.4353 Evaluate side-chains 501 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 477 time to evaluate : 6.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain P residue 159 LYS Chi-restraints excluded: chain N residue 234 HIS Chi-restraints excluded: chain N residue 306 ARG Chi-restraints excluded: chain N residue 307 LEU Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 73 ASP Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Z residue 404 ASP Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 244 MET Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 458 MET Chi-restraints excluded: chain e residue 31 LEU Chi-restraints excluded: chain g residue 255 ASP Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain z residue 415 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 786 optimal weight: 10.0000 chunk 598 optimal weight: 3.9990 chunk 413 optimal weight: 9.9990 chunk 88 optimal weight: 10.0000 chunk 379 optimal weight: 7.9990 chunk 534 optimal weight: 2.9990 chunk 798 optimal weight: 9.9990 chunk 845 optimal weight: 3.9990 chunk 417 optimal weight: 10.0000 chunk 757 optimal weight: 2.9990 chunk 227 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 103 ASN A 164 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 217 ASN a 435 GLN ** b 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 41 GLN ** z 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.0983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 68783 Z= 0.344 Angle : 0.572 10.176 92862 Z= 0.282 Chirality : 0.042 0.208 11047 Planarity : 0.004 0.056 11854 Dihedral : 7.004 179.838 9542 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.99 % Favored : 95.99 % Rotamer: Outliers : 0.79 % Allowed : 8.73 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.09), residues: 8778 helix: 1.99 (0.08), residues: 4457 sheet: 0.12 (0.16), residues: 1172 loop : -0.38 (0.11), residues: 3149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP e 304 HIS 0.011 0.001 HIS z 161 PHE 0.021 0.001 PHE E 16 TYR 0.015 0.001 TYR E 420 ARG 0.008 0.000 ARG N 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 482 time to evaluate : 6.079 Fit side-chains revert: symmetry clash REVERT: P 84 MET cc_start: 0.6175 (ttp) cc_final: 0.5675 (mpp) REVERT: N 182 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7561 (tm-30) REVERT: N 288 ARG cc_start: 0.8090 (ttm110) cc_final: 0.7652 (ttp-170) REVERT: N 290 TYR cc_start: 0.8566 (t80) cc_final: 0.8358 (t80) REVERT: N 314 ARG cc_start: 0.8334 (mtm110) cc_final: 0.8110 (mtm110) REVERT: E 4 MET cc_start: 0.5997 (tmm) cc_final: 0.4951 (mpp) REVERT: E 474 MET cc_start: 0.8448 (tmm) cc_final: 0.8162 (tmt) REVERT: G 47 MET cc_start: 0.8872 (mtp) cc_final: 0.8616 (mtp) REVERT: H 14 ASP cc_start: 0.8394 (t0) cc_final: 0.8137 (t0) REVERT: H 53 ARG cc_start: 0.8436 (mtt180) cc_final: 0.8235 (mtt180) REVERT: H 317 GLU cc_start: 0.7991 (tt0) cc_final: 0.7732 (tt0) REVERT: H 524 ARG cc_start: 0.7603 (mtp-110) cc_final: 0.7340 (mmm160) REVERT: Q 499 ASP cc_start: 0.8538 (m-30) cc_final: 0.8320 (m-30) REVERT: Z 86 ASP cc_start: 0.8249 (m-30) cc_final: 0.7986 (m-30) REVERT: a 47 ASP cc_start: 0.8511 (p0) cc_final: 0.8248 (p0) REVERT: a 473 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7816 (OUTLIER) REVERT: b 452 ASP cc_start: 0.8221 (m-30) cc_final: 0.7894 (m-30) REVERT: e 4 MET cc_start: 0.6276 (mpp) cc_final: 0.5682 (mpp) REVERT: e 21 ASP cc_start: 0.8710 (m-30) cc_final: 0.8451 (m-30) REVERT: e 526 MET cc_start: 0.9205 (ttt) cc_final: 0.8906 (ttt) REVERT: g 152 MET cc_start: 0.9361 (mmp) cc_final: 0.9039 (mmp) REVERT: g 415 GLU cc_start: 0.8248 (mp0) cc_final: 0.8044 (mp0) REVERT: g 527 LYS cc_start: 0.9110 (mtmp) cc_final: 0.8695 (mmmm) REVERT: h 324 MET cc_start: 0.9226 (mmm) cc_final: 0.8886 (mmm) REVERT: z 10 LYS cc_start: 0.9041 (pttm) cc_final: 0.8757 (pmtt) REVERT: z 244 VAL cc_start: 0.8453 (OUTLIER) cc_final: 0.8044 (t) REVERT: z 389 ASP cc_start: 0.8576 (m-30) cc_final: 0.8232 (m-30) outliers start: 58 outliers final: 27 residues processed: 514 average time/residue: 1.5494 time to fit residues: 1034.5723 Evaluate side-chains 488 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 461 time to evaluate : 6.