Starting phenix.real_space_refine on Thu Mar 14 10:38:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sha_40482/03_2024/8sha_40482_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sha_40482/03_2024/8sha_40482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sha_40482/03_2024/8sha_40482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sha_40482/03_2024/8sha_40482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sha_40482/03_2024/8sha_40482_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sha_40482/03_2024/8sha_40482_updated.pdb" } resolution = 3.0 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= 0.052 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 416 5.16 5 C 41964 2.51 5 N 11677 2.21 5 O 12986 1.98 5 F 48 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 529": "OD1" <-> "OD2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 334": "OE1" <-> "OE2" Residue "D GLU 429": "OE1" <-> "OE2" Residue "D TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 467": "OE1" <-> "OE2" Residue "E ASP 58": "OD1" <-> "OD2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "E PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 532": "OD1" <-> "OD2" Residue "G TYR 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 511": "OE1" <-> "OE2" Residue "H GLU 11": "OE1" <-> "OE2" Residue "H GLU 413": "OE1" <-> "OE2" Residue "H GLU 482": "OE1" <-> "OE2" Residue "Q GLU 17": "OE1" <-> "OE2" Residue "Q GLU 75": "OE1" <-> "OE2" Residue "Z GLU 101": "OE1" <-> "OE2" Residue "Z TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 357": "OE1" <-> "OE2" Residue "Z GLU 415": "OE1" <-> "OE2" Residue "a GLU 77": "OE1" <-> "OE2" Residue "a TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 416": "OE1" <-> "OE2" Residue "b GLU 19": "OE1" <-> "OE2" Residue "d ASP 58": "OD1" <-> "OD2" Residue "e GLU 11": "OE1" <-> "OE2" Residue "e TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 21": "OD1" <-> "OD2" Residue "e TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 329": "OE1" <-> "OE2" Residue "e PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 532": "OD1" <-> "OD2" Residue "g ASP 62": "OD1" <-> "OD2" Residue "g ASP 194": "OD1" <-> "OD2" Residue "g TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 521": "OD1" <-> "OD2" Residue "h GLU 11": "OE1" <-> "OE2" Residue "h ASP 70": "OD1" <-> "OD2" Residue "h ASP 451": "OD1" <-> "OD2" Residue "q ASP 193": "OD1" <-> "OD2" Residue "z TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 491": "OE1" <-> "OE2" Residue "P PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 67155 Number of models: 1 Model: "" Number of chains: 50 Chain: "N" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 428 Classifications: {'peptide': 56} Link IDs: {'TRANS': 55} Chain breaks: 5 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: 4094 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 529, 4083 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 18, 'TRANS': 510} Conformer: "C" Number of residues, atoms: 529, 4083 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 18, 'TRANS': 510} bond proxies already assigned to first conformer: 4120 Chain: "G" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4089 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "H" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4054 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 16, 'TRANS': 511} Chain: "Q" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4086 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 18, 'TRANS': 519} Chain: "Z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "a" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4041 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Chain: "b" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3943 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 10, 'TRANS': 514} Chain: "d" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3917 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 4169 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} Conformer: "B" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} bond proxies already assigned to first conformer: 4195 Chain: "g" Number of atoms: 4088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4088 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "h" Number of atoms: 4032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4032 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 16, 'TRANS': 508} Chain: "q" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4053 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 16, 'TRANS': 516} Chain: "z" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4033 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 512} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "P" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1631 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 5, 'TRANS': 199} Chain breaks: 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: 29.08, per 1000 atoms: 0.43 Number of scatterers: 67155 At special positions: 0 Unit cell: (180.918, 176.686, 181.976, 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 416 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 12986 8.00 N 11677 7.00 C 41964 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 "HETATM67062 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66806 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66710 O3A ADP D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66998 O3A ADP e 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66678 O3A ADP B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66742 O3A ADP E 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66934 O3A ADP b 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: 19.66 Conformation dependent library (CDL) restraints added in 10.2 seconds 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16246 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 329 helices and 110 sheets defined 51.1% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 11.10 Creating SS restraints... Processing helix chain 'A' and resid 15 through 35 removed outlier: 3.687A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N SER A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 5.764A 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 removed outlier: 3.732A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 110 removed outlier: 3.787A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 135 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 144 through 156 Processing helix chain 'A' and resid 165 through 179 removed outlier: 4.174A pdb=" N ASN A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 179 " --> pdb=" O ALA A 175 " (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: 3.587A pdb=" N ASP A 261 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ILE A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 382 through 404 Processing helix chain 'A' and resid 414 through 429 removed outlier: 4.641A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N SER A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 455 removed outlier: 3.820A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 5.060A 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: 3.971A 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 removed outlier: 3.958A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 143 Processing helix chain 'B' and resid 152 through 168 Processing helix chain 'B' and resid 171 through 190 removed outlier: 3.672A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS B 176 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ASP B 177 " --> pdb=" O HIS B 174 " (cutoff:3.500A) removed outlier: 3.529A 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: 3.958A 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: 3.934A 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: 3.724A 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: 4.446A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N SER D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 80 Processing helix chain 'D' and resid 86 through 101 Processing helix chain 'D' and resid 106 through 125 removed outlier: 3.633A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 150 Processing helix chain 'D' and resid 160 through 172 Processing helix chain 'D' and resid 180 through 194 Proline residue: D 185 - end of helix removed outlier: 3.779A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) 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: 4.155A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.923A 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: 4.460A pdb=" N GLU D 334 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 3.969A 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: 3.860A pdb=" N THR D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 468 removed outlier: 4.120A pdb=" N VAL D 460 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ILE D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) Proline residue: D 462 - end of helix Processing helix chain 'D' and resid 473 through 486 Processing helix chain 'D' and resid 503 through 506 Processing helix chain 'D' and resid 512 through 531 removed outlier: 3.502A 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: 3.531A pdb=" N LEU E 34 " --> pdb=" O GLY E 30 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR E 50 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N SER E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 80 Processing helix chain 'E' and resid 86 through 101 Processing helix chain 'E' and resid 106 through 126 removed outlier: 4.226A pdb=" N VAL E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 150 Processing helix chain 'E' and resid 163 through 175 removed outlier: 4.637A pdb=" N SER E 175 " --> pdb=" O THR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 180 removed outlier: 3.987A pdb=" N SER E 180 " --> pdb=" O VAL E 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 177 through 180' Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 219 through 221 No H-bonds generated for 'chain 'E' and resid 219 through 221' Processing helix chain 'E' and resid 271 through 295 removed outlier: 3.859A pdb=" N THR E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 316 Processing helix chain 'E' and resid 327 through 337 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 392 through 414 Processing helix chain 'E' and resid 424 through 437 Processing helix chain 'E' and resid 442 through 465 removed outlier: 3.776A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL E 457 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 4.753A 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: 3.901A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N THR G 39 " --> pdb=" O ASP G 35 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N CYS G 40 " --> pdb=" O ILE G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 68 Processing helix chain 'G' and resid 75 through 90 Processing helix chain 'G' and resid 95 through 114 removed outlier: 