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain P residue 159 LYS Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 234 HIS Chi-restraints excluded: chain N residue 252 ASN Chi-restraints excluded: chain N residue 306 ARG Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 324 MET Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Z residue 404 ASP Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 248 LYS Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 458 MET Chi-restraints excluded: chain e residue 31 LEU Chi-restraints excluded: chain g residue 255 ASP Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain z residue 17 GLN Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 415 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 704 optimal weight: 6.9990 chunk 480 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 chunk 629 optimal weight: 4.9990 chunk 348 optimal weight: 10.0000 chunk 721 optimal weight: 0.8980 chunk 584 optimal weight: 0.0370 chunk 0 optimal weight: 50.0000 chunk 431 optimal weight: 0.2980 chunk 759 optimal weight: 0.9990 chunk 213 optimal weight: 0.4980 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 275 GLN A 103 ASN A 164 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 217 ASN ** d 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 68783 Z= 0.124 Angle : 0.509 14.460 92862 Z= 0.248 Chirality : 0.040 0.188 11047 Planarity : 0.003 0.058 11854 Dihedral : 6.632 171.806 9542 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.18 % Favored : 96.80 % Rotamer: Outliers : 0.79 % Allowed : 9.62 % Favored : 89.59 % 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: 8778 helix: 2.10 (0.08), residues: 4437 sheet: 0.13 (0.16), residues: 1167 loop : -0.33 (0.11), residues: 3174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 222 HIS 0.012 0.001 HIS z 161 PHE 0.027 0.001 PHE N 296 TYR 0.029 0.001 TYR A 181 ARG 0.009 0.000 ARG H 425 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 502 time to evaluate : 6.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 84 MET cc_start: 0.6162 (ttp) cc_final: 0.5642 (mtt) REVERT: P 198 MET cc_start: 0.8750 (ppp) cc_final: 0.8506 (ppp) REVERT: N 210 ILE cc_start: 0.8958 (pt) cc_final: 0.8597 (pp) REVERT: N 288 ARG cc_start: 0.8058 (ttm110) cc_final: 0.7561 (ttp-170) REVERT: N 308 TYR cc_start: 0.7946 (m-80) cc_final: 0.7633 (m-80) REVERT: N 314 ARG cc_start: 0.8295 (mtm110) cc_final: 0.8040 (mtm110) REVERT: E 4 MET cc_start: 0.6034 (tmm) cc_final: 0.5320 (ptm) REVERT: E 448 MET cc_start: 0.8948 (mtt) cc_final: 0.8674 (mmm) REVERT: E 474 MET cc_start: 0.8413 (tmm) cc_final: 0.7987 (tmt) REVERT: G 497 GLU cc_start: 0.8310 (pt0) cc_final: 0.8099 (pt0) REVERT: H 14 ASP cc_start: 0.8366 (t0) cc_final: 0.8091 (t0) REVERT: H 53 ARG cc_start: 0.8486 (mtt180) cc_final: 0.8262 (mtt180) REVERT: H 317 GLU cc_start: 0.8008 (tt0) cc_final: 0.7766 (tt0) REVERT: Z 86 ASP cc_start: 0.8151 (m-30) cc_final: 0.7907 (m-30) REVERT: Z 244 VAL cc_start: 0.8465 (OUTLIER) cc_final: 0.8252 (t) REVERT: a 47 ASP cc_start: 0.8574 (p0) cc_final: 0.8233 (p0) REVERT: a 473 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7746 (OUTLIER) REVERT: b 452 ASP cc_start: 0.8176 (m-30) cc_final: 0.7924 (m-30) REVERT: e 4 MET cc_start: 0.6299 (mpp) cc_final: 0.5663 (mpp) REVERT: e 21 ASP cc_start: 0.8632 (m-30) cc_final: 0.8416 (m-30) REVERT: e 80 MET cc_start: 0.8998 (mmt) cc_final: 0.8468 (mtt) REVERT: e 526 MET cc_start: 0.9175 (ttt) cc_final: 0.8894 (ttt) REVERT: g 152 MET cc_start: 0.9289 (mmp) cc_final: 0.8987 (mmp) REVERT: g 527 LYS cc_start: 0.9014 (mtmp) cc_final: 0.8595 (mmmm) REVERT: h 2 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7849 (mmm) REVERT: h 324 MET cc_start: 0.9236 (mmm) cc_final: 0.8870 (mmm) REVERT: z 10 LYS cc_start: 0.9027 (pttm) cc_final: 0.8699 (pmtt) REVERT: z 244 VAL cc_start: 0.8317 (OUTLIER) cc_final: 0.7902 (t) REVERT: z 389 ASP cc_start: 0.8538 (m-30) cc_final: 0.8184 (m-30) outliers start: 58 outliers final: 20 residues processed: 539 average time/residue: 1.5168 time to fit residues: 1074.8517 Evaluate side-chains 502 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 480 time to evaluate : 6.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 234 HIS Chi-restraints excluded: chain N residue 307 LEU Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain Z residue 404 ASP Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain e residue 31 LEU Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain h residue 482 GLU Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 17 GLN Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 284 optimal weight: 8.9990 chunk 761 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 496 optimal weight: 2.9990 chunk 208 optimal weight: 0.0170 chunk 846 optimal weight: 10.0000 chunk 702 optimal weight: 0.0020 chunk 391 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 280 optimal weight: 1.9990 chunk 444 optimal weight: 4.9990 overall best weight: 2.0032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 151 GLN A 164 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 394 ASN ** d 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 41 GLN ** z 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 68783 Z= 0.199 Angle : 0.522 15.277 92862 Z= 0.253 Chirality : 0.040 0.160 11047 Planarity : 0.003 0.056 11854 Dihedral : 6.505 171.549 9542 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.44 % Favored : 96.53 % Rotamer: Outliers : 0.87 % Allowed : 10.29 % Favored : 88.84 % 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: 1.45 (0.09), residues: 8778 helix: 2.10 (0.08), residues: 4440 sheet: 0.13 (0.16), residues: 1179 loop : -0.32 (0.11), residues: 3159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 222 HIS 0.012 0.001 HIS z 161 PHE 0.015 0.001 PHE E 16 TYR 0.020 0.001 TYR Z 353 ARG 0.007 0.000 ARG H 425 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 480 time to evaluate : 6.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 84 MET cc_start: 0.6106 (ttp) cc_final: 0.5605 (mtt) REVERT: N 210 ILE cc_start: 0.8966 (pt) cc_final: 0.8605 (pp) REVERT: N 308 TYR cc_start: 0.8039 (m-80) cc_final: 0.7774 (m-80) REVERT: N 311 ARG cc_start: 0.8649 (mtm-85) cc_final: 0.8406 (mtp-110) REVERT: E 48 MET cc_start: 0.9179 (tpp) cc_final: 0.8971 (mmm) REVERT: E 474 MET cc_start: 0.8391 (tmm) cc_final: 0.8103 (tmt) REVERT: G 47 MET cc_start: 0.8796 (mtp) cc_final: 0.8530 (mtp) REVERT: G 497 GLU cc_start: 0.8310 (pt0) cc_final: 0.8100 (pt0) REVERT: H 14 ASP cc_start: 0.8299 (t0) cc_final: 0.8048 (t0) REVERT: H 53 ARG cc_start: 0.8437 (mtt180) cc_final: 0.8202 (mtt180) REVERT: H 317 GLU cc_start: 0.7993 (tt0) cc_final: 0.7747 (tt0) REVERT: Q 61 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8365 (mp0) REVERT: Z 86 ASP cc_start: 0.8186 (m-30) cc_final: 0.7926 (m-30) REVERT: Z 244 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8300 (t) REVERT: a 416 GLU cc_start: 0.8320 (mp0) cc_final: 0.7804 (mp0) REVERT: a 473 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7759 (OUTLIER) REVERT: b 452 ASP cc_start: 0.8188 (m-30) cc_final: 0.7952 (m-30) REVERT: e 4 MET cc_start: 0.6289 (mpp) cc_final: 0.5722 (mpp) REVERT: e 21 ASP cc_start: 0.8659 (m-30) cc_final: 0.8432 (m-30) REVERT: e 80 MET cc_start: 0.8983 (mmt) cc_final: 0.8770 (mtt) REVERT: e 448 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8520 (mmt) REVERT: g 152 MET cc_start: 0.9323 (mmp) cc_final: 0.8981 (mmp) REVERT: g 527 LYS cc_start: 0.9036 (mtmp) cc_final: 0.8638 (mmmm) REVERT: h 7 ILE cc_start: 0.8731 (OUTLIER) cc_final: 0.8482 (pp) REVERT: h 221 SER cc_start: 0.9159 (m) cc_final: 0.8951 (p) REVERT: h 324 MET cc_start: 0.9240 (mmm) cc_final: 0.8893 (mmm) REVERT: q 208 LEU cc_start: 0.8445 (mt) cc_final: 0.8219 (mt) REVERT: z 10 LYS cc_start: 0.9029 (pttm) cc_final: 0.8724 (pmtt) REVERT: z 244 VAL cc_start: 0.8337 (OUTLIER) cc_final: 0.7925 (t) REVERT: z 389 ASP cc_start: 0.8562 (m-30) cc_final: 0.8190 (m-30) outliers start: 64 outliers final: 32 residues processed: 517 average time/residue: 1.5040 time to fit residues: 1016.6809 Evaluate side-chains 509 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 473 time to evaluate : 5.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain P residue 159 LYS Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 234 HIS Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain Z residue 404 ASP Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 244 MET Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain e residue 448 MET Chi-restraints excluded: chain e residue 522 GLN Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 255 ASP Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 185 MET Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain z residue 17 GLN Chi-restraints excluded: chain z residue 69 ILE Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 415 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 816 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 482 optimal weight: 0.8980 chunk 618 optimal weight: 0.6980 chunk 479 optimal weight: 0.1980 chunk 712 optimal weight: 5.9990 chunk 472 optimal weight: 0.8980 chunk 843 optimal weight: 5.9990 chunk 527 optimal weight: 10.0000 chunk 514 optimal weight: 0.0670 chunk 389 optimal weight: 10.0000 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 56 ASN A 164 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 30 GLN ** h 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 68783 Z= 0.120 Angle : 0.506 12.435 92862 Z= 0.244 Chirality : 0.040 0.160 11047 Planarity : 0.003 0.065 11854 Dihedral : 6.286 163.934 9542 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.99 % Favored : 96.98 % Rotamer: Outliers : 0.77 % Allowed : 10.83 % 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: 1.50 (0.09), residues: 8778 helix: 2.15 (0.08), residues: 4436 sheet: 0.20 (0.16), residues: 1175 loop : -0.31 (0.11), residues: 3167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 222 HIS 0.014 0.000 HIS z 161 PHE 0.013 0.001 PHE g 362 TYR 0.029 0.001 TYR A 181 ARG 0.011 0.000 ARG N 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 508 time to evaluate : 6.115 Fit side-chains revert: symmetry clash REVERT: P 84 MET cc_start: 0.6102 (ttp) cc_final: 0.5568 (mtt) REVERT: N 210 ILE cc_start: 0.8901 (pt) cc_final: 0.8567 (pp) REVERT: N 308 TYR cc_start: 0.8008 (m-80) cc_final: 0.7415 (m-80) REVERT: N 