3.555A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 140 Processing helix chain 'G' and resid 149 through 160 Processing helix chain 'G' and resid 166 through 183 removed outlier: 5.490A pdb=" N SER G 170 " --> pdb=" O ARG G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 198 No H-bonds generated for 'chain 'G' and resid 195 through 198' Processing helix chain 'G' and resid 209 through 211 No H-bonds generated for 'chain 'G' and resid 209 through 211' Processing helix chain 'G' and resid 263 through 285 removed outlier: 4.252A pdb=" N LEU G 285 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 307 removed outlier: 3.852A 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: 4.100A pdb=" N ALA G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 455 removed outlier: 3.742A pdb=" N TRP G 435 " --> pdb=" O VAL G 432 " (cutoff:3.500A) Proline residue: G 436 - end of helix removed outlier: 3.651A pdb=" N GLN G 442 " --> pdb=" O ALA G 439 " (cutoff:3.500A) removed outlier: 3.870A 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 36 removed outlier: 4.056A 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: 3.602A pdb=" N GLU H 89 " --> pdb=" O GLN H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 113 removed outlier: 4.030A pdb=" N THR H 98 " --> pdb=" O THR H 94 " (cutoff:3.500A) Proline residue: H 110 - end of helix Processing helix chain 'H' and resid 118 through 139 Processing helix chain 'H' and resid 148 through 163 Processing helix chain 'H' and resid 169 through 184 removed outlier: 5.491A pdb=" N ALA H 173 " --> pdb=" O GLN H 170 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE H 174 " --> pdb=" O GLN H 171 " (cutoff:3.500A) removed outlier: 3.758A 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: 4.144A pdb=" N THR H 426 " --> pdb=" O ASP H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 453 removed outlier: 3.936A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE H 444 " --> pdb=" O LYS H 440 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N ILE H 445 " --> pdb=" O ALA H 441 " (cutoff:3.500A) Proline residue: H 446 - end of helix Processing helix chain 'H' and resid 457 through 470 Processing helix chain 'H' and resid 496 through 515 Processing helix chain 'Q' and resid 11 through 14 No H-bonds generated for 'chain 'Q' and resid 11 through 14' Processing helix chain 'Q' and resid 24 through 46 removed outlier: 4.342A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ALA Q 46 " --> pdb=" O THR Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 75 Processing helix chain 'Q' and resid 81 through 96 Processing helix chain 'Q' and resid 101 through 121 Processing helix chain 'Q' and resid 125 through 146 Proline residue: Q 144 - end of helix Processing helix chain 'Q' and resid 157 through 170 removed outlier: 4.220A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER Q 170 " --> pdb=" O THR Q 166 " (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: 4.790A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N THR Q 286 " --> pdb=" O ALA Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 299 through 307 Processing helix chain 'Q' and resid 318 through 328 Processing helix chain 'Q' and resid 382 through 404 Processing helix chain 'Q' and resid 414 through 429 removed outlier: 3.612A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 456 removed outlier: 3.532A pdb=" N TYR Q 436 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) Proline residue: Q 449 - end of helix Processing helix chain 'Q' and resid 460 through 473 Processing helix chain 'Q' and resid 492 through 495 No H-bonds generated for 'chain 'Q' and resid 492 through 495' Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'Q' and resid 536 through 538 No H-bonds generated for 'chain 'Q' and resid 536 through 538' Processing helix chain 'Z' and resid 3 through 7 Processing helix chain 'Z' and resid 16 through 37 removed outlier: 3.504A pdb=" N ILE Z 24 " --> pdb=" O ALA Z 21 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG Z 35 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 3.984A 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: 3.631A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLU Z 112 " --> pdb=" O LEU Z 108 " (cutoff:3.500A) Processing helix chain 'Z' and resid 116 through 137 Processing helix chain 'Z' and resid 145 through 159 removed outlier: 4.188A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 162 through 179 removed outlier: 3.806A 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: 4.109A pdb=" N ARG Z 264 " --> pdb=" O VAL Z 260 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS Z 265 " --> pdb=" O LYS Z 261 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N PHE Z 266 " --> pdb=" O ALA Z 262 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ILE Z 267 " --> pdb=" O GLU Z 263 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 299 through 308 removed outlier: 3.895A pdb=" N GLU Z 308 " --> pdb=" O ALA Z 304 " (cutoff:3.500A) Processing helix chain 'Z' and resid 318 through 327 removed outlier: 4.381A pdb=" N GLU Z 322 " --> pdb=" O ARG Z 318 " (cutoff:3.500A) Processing helix chain 'Z' and resid 341 through 343 No H-bonds generated for 'chain 'Z' and resid 341 through 343' Processing helix chain 'Z' and resid 381 through 403 Processing helix chain 'Z' and resid 413 through 428 Proline residue: Z 427 - end of helix Processing helix chain 'Z' and resid 432 through 455 removed outlier: 3.686A 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 498 through 516 Processing helix chain 'a' and resid 15 through 35 removed outlier: 3.714A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N SER a 34 " --> pdb=" O ASN a 30 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N SER a 35 " --> pdb=" O ILE a 31 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 64 Processing helix chain 'a' and resid 70 through 85 Processing helix chain 'a' and resid 92 through 109 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 178 removed outlier: 4.593A pdb=" N ASP a 166 " --> pdb=" O ILE a 163 " (cutoff:3.500A) removed outlier: 4.934A 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: 4.540A pdb=" N ASP a 261 " --> pdb=" O GLU a 258 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE a 270 " --> pdb=" O GLU a 267 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA a 280 " --> pdb=" O LYS a 277 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR a 281 " --> pdb=" O ILE a 278 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 302 Processing helix chain 'a' and resid 313 through 323 Processing helix chain 'a' and resid 342 through 344 No H-bonds generated for 'chain 'a' and resid 342 through 344' Processing helix chain 'a' and resid 382 through 404 Processing helix chain 'a' and resid 414 through 428 removed outlier: 4.267A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) Processing helix chain 'a' and resid 434 through 455 removed outlier: 3.835A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 5.213A 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: 3.705A pdb=" N LYS a 481 " --> pdb=" O PRO a 478 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ASN a 482 " --> pdb=" O GLU a 479 " (cutoff:3.500A) removed outlier: 3.869A 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: 3.595A pdb=" N LYS b 176 " --> pdb=" O THR b 173 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ASP b 177 " --> pdb=" O HIS b 174 " (cutoff:3.500A) removed outlier: 3.502A 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: 3.879A 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: 3.846A pdb=" N ARG b 427 " --> pdb=" O GLN b 423 " (cutoff:3.500A) Processing helix chain 'b' and resid 432 through 454 Proline residue: b 447 - end of helix removed outlier: 3.742A pdb=" N ALA b 454 " --> pdb=" O ILE b 450 " (cutoff:3.500A) Processing helix chain 'b' and resid 458 through 470 Processing helix chain 'b' and resid 488 through 491 No H-bonds generated for 'chain 'b' and resid 488 through 491' Processing helix chain 'b' and resid 497 through 515 Processing helix chain 'd' and resid 29 through 49 Processing helix chain 'd' and resid 74 through 80 Processing helix chain 'd' and resid 86 through 101 Processing helix chain 'd' and resid 106 through 126 removed outlier: 3.768A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.889A 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: 4.487A pdb=" N SER d 173 " --> pdb=" O THR d 169 " (cutoff:3.500A) Processing helix chain 'd' and resid 175 through 177 No H-bonds generated for 'chain 'd' and resid 175 through 177' Processing helix chain 'd' and resid 180 through 192 Proline residue: d 185 - end of helix Processing helix chain 'd' and resid 205 through 207 No H-bonds generated for 'chain 'd' and resid 205 through 207' Processing helix chain 'd' and resid 218 through 220 No H-bonds generated for 'chain 'd' and resid 218 through 220' Processing helix chain 'd' and resid 269 through 293 removed outlier: 4.024A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.872A 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: 4.612A pdb=" N GLU d 334 " --> pdb=" O GLU d 331 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE d 340 " --> pdb=" O CYS d 337 " (cutoff:3.500A) Processing helix chain 'd' and resid 348 through 350 No H-bonds generated for 'chain 'd' and resid 348 through 350' Processing helix chain 'd' and resid 353 through 355 No H-bonds generated for 'chain 'd' and resid 353 through 355' Processing helix chain 'd' and resid 395 through 416 Processing helix chain 'd' and resid 427 through 442 removed outlier: 3.663A pdb=" N THR d 442 " --> pdb=" O GLU d 438 " (cutoff:3.500A) Processing helix chain 'd' and resid 445 through 466 removed outlier: 3.799A pdb=" N ILE d 461 " --> pdb=" O MET d 458 " (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 504 through 506 No H-bonds generated for 'chain 'd' and resid 504 through 506' Processing helix chain 'd' and resid 512 through 530 removed outlier: 4.908A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 51 removed outlier: 3.721A pdb=" N ARG e 49 " --> pdb=" O ASN e 46 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR e 50 " --> pdb=" O THR e 47 " (cutoff:3.500A) Processing helix chain 'e' and resid 74 through 80 Processing helix chain 'e' and resid 86 through 101 Processing helix chain 'e' and resid 108 through 125 removed outlier: 3.612A pdb=" N GLN e 122 " --> pdb=" O GLU e 118 " (cutoff:3.500A) Processing helix chain 'e' and resid 130 through 151 Processing helix chain 'e' and resid 163 through 175 removed outlier: 4.734A pdb=" N SER e 175 " --> pdb=" O THR e 171 " (cutoff:3.500A) Processing helix chain 'e' and resid 177 through 195 removed outlier: 3.847A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ARG e 183 " --> pdb=" O SER e 180 " (cutoff:3.500A) Processing helix chain 'e' and resid 206 through 208 No H-bonds generated for 'chain 'e' and resid 206 through 208' Processing helix chain 'e' and resid 219 through 221 No H-bonds generated for 'chain 'e' and resid 219 through 221' Processing helix chain 'e' and resid 271 through 295 removed outlier: 3.935A