311 ARG cc_start: 0.8607 (mtm-85) cc_final: 0.8375 (mtp180) REVERT: D 179 TYR cc_start: 0.9212 (m-80) cc_final: 0.8974 (m-80) REVERT: D 186 MET cc_start: 0.8592 (ttm) cc_final: 0.8154 (ttm) REVERT: E 4 MET cc_start: 0.6005 (OUTLIER) cc_final: 0.4926 (mtp) REVERT: E 474 MET cc_start: 0.8341 (tmm) cc_final: 0.8089 (tmt) REVERT: H 14 ASP cc_start: 0.8296 (t0) cc_final: 0.8060 (t0) REVERT: H 53 ARG cc_start: 0.8499 (mtt180) cc_final: 0.8256 (mtt180) REVERT: H 317 GLU cc_start: 0.8008 (tt0) cc_final: 0.7773 (tt0) REVERT: Q 61 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8481 (mp0) REVERT: Z 86 ASP cc_start: 0.8136 (m-30) cc_final: 0.7893 (m-30) REVERT: Z 244 VAL cc_start: 0.8368 (OUTLIER) cc_final: 0.8166 (t) REVERT: a 344 MET cc_start: 0.8137 (mmm) cc_final: 0.7611 (mmm) REVERT: a 416 GLU cc_start: 0.8300 (mp0) cc_final: 0.7771 (mp0) REVERT: a 473 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7742 (mp0) REVERT: b 452 ASP cc_start: 0.8074 (m-30) cc_final: 0.7740 (m-30) REVERT: e 4 MET cc_start: 0.6390 (mpp) cc_final: 0.5813 (mpp) REVERT: e 21 ASP cc_start: 0.8618 (m-30) cc_final: 0.8402 (m-30) REVERT: e 80 MET cc_start: 0.8945 (mmt) cc_final: 0.8411 (mtt) REVERT: e 526 MET cc_start: 0.9134 (ttt) cc_final: 0.8722 (ttt) REVERT: g 527 LYS cc_start: 0.8993 (mtmp) cc_final: 0.8600 (mmmm) REVERT: h 7 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8547 (pp) REVERT: h 221 SER cc_start: 0.9110 (m) cc_final: 0.8794 (p) REVERT: h 324 MET cc_start: 0.9249 (mmm) cc_final: 0.8879 (mmm) REVERT: z 10 LYS cc_start: 0.9023 (pttm) cc_final: 0.8686 (pmtt) REVERT: z 244 VAL cc_start: 0.8307 (OUTLIER) cc_final: 0.7892 (t) REVERT: z 389 ASP cc_start: 0.8484 (m-30) cc_final: 0.8141 (m-30) outliers start: 57 outliers final: 18 residues processed: 539 average time/residue: 1.5018 time to fit residues: 1061.5784 Evaluate side-chains 505 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 482 time to evaluate : 6.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 234 HIS Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 185 MET Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 69 ILE Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 415 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 521 optimal weight: 0.9990 chunk 336 optimal weight: 5.9990 chunk 503 optimal weight: 0.9980 chunk 254 optimal weight: 7.9990 chunk 165 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 536 optimal weight: 8.9990 chunk 574 optimal weight: 6.9990 chunk 416 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 662 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 164 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 68783 Z= 0.173 Angle : 0.515 16.279 92862 Z= 0.248 Chirality : 0.040 0.198 11047 Planarity : 0.003 0.057 11854 Dihedral : 6.244 162.137 9542 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.28 % Favored : 96.68 % Rotamer: Outliers : 0.67 % Allowed : 11.43 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.09), residues: 8778 helix: 2.14 (0.08), residues: 4449 sheet: 0.20 (0.16), residues: 1177 loop : -0.31 (0.11), residues: 3152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 222 HIS 0.013 0.001 HIS z 161 PHE 0.028 0.001 PHE N 296 TYR 0.029 0.001 TYR A 181 ARG 0.008 0.000 ARG N 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 485 time to evaluate : 6.692 Fit side-chains revert: symmetry clash REVERT: P 84 MET cc_start: 0.6098 (ttp) cc_final: 0.5556 (mtt) REVERT: N 210 ILE cc_start: 0.8906 (pt) cc_final: 0.8572 (pp) REVERT: N 288 ARG cc_start: 0.8223 (ttm110) cc_final: 0.7858 (ttp-170) REVERT: N 308 TYR cc_start: 0.7889 (m-80) cc_final: 0.7592 (m-80) REVERT: A 156 