pdb=" N THR e 295 " --> pdb=" O GLN e 291 " (cutoff:3.500A) Processing helix chain 'e' and resid 308 through 316 Processing helix chain 'e' and resid 327 through 337 Processing helix chain 'e' and resid 345 through 347 No H-bonds generated for 'chain 'e' and resid 345 through 347' Processing helix chain 'e' and resid 350 through 352 No H-bonds generated for 'chain 'e' and resid 350 through 352' Processing helix chain 'e' and resid 392 through 414 Processing helix chain 'e' and resid 424 through 437 Processing helix chain 'e' and resid 442 through 465 removed outlier: 3.847A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) removed outlier: 3.772A 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 529 Processing helix chain 'g' and resid 20 through 36 Processing helix chain 'g' and resid 38 through 40 No H-bonds generated for 'chain 'g' and resid 38 through 40' Processing helix chain 'g' and resid 63 through 69 removed outlier: 3.881A 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: 3.572A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.749A 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: 3.807A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N SER g 170 " --> pdb=" O ARG g 167 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU g 171 " --> pdb=" O TRP g 168 " (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: 4.360A pdb=" N PHE g 264 " --> pdb=" O GLU g 261 " (cutoff:3.500A) Processing helix chain 'g' and resid 298 through 307 removed outlier: 3.680A pdb=" N ALA g 307 " --> pdb=" O TYR g 303 " (cutoff:3.500A) Processing helix chain 'g' and resid 317 through 327 Processing helix chain 'g' and resid 335 through 337 No H-bonds generated for 'chain 'g' and resid 335 through 337' Processing helix chain 'g' and resid 340 through 342 No H-bonds generated for 'chain 'g' and resid 340 through 342' Processing helix chain 'g' and resid 381 through 403 Processing helix chain 'g' and resid 413 through 428 removed outlier: 3.635A pdb=" N LYS g 427 " --> pdb=" O THR g 423 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA g 428 " --> pdb=" O GLU g 424 " (cutoff:3.500A) Processing helix chain 'g' and resid 434 through 455 removed outlier: 3.892A pdb=" N LEU g 444 " --> pdb=" O VAL g 440 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N GLU g 445 " --> pdb=" O ALA g 441 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N VAL g 446 " --> pdb=" O GLN g 442 " (cutoff:3.500A) removed outlier: 5.251A 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: 3.549A pdb=" N ALA h 35 " --> pdb=" O VAL h 31 " (cutoff:3.500A) removed outlier: 3.998A 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: 3.600A pdb=" N VAL h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 113 removed outlier: 4.237A 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: 5.701A pdb=" N ALA h 173 " --> pdb=" O GLN h 170 " (cutoff:3.500A) removed outlier: 3.791A 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: 4.208A pdb=" N THR h 426 " --> pdb=" O ASP h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 430 through 453 removed outlier: 4.143A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU h 443 " --> pdb=" O ALA h 439 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ILE h 444 " --> pdb=" O LYS h 440 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE h 445 " --> pdb=" O ALA h 441 " (cutoff:3.500A) Proline residue: h 446 - end of helix Processing helix chain 'h' and resid 457 through 470 Processing helix chain 'h' and resid 496 through 515 Processing helix chain 'q' and resid 11 through 14 No H-bonds generated for 'chain 'q' and resid 11 through 14' Processing helix chain 'q' and resid 25 through 46 removed outlier: 3.939A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) removed outlier: 5.666A 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: 4.371A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.552A 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: 4.731A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) removed outlier: 3.867A 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: 3.909A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 434 through 456 removed outlier: 3.817A pdb=" N PHE q 445 " --> pdb=" O PHE q 441 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU q 446 " --> pdb=" O ALA q 442 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ALA q 447 " --> pdb=" O GLU q 443 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ILE q 448 " --> pdb=" O ALA q 444 " (cutoff:3.500A) Proline residue: q 449 - end of helix Processing helix chain 'q' and resid 460 through 473 Processing helix chain 'q' and resid 492 through 495 No H-bonds generated for 'chain 'q' and resid 492 through 495' Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'z' and resid 3 through 7 Processing helix chain 'z' and resid 16 through 37 removed outlier: 3.806A pdb=" N ARG z 35 " --> pdb=" O ASP z 32 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N THR z 36 " --> pdb=" O VAL z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 60 through 65 Processing helix chain 'z' and resid 72 through 87 Processing helix chain 'z' and resid 92 through 112 removed outlier: 3.586A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLU z 112 " --> pdb=" O LEU z 108 " (cutoff:3.500A) Processing helix chain 'z' and resid 116 through 137 Processing helix chain 'z' and resid 145 through 159 removed outlier: 4.122A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 162 through 179 removed outlier: 3.663A 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: 4.062A pdb=" N ARG z 264 " --> pdb=" O VAL z 260 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS z 265 " --> pdb=" O LYS z 261 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N PHE z 266 " --> pdb=" O ALA z 262 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N ILE z 267 " --> pdb=" O GLU z 263 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 299 through 308 removed outlier: 3.835A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 318 through 327 removed outlier: 4.224A pdb=" N GLU z 322 " --> pdb=" O ARG z 318 " (cutoff:3.500A) Processing helix chain 'z' and resid 341 through 343 No H-bonds generated for 'chain 'z' and resid 341 through 343' Processing helix chain 'z' and resid 381 through 403 Processing helix chain 'z' and resid 413 through 428 Proline residue: z 427 - end of helix Processing helix chain 'z' and resid 432 through 455 removed outlier: 3.839A 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 517 Processing helix chain 'P' and resid 58 through 61 No H-bonds generated for 'chain 'P' and resid 58 through 61' Processing helix chain 'P' and resid 63 through 83 removed outlier: 3.592A pdb=" N LEU P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 139 No H-bonds generated for 'chain 'P' and resid 137 through 139' Processing helix chain 'P' and resid 141 through 151 removed outlier: 3.555A pdb=" N ARG P 144 " --> pdb=" O ARG P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 175 Processing helix chain 'P' and resid 195 through 208 Processing helix chain 'P' and resid 219 through 222 No H-bonds generated for 'chain 'P' and resid 219 through 222' Processing helix chain 'P' and resid 226 through 231 Processing helix chain 'P' and resid 251 through 254 No H-bonds generated for 'chain 'P' and resid 251 through 254' Processing helix chain 'P' and resid 261 through 270 Processing sheet with id= A, first strand: chain 'N' and resid 200 through 203 removed outlier: 4.157A pdb=" N ALA N 200 " --> pdb=" O ALA N 213 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA N 213 " --> pdb=" O ALA N 200 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER N 202 " --> pdb=" O LEU N 211 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS N 219 " --> pdb=" O PHE N 233 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLN N 231 " --> pdb=" O LEU N 221 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'N' and resid 264 through 267 removed outlier: 3.615A pdb=" N GLN N 275 " --> pdb=" O VAL N 265 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASP N 267 " --> pdb=" O CYS N 273 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N CYS N 273 " --> pdb=" O ASP N 267 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 9 through 13 Processing sheet with id= D, first strand: chain 'A' and resid 43 through 46 Processing sheet with id= E, first strand: chain 'A' and resid 137 through 139 Processing sheet with id= F, first strand: chain 'A' and resid 180 through 182 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: 6.557A pdb=" N VAL A 285 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU A 237 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU A 287 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N MET A 306 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N THR A 288 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 308 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 486 through 489 Processing sheet with id= K, first strand: chain 'B' and resid 17 through 19 Processing sheet with id= L, first strand: chain 'B' and resid 50 through 53 Processing sheet with id= M, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.363A pdb=" N CYS B 371 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N ILE B 202 " --> pdb=" O CYS B 371 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ILE B 373 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LYS B 204 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LEU B 375 " --> pdb=" O LYS B 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'B' and resid 218 through 220 Processing sheet with id= O, first strand: chain 'B' and resid 344 through 346 removed outlier: 3.510A pdb=" N CYS B 346 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N CYS B 289 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ALA B 240 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ILE B 291 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N MET B 310 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N ASN B 292 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 312 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 406 through 408 Processing sheet with id= Q, first strand: chain 'B' and resid 476 through 479 removed outlier: 3.553A pdb=" N THR B 484 " --> pdb=" O ASP B 479 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 59 through 62 Processing sheet with id= S, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.699A pdb=" N VAL D 386 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N VAL D 211 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ILE D 388 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS D 213 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL D 390 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 227 through 229 Processing sheet with id= U, first strand: chain 'D' and resid 246 through 249 removed outlier: 6.937A pdb=" N VAL D 297 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE D 249 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU D 299 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N MET D 323 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ILE D 300 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ILE D 325 " --> pdb=" O ILE D 300 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'D' and resid 421 through 423 Processing sheet with id= W, first strand: chain 'D' and resid 491 through 494 Processing sheet with id= X, first strand: chain 'E' and resid 59 through 62 Processing sheet with id= Y, first strand: chain 'E' and resid 209 through 215 removed outlier: 7.108A pdb=" N VAL E 383 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLU E 212 " --> pdb=" O VAL E 383 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N ILE E 385 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LYS E 214 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE E 387 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 228 through 230 Processing sheet with id= AA, first strand: chain 'E' and resid 354 through 356 removed outlier: 6.877A pdb=" N LEU E 299 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 48 through 51 Processing sheet with id= AC, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.477A pdb=" N CYS G 372 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N GLU G 202 " --> pdb=" O CYS G 372 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ILE G 374 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE G 204 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU G 376 " --> pdb=" O ILE G 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'G' and resid 238 through 241 removed outlier: 6.626A pdb=" N VAL G 289 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LEU G 241 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE G 291 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR G 310 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N THR G 292 " --> pdb=" O THR G 310 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE G 312 " --> pdb=" O THR G 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'G' and resid 351 through 355 Processing sheet with id= AF, first strand: chain 'G' and resid 407 through 409 Processing sheet with id= AG, first strand: chain 'G' and resid 478 through 480 Processing sheet with id= AH, first strand: chain 'H' and resid 14 through 17 Processing sheet with id= AI, first strand: chain 'H' and resid 47 through 50 Processing sheet with id= AJ, first strand: chain 'H' and resid 195 through 201 removed outlier: 6.463A pdb=" N CYS H 370 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 8.073A 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: 7.374A pdb=" N VAL H 200 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU H 374 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'H' and resid 214 through 217 Processing sheet with id= AL, first strand: chain 'H' and resid 237 through 240 removed outlier: 6.973A pdb=" N VAL H 288 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 7.464A pdb=" N LEU H 240 " --> pdb=" O VAL H 288 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N LEU H 290 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE H 309 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N SER H 291 " --> pdb=" O PHE H 309 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA H 311 " --> pdb=" O SER H 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'H' and resid 405 through 407 Processing sheet with id= AN, first strand: chain 'H' and resid 475 through 478 Processing sheet with id= AO, first strand: chain 'Q' and resid 20 through 23 Processing sheet with id= AP, first strand: chain 'Q' and resid 54 through 57 Processing sheet with id= AQ, first strand: chain 'Q' and resid 202 through 206 removed outlier: 6.551A pdb=" N SER Q 373 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N CYS Q 205 " --> pdb=" O SER Q 373 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE Q 375 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'Q' and resid 220 through 223 Processing sheet with id= AS, first strand: chain 'Q' and resid 240 through 242 removed outlier: 6.027A pdb=" N MET Q 311 " --> pdb=" O VAL Q 291 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR Q 293 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL Q 313 " --> pdb=" O THR Q 293 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Q' and resid 498 through 500 removed outlier: 4.024A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N VAL Q 147 " --> pdb=" O PRO Q 410 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id= AV, first strand: chain 'Z' and resid 12 through 15 removed outlier: 3.570A pdb=" N GLU Z 12 " --> pdb=" O ARG Z 523 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'Z' and resid 45 through 48 Processing sheet with id= AX, first strand: chain 'Z' and resid 191 through 196 removed outlier: 7.094A pdb=" N VAL Z 372 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 8.325A pdb=" N MET Z 194 " --> pdb=" O VAL Z 372 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU Z 374 " --> pdb=" O MET Z 194 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N MET Z 196 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N ILE Z 376 " --> pdb=" O MET Z 196 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER Z 205 " --> pdb=" O LEU Z 375 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id= AZ, first strand: chain 'Z' and resid 345 through 347 Processing sheet with id= BA, first strand: chain 'Z' and resid 477 through 479 Processing sheet with id= BB, first strand: chain 'a' and resid 9 through 13 Processing sheet with id= BC, first strand: chain 'a' and resid 43 through 46 Processing sheet with id= BD, first strand: chain 'a' and resid 137 through 139 Processing sheet with id= BE, first strand: chain 'a' and resid 180 through 182 Processing sheet with id= BF, first strand: chain 'a' and resid 196 through 199 Processing sheet with id= BG, first strand: chain 'a' and resid 213 through 216 Processing sheet with id= BH, first strand: chain 'a' and resid 346 through 348 removed outlier: 6.590A pdb=" N VAL a 285 " --> pdb=" O ALA a 235 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N LEU a 237 " --> pdb=" O VAL a 285 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU a 287 " --> pdb=" O LEU a 237 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N MET a 306 " --> pdb=" O ILE a 286 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N THR a 288 " --> pdb=" O MET a 306 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N VAL a 308 " --> pdb=" O THR a 288 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'a' and resid 486 through 489 Processing sheet with id= BJ, first strand: chain 'b' and resid 17 through 19 Processing sheet with id= BK, first strand: chain 'b' and resid 50 through 53 Processing sheet with id= BL, first strand: chain 'b' and resid 199 through 205 removed outlier: 6.350A pdb=" N CYS b 371 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ILE b 202 " --> pdb=" O CYS b 371 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE b 373 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LYS b 204 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LEU b 375 " --> pdb=" O LYS b 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= BL Processing sheet with id= BM, first strand: chain 'b' and resid 218 through 220 removed outlier: 3.622A pdb=" N ASP b 357 " --> pdb=" O ILE b 354 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'b' and resid 344 through 346 removed outlier: 6.661A pdb=" N CYS b 289 " --> pdb=" O LEU b 238 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ALA b 240 " --> pdb=" O CYS b 289 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE b 291 " --> pdb=" O ALA b 240 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N MET b 310 " --> pdb=" O PHE b 290 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ASN b 292 " --> pdb=" O MET b 310 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE b 312 " --> pdb=" O ASN b 292 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'b' and resid 406 through 408 Processing sheet with id= BP, first strand: chain 'b' and resid 476 through 479 Processing sheet with id= BQ, first strand: chain 'd' and resid 59 through 62 Processing sheet with id= BR, first strand: chain 'd' and resid 208 through 214 removed outlier: 6.804A pdb=" N VAL d 386 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N VAL d 211 " --> pdb=" O VAL d 386 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE d 388 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LYS d 213 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL d 390 " --> pdb=" O LYS d 213 " (cutoff:3.500A) No H-bonds generated for sheet with id= BR Processing sheet with id= BS, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.626A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'd' and resid 357 through 359 removed outlier: 6.671A pdb=" N VAL d 297 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ILE d 249 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU d 299 " --> pdb=" O ILE d 249 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N MET d 323 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE d 300 " --> pdb=" O MET d 323 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE d 325 " --> pdb=" O ILE d 300 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 'd' and resid 421 through 423 Processing sheet with id= BV, first strand: chain 'd' and resid 491 through 494 Processing sheet with id= BW, first strand: chain 'e' and resid 26 through 29 Processing sheet with id= BX, first strand: chain 'e' and resid 59 through 62 Processing sheet with id= BY, first strand: chain 'e' and resid 209 through 215 removed outlier: 6.783A pdb=" N VAL e 383 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N GLU e 212 " --> pdb=" O VAL e 383 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ILE e 385 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N LYS e 214 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ILE e 387 " --> pdb=" O LYS e 214 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'e' and resid 228 through 230 Processing sheet with id= CA, first strand: chain 'e' and resid 248 through 250 removed outlier: 7.088A pdb=" N LEU e 299 " --> pdb=" O ALA e 249 " (cutoff:3.500A) No H-bonds generated for sheet with id= CA Processing sheet with id= CB, first strand: chain 'e' and resid 418 through 420 Processing sheet with id= CC, first strand: chain 'g' and resid 15 through 18 Processing sheet with id= CD, first strand: chain 'g' and resid 48 through 51 Processing sheet with id= CE, first strand: chain 'g' and resid 185 through 187 Processing sheet with id= CF, first strand: chain 'g' and resid 200 through 205 removed outlier: 3.853A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'g' and resid 218 through 220 Processing sheet with id= CH, first strand: chain 'g' and resid 238 through 241 removed outlier: 6.381A pdb=" N VAL g 289 " --> pdb=" O VAL g 239 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU g 241 " --> pdb=" O VAL g 289 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE g 291 " --> pdb=" O LEU g 241 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N THR g 310 " --> pdb=" O VAL g 290 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N THR g 292 " --> pdb=" O THR g 310 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE g 312 " --> pdb=" O THR g 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= CH Processing sheet with id= CI, first strand: chain 'g' and resid 407 through 409 Processing sheet with id= CJ, first strand: chain 'g' and resid 478 through 480 Processing sheet with id= CK, first strand: chain 'h' and resid 14 through 17 Processing sheet with id= CL, first strand: chain 'h' and resid 47 through 50 Processing sheet with id= CM, first strand: chain 'h' and resid 195 through 201 removed outlier: 6.620A pdb=" N CYS h 370 " --> pdb=" O GLY h 196 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N LYS h 198 " --> pdb=" O CYS h 370 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N PHE h 372 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL h 200 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU h 374 " --> pdb=" O VAL h 200 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'h' and resid 214 through 217 Processing sheet with id= CO, first strand: chain 'h' and resid 342 through 344 removed outlier: 6.816A pdb=" N VAL h 288 " --> pdb=" O ALA h 238 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU h 240 " --> pdb=" O VAL h 288 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N LEU h 290 " --> pdb=" O LEU h 240 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N PHE h 309 " --> pdb=" O VAL h 289 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N SER h 291 " --> pdb=" O PHE h 309 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA h 311 " --> pdb=" O SER h 291 " (cutoff:3.500A) Processing sheet with id= CP, first strand: chain 'h' and resid 405 through 407 Processing sheet with id= CQ, first strand: chain 'h' and resid 475 through 478 Processing sheet with id= CR, first strand: chain 'q' and resid 20 through 23 Processing sheet with id= CS, first strand: chain 'q' and resid 54 through 57 Processing sheet with id= CT, first strand: chain 'q' and resid 202 through 208 removed outlier: 6.501A pdb=" N SER q 373 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N CYS q 205 " --> pdb=" O SER q 373 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ILE q 375 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ILE q 207 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N LEU q 377 " --> pdb=" O ILE q 207 " (cutoff:3.500A) Processing sheet with id= CU, first strand: chain 'q' and resid 220 through 223 Processing sheet with id= CV, first strand: chain 'q' and resid 240 through 242 removed outlier: 6.158A pdb=" N MET q 311 " --> pdb=" O VAL q 291 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N THR q 293 " --> pdb=" O MET q 311 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL q 313 " --> pdb=" O THR q 293 " (cutoff:3.500A) Processing sheet with id= CW, first strand: chain 'q' and resid 498 through 500 removed outlier: 3.804A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N VAL q 147 " --> pdb=" O PRO q 410 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain 'q' and resid 478 through 480 Processing sheet with id= CY, first strand: chain 'z' and resid 12 through 15 Processing sheet with id= CZ, first strand: chain 'z' and resid 45 through 48 Processing sheet with id= DA, first strand: chain 'z' and resid 191 through 196 removed outlier: 6.914A pdb=" N VAL z 372 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N MET z 194 " --> pdb=" O VAL z 372 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU z 374 " --> pdb=" O MET z 194 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N MET z 196 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ILE z 376 " --> pdb=" O MET z 196 " (cutoff:3.500A) Processing sheet with id= DB, first strand: chain 'z' and resid 210 through 212 Processing sheet with id= DC, first strand: chain 'z' and resid 345 through 347 Processing sheet with id= DD, first strand: chain 'z' and resid 407 through 409 Processing sheet with id= DE, first strand: chain 'z' and resid 477 through 479 Processing sheet with id= DF, first strand: chain 'P' and resid 162 through 164 removed outlier: 4.262A pdb=" N LYS P 218 " --> pdb=" O ILE P 164 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE P 187 " --> pdb=" O ALA P 235 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA P 235 " --> pdb=" O ILE P 187 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY P 246 " --> pdb=" O ILE P 238 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LYS P 240 " --> pdb=" O LEU P 244 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU P 244 " --> pdb=" O LYS P 240 " (cutoff:3.500A) 3461 hydrogen bonds defined for protein. 9081 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: 26.71 Time building geometry restraints manager: 21.60 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: 22561 1.34 - 1.46: 8787 1.46 - 1.58: 35784 1.58 - 1.69: 48 1.69 - 1.81: 735 Bond restraints: 67915 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 6.49e+01 bond pdb=" F2 AF3 g 603 " pdb="AL AF3 g 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 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 6.40e+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 D 603 " pdb="AL AF3 D 603 " ideal model delta sigma weight residual 1.637 1.795 -0.158 2.00e-02 2.50e+03 6.24e+01 ... (remaining 67910 not shown) Histogram of bond angle deviations from ideal: 97.35 - 105.26: 1046 105.26 - 113.18: 39586 113.18 - 121.09: 33797 121.09 - 129.01: 16970 129.01 - 136.92: 291 Bond angle restraints: 91690 Sorted by residual: angle pdb=" N GLY q 209 " pdb=" CA GLY q 209 " pdb=" C GLY q 209 " ideal model delta sigma weight residual 113.18 121.99 -8.81 2.37e+00 1.78e-01 1.38e+01 angle pdb=" N GLY Q 209 " pdb=" CA GLY Q 209 " pdb=" C GLY Q 209 " ideal model delta sigma weight residual 113.18 121.42 -8.24 2.37e+00 1.78e-01 1.21e+01 angle pdb=" CB MET E 60 " pdb=" CG MET E 60 " pdb=" SD MET E 60 " ideal model delta sigma weight residual 112.70 103.16 9.54 3.00e+00 1.11e-01 1.01e+01 angle pdb=" C GLN q 472 " pdb=" N GLU q 473 " pdb=" CA GLU q 473 " ideal model delta sigma weight residual 121.18 115.08 6.10 1.98e+00 2.55e-01 9.50e+00 angle pdb=" CB MET b 488 " pdb=" CG MET b 488 " pdb=" SD MET b 488 " ideal model delta sigma weight residual 112.70 103.55 9.15 3.00e+00 1.11e-01 9.30e+00 ... (remaining 91685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.15: 41168 35.15 - 70.30: 742 70.30 - 105.45: 64 105.45 - 140.60: 10 140.60 - 175.75: 7 Dihedral angle restraints: 41991 sinusoidal: 16914 harmonic: 25077 Sorted by residual: dihedral pdb=" O2A ADP q 601 " pdb=" O3A ADP q 601 " pdb=" PA ADP q 601 " pdb=" PB ADP q 601 " ideal model delta sinusoidal sigma weight residual 300.00 124.25 175.75 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O1B ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PB ADP B 601 " pdb=" PA ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 114.15 -174.15 1 2.00e+01 2.50e-03 4.79e+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 -60.00 111.72 -171.72 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 41988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 7989 0.043 - 0.085: 2131 0.085 - 0.128: 749 0.128 - 0.171: 49 0.171 - 0.214: 2 Chirality restraints: 10920 Sorted by residual: chirality pdb=" CB THR h 57 " pdb=" CA THR h 57 " pdb=" OG1 THR h 57 " pdb=" CG2 THR h 57 " both_signs ideal model delta sigma weight residual False 2.55 2.34 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA GLU A 77 " pdb=" N GLU A 77 " pdb=" C GLU A 77 " pdb=" CB GLU A 77 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.74e-01 chirality pdb=" CB VAL g 183 " pdb=" CA VAL g 183 " pdb=" CG1 VAL g 183 " pdb=" CG2 VAL g 183 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 10917 not shown) Planarity restraints: 11702 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN a 477 " 0.079 5.00e-02 4.00e+02 1.19e-01 2.26e+01 pdb=" N PRO a 478 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO a 478 " 0.063 5.00e-02 4.00e+02 pdb=" CD PRO a 478 " 0.064 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS a 69 " -0.032 5.00e-02 4.00e+02 4.84e-02 3.75e+00 pdb=" N PRO a 70 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO a 70 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO a 70 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG G 438 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C ARG G 438 " -0.033 2.00e-02 2.50e+03 pdb=" O ARG G 438 " 0.012 2.00e-02 2.50e+03 pdb=" N ALA G 439 " 0.011 2.00e-02 2.50e+03 ... (remaining 11699 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 489 2.50 - 3.10: 49933 3.10 - 3.70: 102493 3.70 - 4.30: 151527 4.30 - 4.90: 257250 Nonbonded interactions: 561692 Sorted by model distance: nonbonded pdb="MG MG B 602 " pdb=" F1 AF3 B 603 " model vdw 1.897 2.120 nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.906 2.120 nonbonded pdb="MG MG D 602 " pdb=" F2 AF3 D 603 " model vdw 1.908 2.120 nonbonded pdb="MG MG e 602 " pdb=" F1 AF3 e 603 " model vdw 1.923 2.120 nonbonded pdb=" OD2 ASP b 97 " pdb="MG MG b 602 " model vdw 1.931 2.170 ... (remaining 561687 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 8 or resid 10 through 536 or resid 601 through 603)) selection = (chain 'e' and (resid 8 or resid 10 through 536 or resid 601 through 603)) } 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 8.400 Check model and map are aligned: 0.730 Set scattering table: 0.460 Process input model: 142.930 Find NCS groups from input model: 6.550 Set up NCS constraints: 0.580 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:10.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 171.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 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 : 0.006 0.161 67915 Z= 0.417 Angle : 0.599 9.543 91690 Z= 0.296 Chirality : 0.043 0.214 10920 Planarity : 0.003 0.119 11702 Dihedral : 14.840 175.754 25745 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.11 % Favored : 95.88 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.09), residues: 8670 helix: 2.16 (0.08), residues: 4447 sheet: -0.10 (0.16), residues: 1155 loop : -0.61 (0.11), residues: 3068 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 0.027 0.001 PHE B 12 TYR 0.017 0.001 TYR G 437 ARG 0.015 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 563 time to evaluate : 5.904 Fit side-chains revert: symmetry clash REVERT: N 226 SER cc_start: 0.9049 (t) cc_final: 0.8754 (t) REVERT: N 228 GLN cc_start: 0.8653 (mm110) cc_final: 0.8278 (mp10) REVERT: A 171 MET cc_start: 0.8973 (ttm) cc_final: 0.8743 (ttm) REVERT: B 384 ASP cc_start: 0.8262 (m-30) cc_final: 0.8047 (m-30) REVERT: D 24 TYR cc_start: 0.8867 (t80) cc_final: 0.8614 (t80) REVERT: D 467 GLU cc_start: 0.8382 (tp30) cc_final: 0.8126 (tp30) REVERT: G 255 ASP cc_start: 0.8044 (m-30) cc_final: 0.7086 (m-30) REVERT: H 194 MET cc_start: 0.8827 (mmp) cc_final: 0.8411 (mmp) REVERT: H 403 ASP cc_start: 0.7885 (p0) cc_final: 0.7529 (p0) REVERT: H 524 ARG cc_start: 0.7537 (tmm-80) cc_final: 0.7302 (tmm-80) REVERT: Q 393 ASP cc_start: 0.8302 (t70) cc_final: 0.8024 (t0) REVERT: Z 522 MET cc_start: 0.8417 (mtm) cc_final: 0.7925 (mtm) REVERT: b 384 ASP cc_start: 0.8452 (m-30) cc_final: 0.8099 (m-30) REVERT: b 445 MET cc_start: 0.8826 (tpp) cc_final: 0.8540 (mmm) REVERT: d 446 MET cc_start: 0.8214 (mtt) cc_final: 0.7951 (mtt) REVERT: e 125 ASP cc_start: 0.8097 (m-30) cc_final: 0.7790 (m-30) REVERT: g 358 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8258 (mt-10) REVERT: g 395 MET cc_start: 0.9310 (mtm) cc_final: 0.9063 (mtm) REVERT: h 524 ARG cc_start: 0.7663 (mmm160) cc_final: 0.7193 (tpt90) REVERT: z 272 LYS cc_start: 0.8700 (mtpt) cc_final: 0.8483 (mppt) REVERT: z 364 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7691 (mm-30) REVERT: P 173 MET cc_start: 0.7891 (ttt) cc_final: 0.7353 (tpp) outliers start: 0 outliers final: 1 residues processed: 563 average time/residue: 1.4750 time to fit residues: 1087.0630 Evaluate side-chains 471 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 470 time to evaluate : 5.