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8709 (mtp) REVERT: D 186 MET cc_start: 0.8609 (ttm) cc_final: 0.8177 (ttm) REVERT: E 4 MET cc_start: 0.6072 (tmm) cc_final: 0.5283 (ptm) REVERT: E 48 MET cc_start: 0.9130 (tpp) cc_final: 0.8922 (mmm) REVERT: E 474 MET cc_start: 0.8351 (tmm) cc_final: 0.8104 (tmt) REVERT: H 14 ASP cc_start: 0.8296 (t0) cc_final: 0.8058 (t0) REVERT: H 53 ARG cc_start: 0.8467 (mtt180) cc_final: 0.8225 (mtt180) REVERT: H 317 GLU cc_start: 0.8014 (tt0) cc_final: 0.7772 (tt0) REVERT: Q 61 GLU cc_start: 0.8869 (OUTLIER) cc_final: 0.8487 (mp0) REVERT: Z 86 ASP cc_start: 0.8173 (m-30) cc_final: 0.7912 (m-30) REVERT: a 416 GLU cc_start: 0.8304 (mp0) cc_final: 0.7778 (mp0) REVERT: a 473 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7750 (mp0) REVERT: b 452 ASP cc_start: 0.8097 (m-30) cc_final: 0.7776 (m-30) REVERT: b 488 MET cc_start: 0.8978 (mmt) cc_final: 0.7634 (mmt) REVERT: e 4 MET cc_start: 0.6401 (mpp) cc_final: 0.5772 (mpp) REVERT: e 21 ASP cc_start: 0.8634 (m-30) cc_final: 0.8415 (m-30) REVERT: e 526 MET cc_start: 0.9172 (ttt) cc_final: 0.8810 (ttt) REVERT: g 254 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.7991 (p) REVERT: g 527 LYS cc_start: 0.9003 (mtmp) cc_final: 0.8619 (mmmm) REVERT: h 7 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8532 (pp) REVERT: h 221 SER cc_start: 0.9119 (m) cc_final: 0.8828 (p) REVERT: h 324 MET cc_start: 0.9230 (mmm) cc_final: 0.8880 (mmm) REVERT: z 10 LYS cc_start: 0.9009 (pttm) cc_final: 0.8686 (pmtt) REVERT: z 244 VAL cc_start: 0.8348 (OUTLIER) cc_final: 0.7864 (t) REVERT: z 389 ASP cc_start: 0.8494 (m-30) cc_final: 0.8143 (m-30) outliers start: 49 outliers final: 21 residues processed: 512 average time/residue: 1.5457 time to fit residues: 1038.3069 Evaluate side-chains 499 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 473 time to evaluate : 6.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 234 HIS Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain e residue 501 MET Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain g residue 255 ASP Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 69 ILE Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 415 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 767 optimal weight: 0.1980 chunk 807 optimal weight: 3.9990 chunk 737 optimal weight: 7.9990 chunk 785 optimal weight: 3.9990 chunk 473 optimal weight: 2.9990 chunk 342 optimal weight: 0.9990 chunk 617 optimal weight: 5.9990 chunk 241 optimal weight: 5.9990 chunk 710 optimal weight: 0.8980 chunk 743 optimal weight: 9.9990 chunk 783 optimal weight: 8.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 68783 Z= 0.187 Angle : 0.524 14.499 92862 Z= 0.254 Chirality : 0.040 0.210 11047 Planarity : 0.003 0.057 11854 Dihedral : 6.235 159.040 9542 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.33 % Favored : 96.65 % Rotamer: Outliers : 0.54 % Allowed : 11.62 % Favored : 87.84 % 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: 1.50 (0.09), residues: 8778 helix: 2.14 (0.08), residues: 4449 sheet: 0.18 (0.16), residues: 1187 loop : -0.31 (0.11), residues: 3142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 222 HIS 0.014 0.001 HIS z 161 PHE 0.014 0.001 PHE E 16 TYR 0.030 0.001 TYR A 181 ARG 0.014 0.000 ARG N 314 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 478 time to evaluate : 6.212 Fit side-chains revert: symmetry clash REVERT: P 84 MET cc_start: 0.6116 (ttp) cc_final: 0.5565 (mtt) REVERT: P 148 MET cc_start: 0.8249 (tmm) cc_final: 0.8039 (pmm) REVERT: N 210 ILE cc_start: 0.8893 (pt) cc_final: 0.8567 (pp) REVERT: N 268 MET cc_start: 0.9048 (pmm) cc_final: 0.8847 (mpp) REVERT: N 308 TYR cc_start: 0.7826 (m-80) cc_final: 0.7481 (m-80) REVERT: A 156 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8629 (mtp) REVERT: E 4 MET cc_start: 0.6044 (tmm) cc_final: 0.4946 (mpp) REVERT: E 48 MET cc_start: 0.9162 (tpp) cc_final: 0.8946 (mmm) REVERT: E 474 MET cc_start: 0.8363 (tmm) cc_final: 0.8087 (tmt) REVERT: H 14 ASP cc_start: 0.8310 (t0) cc_final: 0.8058 (t0) REVERT: H 53 ARG cc_start: 0.8469 (mtt180) cc_final: 0.8220 (mtt180) REVERT: H 317 GLU cc_start: 0.8025 (tt0) cc_final: 0.7780 (tt0) REVERT: Q 61 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8506 (mp0) REVERT: Z 86 ASP cc_start: 0.8191 (m-30) cc_final: 0.7928 (m-30) REVERT: a 344 MET cc_start: 0.8278 (mmm) cc_final: 0.7663 (mmm) REVERT: a 416 GLU cc_start: 0.8309 (mp0) cc_final: 0.7808 (mp0) REVERT: a 473 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7742 (OUTLIER) REVERT: b 452 ASP cc_start: 0.8119 (m-30) cc_final: 0.7805 (m-30) REVERT: e 4 MET cc_start: 0.6464 (mpp) cc_final: 0.5878 (mpp) REVERT: e 21 ASP cc_start: 0.8635 (m-30) cc_final: 0.8415 (m-30) REVERT: e 526 MET cc_start: 0.9196 (ttt) cc_final: 0.8868 (ttt) REVERT: g 254 THR cc_start: 0.8357 (OUTLIER) cc_final: 0.8000 (p) REVERT: g 527 LYS cc_start: 0.9017 (mtmp) cc_final: 0.8610 (mmmm) REVERT: h 7 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8543 (pp) REVERT: h 221 SER cc_start: 0.9117 (m) cc_final: 0.8843 (p) REVERT: h 324 MET cc_start: 0.9210 (mmm) cc_final: 0.8833 (mmm) REVERT: z 10 LYS cc_start: 0.9013 (pttm) cc_final: 0.8694 (pmtt) REVERT: z 244 VAL cc_start: 0.8333 (OUTLIER) cc_final: 0.7853 (t) REVERT: z 389 ASP cc_start: 0.8524 (m-30) cc_final: 0.8168 (m-30) outliers start: 40 outliers final: 27 residues processed: 502 average time/residue: 1.5326 time to fit residues: 1017.0087 Evaluate side-chains 502 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 471 time to evaluate : 6.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 234 HIS Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Z residue 404 ASP Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain e residue 501 MET Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain g residue 255 ASP Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 69 ILE Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 415 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 516 optimal weight: 0.9980 chunk 831 optimal weight: 1.9990 chunk 507 optimal weight: 0.9980 chunk 394 optimal weight: 0.9990 chunk 577 optimal weight: 0.6980 chunk 871 optimal weight: 0.7980 chunk 802 optimal weight: 2.9990 chunk 694 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 536 optimal weight: 9.9990 chunk 425 optimal weight: 0.0050 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 459 ASN ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 331 GLN z 65 HIS ** z 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 68783 Z= 0.130 Angle : 0.513 17.640 92862 Z= 0.248 Chirality : 0.040 0.187 11047 Planarity : 0.003 0.056 11854 Dihedral : 6.064 150.096 9542 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.98 % Favored : 96.99 % Rotamer: Outliers : 0.39 % Allowed : 11.92 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.09), residues: 8778 helix: 2.15 (0.08), residues: 4445 sheet: 0.25 (0.16), residues: 1172 loop : -0.29 (0.11), residues: 3161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 222 HIS 0.017 0.000 HIS z 161 PHE 0.034 0.001 PHE N 296 TYR 0.028 0.001 TYR A 181 ARG 0.015 0.000 ARG N 314 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17556 Ramachandran restraints generated. 8778 Oldfield, 0 Emsley, 8778 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 504 time to evaluate : 6.