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain z residue 415 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 863 random chunks: chunk 728 optimal weight: 10.0000 chunk 654 optimal weight: 7.9990 chunk 362 optimal weight: 8.9990 chunk 223 optimal weight: 1.9990 chunk 441 optimal weight: 0.2980 chunk 349 optimal weight: 8.9990 chunk 676 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 411 optimal weight: 8.9990 chunk 503 optimal weight: 7.9990 chunk 783 optimal weight: 10.0000 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 231 GLN ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS G 12 GLN G 28 ASN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 HIS ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 217 ASN ** d 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 263 GLN ** d 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 526 HIS ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 130 GLN h 134 ASN z 161 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.0574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 67915 Z= 0.459 Angle : 0.636 10.577 91690 Z= 0.319 Chirality : 0.045 0.185 10920 Planarity : 0.004 0.070 11702 Dihedral : 7.979 175.037 9425 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.95 % Favored : 96.04 % Rotamer: Outliers : 1.06 % Allowed : 6.31 % Favored : 92.63 % 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: 0.97 (0.09), residues: 8670 helix: 1.78 (0.08), residues: 4472 sheet: -0.25 (0.16), residues: 1135 loop : -0.66 (0.11), residues: 3063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 266 HIS 0.010 0.001 HIS Z 161 PHE 0.023 0.002 PHE P 170 TYR 0.019 0.002 TYR G 437 ARG 0.010 0.000 ARG G 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 495 time to evaluate : 5.979 Fit side-chains revert: symmetry clash REVERT: N 226 SER cc_start: 0.9062 (t) cc_final: 0.8772 (t) REVERT: N 228 GLN cc_start: 0.8631 (mm110) cc_final: 0.8267 (mp10) REVERT: N 231 GLN cc_start: 0.8822 (pt0) cc_final: 0.8550 (pt0) REVERT: B 384 ASP cc_start: 0.8344 (m-30) cc_final: 0.8123 (m-30) REVERT: D 24 TYR cc_start: 0.8975 (t80) cc_final: 0.8730 (t80) REVERT: D 93 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7863 (mt-10) REVERT: D 467 GLU cc_start: 0.8396 (tp30) cc_final: 0.8119 (tp30) REVERT: E 91 MET cc_start: 0.9373 (OUTLIER) cc_final: 0.9068 (mmp) REVERT: H 403 ASP cc_start: 0.8031 (p0) cc_final: 0.7599 (p0) REVERT: H 524 ARG cc_start: 0.7637 (tmm-80) cc_final: 0.7287 (tmm-80) REVERT: Q 393 ASP cc_start: 0.8351 (t70) cc_final: 0.8064 (t0) REVERT: Z 32 ASP cc_start: 0.8144 (m-30) cc_final: 0.7773 (m-30) REVERT: Z 46 MET cc_start: 0.8751 (ttm) cc_final: 0.8450 (ttt) REVERT: b 384 ASP cc_start: 0.8473 (m-30) cc_final: 0.8243 (m-30) REVERT: b 445 MET cc_start: 0.8907 (tpp) cc_final: 0.8630 (mmm) REVERT: e 21 ASP cc_start: 0.7645 (t70) cc_final: 0.7415 (t0) REVERT: g 358 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8141 (mt-10) REVERT: g 395 MET cc_start: 0.9265 (mtm) cc_final: 0.9053 (mtm) REVERT: h 440 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8619 (tppp) REVERT: h 524 ARG cc_start: 0.7715 (mmm160) cc_final: 0.7226 (tpt90) REVERT: z 244 VAL cc_start: 0.8968 (OUTLIER) cc_final: 0.8649 (t) REVERT: z 272 LYS cc_start: 0.8712 (mtpt) cc_final: 0.8501 (mppt) REVERT: z 364 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7604 (mm-30) REVERT: P 173 MET cc_start: 0.7931 (ttt) cc_final: 0.7437 (tpp) REVERT: P 236 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.8007 (tm) outliers start: 77 outliers final: 31 residues processed: 525 average time/residue: 1.4614 time to fit residues: 1005.2792 Evaluate side-chains 504 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 468 time to evaluate : 5.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 233 HIS Chi-restraints excluded: chain H residue 497 MET Chi-restraints excluded: chain H residue 499 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 236 ASP Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain b residue 413 SER Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 191 VAL Chi-restraints excluded: chain e residue 443 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 283 HIS Chi-restraints excluded: chain h residue 440 LYS Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 266 MET Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 170 PHE Chi-restraints excluded: chain P residue 236 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 863 random chunks: chunk 435 optimal weight: 0.7980 chunk 243 optimal weight: 0.8980 chunk 652 optimal weight: 0.0570 chunk 533 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 785 optimal weight: 1.9990 chunk 848 optimal weight: 5.9990 chunk 699 optimal weight: 0.9980 chunk 778 optimal weight: 2.9990 chunk 267 optimal weight: 8.9990 chunk 629 optimal weight: 6.9990 overall best weight: 0.9500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN G 12 GLN G 28 ASN ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 251 GLN ** d 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 139 GLN h 30 GLN h 134 ASN ** z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.0829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 67915 Z= 0.141 Angle : 0.518 8.838 91690 Z= 0.256 Chirality : 0.040 0.156 10920 Planarity : 0.004 0.051 11702 Dihedral : 7.341 176.920 9422 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.22 % Favored : 96.77 % Rotamer: Outliers : 0.82 % Allowed : 8.29 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.09), residues: 8670 helix: 1.95 (0.08), residues: 4432 sheet: -0.09 (0.16), residues: 1135 loop : -0.55 (0.11), residues: 3103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g 168 HIS 0.014 0.001 HIS Z 161 PHE 0.026 0.001 PHE P 136 TYR 0.014 0.001 TYR z 498 ARG 0.006 0.000 ARG H 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 542 time to evaluate : 5.863 Fit side-chains revert: symmetry clash REVERT: N 226 SER cc_start: 0.9069 (t) cc_final: 0.8865 (t) REVERT: N 228 GLN cc_start: 0.8651 (mm110) cc_final: 0.8389 (mp10) REVERT: A 47 ASP cc_start: 0.7677 (t0) cc_final: 0.7161 (t0) REVERT: A 246 MET cc_start: 0.8545 (mmm) cc_final: 0.8280 (mmm) REVERT: D 24 TYR cc_start: 0.8779 (t80) cc_final: 0.8533 (t80) REVERT: D 467 GLU cc_start: 0.8323 (tp30) cc_final: 0.8038 (tp30) REVERT: H 403 ASP cc_start: 0.7944 (p0) cc_final: 0.7516 (p0) REVERT: H 524 ARG cc_start: 0.7573 (tmm-80) cc_final: 0.7159 (tmm-80) REVERT: Q 393 ASP cc_start: 0.8195 (t70) cc_final: 0.7981 (t0) REVERT: Z 32 ASP cc_start: 0.8138 (m-30) cc_final: 0.7703 (m-30) REVERT: b 87 MET cc_start: 0.8994 (ttp) cc_final: 0.8747 (ttp) REVERT: b 384 ASP cc_start: 0.8439 (m-30) cc_final: 0.8204 (m-30) REVERT: b 445 MET cc_start: 0.8648 (tpp) cc_final: 0.8320 (mmm) REVERT: e 21 ASP cc_start: 0.7592 (t70) cc_final: 0.7321 (t0) REVERT: g 358 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8134 (mt-10) REVERT: h 70 ASP cc_start: 0.7272 (t0) cc_final: 0.7053 (t0) REVERT: h 440 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8611 (tppp) REVERT: h 524 ARG cc_start: 0.7631 (mmm160) cc_final: 0.7307 (mmm-85) REVERT: z 272 LYS cc_start: 0.8675 (mtpt) cc_final: 0.8442 (mppt) REVERT: P 173 MET cc_start: 0.7950 (ttt) cc_final: 0.7656 (tpp) outliers start: 60 outliers final: 22 residues processed: 573 average time/residue: 1.4205 time to fit residues: 1075.9486 Evaluate side-chains 512 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 489 time to evaluate : 5.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 499 ARG Chi-restraints excluded: chain Q residue 236 ASP Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 134 GLU Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 283 HIS Chi-restraints excluded: chain h residue 440 LYS Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 170 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 863 random chunks: chunk 775 optimal weight: 8.9990 chunk 590 optimal weight: 8.9990 chunk 407 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 374 optimal weight: 4.9990 chunk 527 optimal weight: 8.9990 chunk 787 optimal weight: 8.9990 chunk 834 optimal weight: 9.9990 chunk 411 optimal weight: 8.9990 chunk 746 optimal weight: 5.9990 chunk 224 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 12 GLN G 226 HIS Z 71 HIS ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 334 ASN b 380 GLN ** d 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 139 GLN g 390 ASN q 359 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.0868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 67915 Z= 0.548 Angle : 0.677 11.826 91690 Z= 0.336 Chirality : 0.046 0.167 10920 Planarity : 0.004 0.052 11702 Dihedral : 7.562 173.345 9422 Min Nonbonded Distance : 1.751 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.39 % Favored : 95.60 % Rotamer: Outliers : 1.46 % Allowed : 10.26 % Favored : 88.29 % 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: 0.81 (0.09), residues: 8670 helix: 1.63 (0.08), residues: 4470 sheet: -0.31 (0.16), residues: 1148 loop : -0.71 (0.11), residues: 3052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 474 HIS 0.012 0.001 HIS Z 161 PHE 0.022 0.002 PHE P 170 TYR 0.020 0.002 TYR z 498 ARG 0.006 0.000 ARG H 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 476 time to evaluate : 5.865 Fit side-chains REVERT: N 228 GLN cc_start: 0.8600 (mm110) cc_final: 0.8223 (mp10) REVERT: A 47 ASP cc_start: 0.7856 (t0) cc_final: 0.7398 (t0) REVERT: A 48 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7773 (p0) REVERT: B 387 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7829 (tt0) REVERT: D 24 TYR cc_start: 0.9087 (t80) cc_final: 0.8816 (t80) REVERT: D 60 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8803 (ttm) REVERT: D 93 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7836 (mt-10) REVERT: D 467 GLU cc_start: 0.8384 (tp30) cc_final: 0.8065 (tp30) REVERT: G 422 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9191 (tp) REVERT: H 194 MET cc_start: 0.8848 (mmp) cc_final: 0.8506 (mmp) REVERT: H 320 LYS cc_start: 0.9004 (mttp) cc_final: 0.8783 (mttp) REVERT: H 403 ASP cc_start: 0.8079 (p0) cc_final: 0.7595 (p0) REVERT: Q 393 ASP cc_start: 0.8313 (t70) cc_final: 0.8011 (t0) REVERT: Z 32 ASP cc_start: 0.8264 (m-30) cc_final: 0.7858 (m-30) REVERT: Z 526 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.7596 (ptp) REVERT: a 156 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8678 (mtp) REVERT: b 10 ASN cc_start: 0.8954 (p0) cc_final: 0.8743 (p0) REVERT: b 87 MET cc_start: 0.9134 (ttp) cc_final: 0.8923 (ttp) REVERT: b 384 ASP cc_start: 0.8470 (m-30) cc_final: 0.8230 (m-30) REVERT: b 445 MET cc_start: 0.8989 (tpp) cc_final: 0.8707 (mmm) REVERT: d 279 GLU cc_start: 0.8078 (tt0) cc_final: 0.7742 (tt0) REVERT: e 21 ASP cc_start: 0.7668 (t70) cc_final: 0.7356 (t0) REVERT: g 8 LEU cc_start: 0.8665 (mt) cc_final: 0.8437 (tp) REVERT: g 358 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8189 (mt-10) REVERT: h 70 ASP cc_start: 0.7401 (t0) cc_final: 0.7191 (t0) REVERT: h 440 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8664 (tppp) REVERT: h 524 ARG cc_start: 0.7737 (mmm160) cc_final: 0.7407 (tpt90) REVERT: z 207 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8923 (mm) REVERT: z 244 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8738 (t) REVERT: z 272 LYS cc_start: 0.8734 (mtpt) cc_final: 0.8473 (mppt) REVERT: z 430 LYS cc_start: 0.8798 (tmtt) cc_final: 0.8586 (tmtm) REVERT: P 173 MET cc_start: 0.7997 (ttt) cc_final: 0.7664 (tpp) outliers start: 106 outliers final: 50 residues processed: 536 average time/residue: 1.4317 time to fit residues: 1011.2018 Evaluate side-chains 519 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 459 time to evaluate : 5.