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: P 84 MET cc_start: 0.6205 (ttp) cc_final: 0.5677 (mtt) REVERT: N 210 ILE cc_start: 0.8851 (pt) cc_final: 0.8552 (pp) REVERT: N 296 PHE cc_start: 0.8706 (p90) cc_final: 0.8399 (p90) REVERT: N 308 TYR cc_start: 0.7864 (m-80) cc_final: 0.7535 (m-80) REVERT: A 156 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8606 (mtp) REVERT: E 4 MET cc_start: 0.6069 (tmm) cc_final: 0.5167 (ptm) REVERT: E 48 MET cc_start: 0.9150 (tpp) cc_final: 0.8900 (mmm) REVERT: E 474 MET cc_start: 0.8295 (tmm) cc_final: 0.8057 (tmt) REVERT: H 14 ASP cc_start: 0.8291 (t0) cc_final: 0.8062 (t0) REVERT: H 317 GLU cc_start: 0.8020 (tt0) cc_final: 0.7775 (tt0) REVERT: H 524 ARG cc_start: 0.7273 (mmm160) cc_final: 0.7060 (mmm160) REVERT: Q 61 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8481 (mp0) REVERT: Z 86 ASP cc_start: 0.8143 (m-30) cc_final: 0.7881 (m-30) REVERT: a 416 GLU cc_start: 0.8291 (mp0) cc_final: 0.7803 (mp0) REVERT: a 473 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7719 (mp0) REVERT: b 452 ASP cc_start: 0.8044 (m-30) cc_final: 0.7725 (m-30) REVERT: e 4 MET cc_start: 0.6486 (mpp) cc_final: 0.5915 (mpp) REVERT: e 21 ASP cc_start: 0.8621 (m-30) cc_final: 0.8410 (m-30) REVERT: e 526 MET cc_start: 0.9170 (ttt) cc_final: 0.8822 (ttt) REVERT: g 527 LYS cc_start: 0.8986 (mtmp) cc_final: 0.8578 (mmmm) REVERT: h 324 MET cc_start: 0.9241 (mmm) cc_final: 0.8920 (mmm) REVERT: z 10 LYS cc_start: 0.9011 (pttm) cc_final: 0.8690 (pmtt) REVERT: z 244 VAL cc_start: 0.8332 (OUTLIER) cc_final: 0.7917 (t) REVERT: z 389 ASP cc_start: 0.8508 (m-30) cc_final: 0.8137 (m-30) outliers start: 29 outliers final: 16 residues processed: 521 average time/residue: 1.5287 time to fit residues: 1049.2741 Evaluate side-chains 503 residues out of total 7365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 484 time to evaluate : 6.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 234 HIS Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain g residue 83 ILE Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 212 ILE Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 69 ILE Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 551 optimal weight: 10.0000 chunk 739 optimal weight: 3.9990 chunk 212 optimal weight: 7.9990 chunk 640 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 192 optimal weight: 4.9990 chunk 695 optimal weight: 10.0000 chunk 290 optimal weight: 0.7980 chunk 713 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 128 optimal weight: 0.2980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 41 GLN ** z 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.071343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.056252 restraints weight = 233878.950| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 3.49 r_work: 0.2556 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 68783 Z= 0.163 Angle : 0.519 16.037 92862 Z= 0.250 Chirality : 0.040 0.198 11047 Planarity : 0.003 0.057 11854 Dihedral : 6.018 148.346 9542 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.17 % Favored : 96.80 % Rotamer: Outliers : 0.35 % Allowed : 12.09 % Favored : 87.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.09), residues: 8778 helix: 2.17 (0.08), residues: 4451 sheet: 0.24 (0.16), residues: 1185 loop : -0.30 (0.11), residues: 3142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 222 HIS 0.016 0.001 HIS z 161 PHE 0.032 0.001 PHE N 296 TYR 0.029 0.001 TYR A 181 ARG 0.015 0.000 ARG N 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16790.06 seconds wall clock time: 295 minutes 52.30 seconds (17752.30 seconds total)