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 202 SER Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 146 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 155 SER Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 499 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 236 ASP Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 158 THR Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 526 MET Chi-restraints excluded: chain a residue 134 GLU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 320 VAL Chi-restraints excluded: chain b residue 413 SER Chi-restraints excluded: chain d residue 71 THR Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 191 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 283 HIS Chi-restraints excluded: chain h residue 440 LYS Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 207 ILE Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 415 GLU Chi-restraints excluded: chain P residue 170 PHE Chi-restraints excluded: chain P residue 263 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 863 random chunks: chunk 694 optimal weight: 6.9990 chunk 473 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 621 optimal weight: 0.9980 chunk 344 optimal weight: 6.9990 chunk 711 optimal weight: 6.9990 chunk 576 optimal weight: 5.9990 chunk 0 optimal weight: 40.0000 chunk 425 optimal weight: 1.9990 chunk 748 optimal weight: 0.7980 chunk 210 optimal weight: 3.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 515 GLN G 12 GLN G 28 ASN Z 161 HIS ** d 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 139 GLN g 390 ASN h 431 GLN P 287 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 67915 Z= 0.192 Angle : 0.538 9.186 91690 Z= 0.265 Chirality : 0.041 0.180 10920 Planarity : 0.003 0.049 11702 Dihedral : 7.285 173.793 9422 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.43 % Favored : 96.56 % Rotamer: Outliers : 1.17 % Allowed : 11.45 % Favored : 87.38 % 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: 1.06 (0.09), residues: 8670 helix: 1.83 (0.08), residues: 4464 sheet: -0.17 (0.16), residues: 1139 loop : -0.60 (0.11), residues: 3067 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.012 0.001 HIS Z 161 PHE 0.021 0.001 PHE P 170 TYR 0.017 0.001 TYR z 498 ARG 0.006 0.000 ARG Z 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 499 time to evaluate : 6.113 Fit side-chains revert: symmetry clash REVERT: N 228 GLN cc_start: 0.8576 (mm110) cc_final: 0.8371 (mp10) REVERT: A 47 ASP cc_start: 0.7784 (t0) cc_final: 0.7540 (t0) REVERT: A 246 MET cc_start: 0.8594 (mmm) cc_final: 0.8354 (mmm) REVERT: B 10 ASN cc_start: 0.8860 (OUTLIER) cc_final: 0.8343 (p0) REVERT: B 387 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7723 (tt0) REVERT: D 24 TYR cc_start: 0.8912 (t80) cc_final: 0.8681 (t80) REVERT: D 467 GLU cc_start: 0.8350 (tp30) cc_final: 0.8035 (tp30) REVERT: E 91 MET cc_start: 0.9317 (OUTLIER) cc_final: 0.9014 (mmp) REVERT: H 403 ASP cc_start: 0.8041 (p0) cc_final: 0.7582 (p0) REVERT: H 524 ARG cc_start: 0.7682 (tmm-80) cc_final: 0.7332 (tmm-80) REVERT: Q 393 ASP cc_start: 0.8206 (t70) cc_final: 0.7943 (t0) REVERT: Z 32 ASP cc_start: 0.8209 (m-30) cc_final: 0.7764 (m-30) REVERT: a 156 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8598 (mtp) REVERT: b 87 MET cc_start: 0.9099 (ttp) cc_final: 0.8887 (ttp) REVERT: b 384 ASP cc_start: 0.8399 (m-30) cc_final: 0.8175 (m-30) REVERT: b 445 MET cc_start: 0.8844 (tpp) cc_final: 0.8568 (mmm) REVERT: e 21 ASP cc_start: 0.7640 (t70) cc_final: 0.7311 (t0) REVERT: e 121 GLU cc_start: 0.7821 (tp30) cc_final: 0.7559 (tm-30) REVERT: g 8 LEU cc_start: 0.8548 (mt) cc_final: 0.8314 (tp) REVERT: g 15 LYS cc_start: 0.8566 (mmtt) cc_final: 0.8361 (mmtm) REVERT: g 229 MET cc_start: 0.9042 (mtt) cc_final: 0.8571 (mtt) REVERT: g 358 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8096 (mt-10) REVERT: h 70 ASP cc_start: 0.7388 (t0) cc_final: 0.7180 (t0) REVERT: h 440 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8595 (tppp) REVERT: h 524 ARG cc_start: 0.7715 (mmm160) cc_final: 0.7355 (tpt90) REVERT: z 207 ILE cc_start: 0.9087 (OUTLIER) cc_final: 0.8852 (mm) REVERT: z 244 VAL cc_start: 0.8830 (OUTLIER) cc_final: 0.8482 (t) REVERT: z 272 LYS cc_start: 0.8691 (mtpt) cc_final: 0.8417 (mppt) REVERT: z 430 LYS cc_start: 0.8779 (tmtt) cc_final: 0.8575 (tmtm) REVERT: P 173 MET cc_start: 0.8004 (ttt) cc_final: 0.7671 (tpp) outliers start: 85 outliers final: 40 residues processed: 548 average time/residue: 1.4655 time to fit residues: 1065.6269 Evaluate side-chains 525 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 478 time to evaluate : 5.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 499 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 236 ASP Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Z residue 17 GLN Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 134 GLU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 320 VAL Chi-restraints excluded: chain b residue 413 SER Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 497 LYS Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 283 HIS Chi-restraints excluded: chain h residue 440 LYS Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain z residue 207 ILE Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 170 PHE Chi-restraints excluded: chain P residue 263 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 863 random chunks: chunk 280 optimal weight: 7.9990 chunk 751 optimal weight: 10.0000 chunk 164 optimal weight: 5.9990 chunk 489 optimal weight: 6.9990 chunk 205 optimal weight: 9.9990 chunk 834 optimal weight: 10.0000 chunk 693 optimal weight: 4.9990 chunk 386 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 chunk 276 optimal weight: 10.0000 chunk 438 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 12 GLN Z 161 HIS Z 386 GLN a 217 ASN ** d 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 501 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 67915 Z= 0.451 Angle : 0.626 9.981 91690 Z= 0.309 Chirality : 0.044 0.162 10920 Planarity : 0.004 0.049 11702 Dihedral : 7.399 175.729 9422 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.36 % Favored : 95.63 % Rotamer: Outliers : 1.47 % Allowed : 12.21 % Favored : 86.32 % 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: 0.87 (0.09), residues: 8670 helix: 1.70 (0.08), residues: 4458 sheet: -0.34 (0.15), residues: 1154 loop : -0.70 (0.11), residues: 3058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 474 HIS 0.013 0.001 HIS Z 161 PHE 0.020 0.002 PHE P 170 TYR 0.020 0.002 TYR z 498 ARG 0.006 0.000 ARG H 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 589 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 482 time to evaluate : 6.969 Fit side-chains REVERT: N 228 GLN cc_start: 0.8552 (mm110) cc_final: 0.8338 (mp10) REVERT: A 47 ASP cc_start: 0.7956 (t0) cc_final: 0.7744 (t0) REVERT: B 10 ASN cc_start: 0.8893 (OUTLIER) cc_final: 0.8426 (p0) REVERT: B 387 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7780 (tt0) REVERT: D 24 TYR cc_start: 0.9052 (t80) cc_final: 0.8814 (t80) REVERT: D 93 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: D 467 GLU cc_start: 0.8356 (tp30) cc_final: 0.8032 (tp30) REVERT: G 422 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9184 (tp) REVERT: Q 393 ASP cc_start: 0.8261 (t70) cc_final: 0.7974 (t0) REVERT: Z 32 ASP cc_start: 0.8251 (m-30) cc_final: 0.7802 (m-30) REVERT: Z 526 MET cc_start: 0.7812 (pmm) cc_final: 0.7545 (ptp) REVERT: a 156 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8626 (mtp) REVERT: b 10 ASN cc_start: 0.8981 (p0) cc_final: 0.8736 (p0) REVERT: b 87 MET cc_start: 0.9158 (ttp) cc_final: 0.8928 (ttp) REVERT: b 384 ASP cc_start: 0.8424 (m-30) cc_final: 0.8195 (m-30) REVERT: b 445 MET cc_start: 0.8930 (tpp) cc_final: 0.8634 (mmm) REVERT: e 21 ASP cc_start: 0.7667 (t70) cc_final: 0.7344 (t0) REVERT: e 121 GLU cc_start: 0.7918 (tp30) cc_final: 0.7559 (tm-30) REVERT: g 15 LYS cc_start: 0.8558 (mmtt) cc_final: 0.8358 (mmtm) REVERT: g 182 MET cc_start: 0.8588 (ptt) cc_final: 0.8098 (ptt) REVERT: g 358 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8172 (mt-10) REVERT: h 70 ASP cc_start: 0.7416 (t0) cc_final: 0.7180 (t0) REVERT: h 440 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8640 (tppp) REVERT: h 482 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7945 (mm-30) REVERT: h 524 ARG cc_start: 0.7751 (mmm160) cc_final: 0.7408 (tpt90) REVERT: z 207 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8899 (mm) REVERT: z 244 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8677 (t) REVERT: z 272 LYS cc_start: 0.8726 (mtpt) cc_final: 0.8460 (mppt) REVERT: P 173 MET cc_start: 0.7976 (ttt) cc_final: 0.7643 (OUTLIER) outliers start: 107 outliers final: 61 residues processed: 549 average time/residue: 1.4543 time to fit residues: 1053.3061 Evaluate side-chains 534 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 465 time to evaluate : 5.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 202 SER Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 52 ASP Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain G residue 422 LEU Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 233 HIS Chi-restraints excluded: chain H residue 497 MET Chi-restraints excluded: chain H residue 499 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 236 ASP Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Z residue 17 GLN Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 196 MET Chi-restraints excluded: chain a residue 134 GLU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 320 VAL Chi-restraints excluded: chain b residue 413 SER Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 191 VAL Chi-restraints excluded: chain d residue 497 LYS Chi-restraints excluded: chain d residue 538 THR Chi-restraints excluded: chain e residue 307 ASP Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 429 MET Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 283 HIS Chi-restraints excluded: chain h residue 440 LYS Chi-restraints excluded: chain h residue 482 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 207 ILE Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 415 GLU Chi-restraints excluded: chain P residue 170 PHE Chi-restraints excluded: chain P residue 263 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 863 random chunks: chunk 805 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 475 optimal weight: 4.9990 chunk 609 optimal weight: 8.9990 chunk 472 optimal weight: 0.0870 chunk 702 optimal weight: 5.9990 chunk 466 optimal weight: 0.9980 chunk 831 optimal weight: 2.9990 chunk 520 optimal weight: 0.8980 chunk 507 optimal weight: 2.9990 chunk 384 optimal weight: 5.9990 overall best weight: 1.5962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 ASN G 12 GLN G 28 ASN Z 161 HIS Z 386 GLN a 217 ASN ** d 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 522 GLN h 501 ASN ** z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 287 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 67915 Z= 0.178 Angle : 0.536 10.086 91690 Z= 0.263 Chirality : 0.041 0.156 10920 Planarity : 0.003 0.049 11702 Dihedral : 7.142 178.410 9422 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.29 % Favored : 96.70 % Rotamer: Outliers : 1.18 % Allowed : 12.76 % Favored : 86.06 % 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: 1.07 (0.09), residues: 8670 helix: 1.86 (0.08), residues: 4455 sheet: -0.19 (0.16), residues: 1138 loop : -0.61 (0.11), residues: 3077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 222 HIS 0.017 0.001 HIS Z 161 PHE 0.020 0.001 PHE P 170 TYR 0.019 0.001 TYR z 498 ARG 0.006 0.000 ARG Z 15 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 500 time to evaluate : 5.925 Fit side-chains revert: symmetry clash REVERT: N 211 LEU cc_start: 0.6139 (mp) cc_final: 0.5735 (mp) REVERT: A 47 ASP cc_start: 0.7870 (t0) cc_final: 0.7659 (t0) REVERT: B 387 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: D 24 TYR cc_start: 0.8900 (t80) cc_final: 0.8687 (t80) REVERT: D 93 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7825 (mt-10) REVERT: D 320 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8849 (mtt) REVERT: E 91 MET cc_start: 0.9304 (OUTLIER) cc_final: 0.8971 (mmp) REVERT: H 194 MET cc_start: 0.8843 (mmp) cc_final: 0.8504 (mmp) REVERT: H 403 ASP cc_start: 0.8049 (p0) cc_final: 0.7577 (p0) REVERT: H 524 ARG cc_start: 0.7658 (tmm-80) cc_final: 0.7359 (tmm-80) REVERT: Q 393 ASP cc_start: 0.8197 (t70) cc_final: 0.7937 (t0) REVERT: Z 32 ASP cc_start: 0.8218 (m-30) cc_final: 0.7743 (m-30) REVERT: Z 526 MET cc_start: 0.7813 (pmm) cc_final: 0.7483 (ptp) REVERT: a 156 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.8540 (mtp) REVERT: b 87 MET cc_start: 0.9115 (ttp) cc_final: 0.8907 (ttp) REVERT: b 384 ASP cc_start: 0.8397 (m-30) cc_final: 0.8173 (m-30) REVERT: b 445 MET cc_start: 0.8804 (tpp) cc_final: 0.8529 (mmm) REVERT: e 21 ASP cc_start: 0.7656 (t70) cc_final: 0.7319 (OUTLIER) REVERT: e 121 GLU cc_start: 0.7874 (tp30) cc_final: 0.7512 (tm-30) REVERT: g 15 LYS cc_start: 0.8518 (mmtt) cc_final: 0.8312 (mmtm) REVERT: g 358 GLU cc_start: 0.8356 (mt-10) cc_final: 0.8121 (mt-10) REVERT: h 70 ASP cc_start: 0.7342 (t0) cc_final: 0.7086 (t0) REVERT: h 324 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.7920 (mpp) REVERT: h 440 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8585 (tppp) REVERT: h 482 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7938 (mm-30) REVERT: h 524 ARG cc_start: 0.7746 (mmm160) cc_final: 0.7395 (tpt90) REVERT: z 207 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8833 (mm) REVERT: z 244 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8455 (t) REVERT: z 272 LYS cc_start: 0.8691 (mtpt) cc_final: 0.8411 (mppt) REVERT: P 144 ARG cc_start: 0.7201 (mmm160) cc_final: 0.6981 (mmm160) REVERT: P 173 MET cc_start: 0.7971 (ttt) cc_final: 0.7604 (tpp) outliers start: 86 outliers final: 45 residues processed: 549 average time/residue: 1.4467 time to fit residues: 1050.2043 Evaluate side-chains 532 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 478 time to evaluate : 5.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 497 MET Chi-restraints excluded: chain H residue 499 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Z residue 17 GLN Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 134 GLU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 320 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 522 GLN Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 283 HIS Chi-restraints excluded: chain h residue 324 MET Chi-restraints excluded: chain h residue 440 LYS Chi-restraints excluded: chain h residue 482 GLU Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 207 ILE Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 170 PHE Chi-restraints excluded: chain P residue 263 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 863 random chunks: chunk 514 optimal weight: 5.9990 chunk 332 optimal weight: 7.9990 chunk 496 optimal weight: 4.9990 chunk 250 optimal weight: 7.9990 chunk 163 optimal weight: 0.9990 chunk 161 optimal weight: 7.9990 chunk 528 optimal weight: 0.9990 chunk 566 optimal weight: 4.9990 chunk 411 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 653 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 228 GLN ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 ASN G 12 GLN Z 161 HIS a 534 HIS ** d 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 522 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 67915 Z= 0.260 Angle : 0.558 11.024 91690 Z= 0.272 Chirality : 0.041 0.155 10920 Planarity : 0.003 0.047 11702 Dihedral : 7.091 178.487 9422 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.88 % Favored : 96.11 % Rotamer: Outliers : 1.26 % Allowed : 13.14 % Favored : 85.59 % 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: 1.06 (0.09), residues: 8670 helix: 1.86 (0.08), residues: 4460 sheet: -0.16 (0.16), residues: 1149 loop : -0.63 (0.11), residues: 3061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.015 0.001 HIS Z 161 PHE 0.020 0.001 PHE P 170 TYR 0.018 0.001 TYR z 498 ARG 0.007 0.000 ARG H 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 485 time to evaluate : 6.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 211 LEU cc_start: 0.6213 (mp) cc_final: 0.5960 (mp) REVERT: B 10 ASN cc_start: 0.8903 (OUTLIER) cc_final: 0.8466 (p0) REVERT: B 323 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9252 (mm) REVERT: B 387 GLU cc_start: 0.8167 (OUTLIER) cc_final: 0.7722 (tt0) REVERT: D 24 TYR cc_start: 0.8942 (t80) cc_final: 0.8720 (t80) REVERT: D 93 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7837 (mt-10) REVERT: D 320 MET cc_start: 0.9221 (OUTLIER) cc_final: 0.8846 (mtt) REVERT: E 91 MET cc_start: 0.9314 (OUTLIER) cc_final: 0.9017 (mmp) REVERT: H 194 MET cc_start: 0.8859 (mmp) cc_final: 0.8491 (mmp) REVERT: H 227 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8733 (mtp) REVERT: H 320 LYS cc_start: 0.8926 (mttm) cc_final: 0.8666 (mttp) REVERT: H 524 ARG cc_start: 0.7705 (tmm-80) cc_final: 0.7369 (tmm-80) REVERT: Q 393 ASP cc_start: 0.8199 (t70) cc_final: 0.7935 (t0) REVERT: Z 32 ASP cc_start: 0.8265 (m-30) cc_final: 0.7790 (m-30) REVERT: Z 526 MET cc_start: 0.7833 (pmm) cc_final: 0.7507 (ptp) REVERT: a 156 MET cc_start: 0.8848 (OUTLIER) cc_final: 0.8592 (mtp) REVERT: b 87 MET cc_start: 0.9126 (ttp) cc_final: 0.8923 (ttp) REVERT: b 384 ASP cc_start: 0.8408 (m-30) cc_final: 0.8178 (m-30) REVERT: b 445 MET cc_start: 0.8820 (tpp) cc_final: 0.8527 (mmm) REVERT: e 21 ASP cc_start: 0.7666 (t70) cc_final: 0.7344 (t0) REVERT: e 121 GLU cc_start: 0.7919 (tp30) cc_final: 0.7553 (tm-30) REVERT: g 15 LYS cc_start: 0.8515 (mmtt) cc_final: 0.8305 (mmtm) REVERT: g 358 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8155 (mt-10) REVERT: h 70 ASP cc_start: 0.7400 (t0) cc_final: 0.7101 (t0) REVERT: h 440 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8594 (tppp) REVERT: h 482 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7912 (mm-30) REVERT: h 524 ARG cc_start: 0.7748 (mmm160) cc_final: 0.7406 (tpt90) REVERT: z 207 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8861 (mm) REVERT: z 244 VAL cc_start: 0.8838 (OUTLIER) cc_final: 0.8502 (t) REVERT: z 272 LYS cc_start: 0.8706 (mtpt) cc_final: 0.8424 (mppt) REVERT: P 173 MET cc_start: 0.7964 (ttt) cc_final: 0.7644 (OUTLIER) outliers start: 92 outliers final: 53 residues processed: 539 average time/residue: 1.4350 time to fit residues: 1029.5318 Evaluate side-chains 543 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 479 time to evaluate : 5.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 172 ASN Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 332 VAL Chi-restraints excluded: chain G residue 364 THR Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 497 MET Chi-restraints excluded: chain H residue 499 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Z residue 17 GLN Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 134 GLU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 320 VAL Chi-restraints excluded: chain b residue 413 SER Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 538 THR Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 307 ASP Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 283 HIS Chi-restraints excluded: chain h residue 440 LYS Chi-restraints excluded: chain h residue 482 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 207 ILE Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 374 LEU Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 170 PHE Chi-restraints excluded: chain P residue 263 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 863 random chunks: chunk 756 optimal weight: 10.0000 chunk 796 optimal weight: 8.9990 chunk 727 optimal weight: 4.9990 chunk 775 optimal weight: 8.9990 chunk 466 optimal weight: 10.0000 chunk 337 optimal weight: 0.0040 chunk 608 optimal weight: 10.0000 chunk 237 optimal weight: 2.9990 chunk 700 optimal weight: 6.9990 chunk 733 optimal weight: 5.9990 chunk 772 optimal weight: 9.9990 overall best weight: 4.2000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 12 GLN Z 161 HIS ** a 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 522 GLN h 501 ASN q 346 HIS P 287 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 67915 Z= 0.363 Angle : 0.600 11.257 91690 Z= 0.294 Chirality : 0.043 0.178 10920 Planarity : 0.004 0.047 11702 Dihedral : 7.192 175.595 9422 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.95 % Favored : 96.04 % Rotamer: Outliers : 1.24 % Allowed : 13.45 % Favored : 85.32 % 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: 0.96 (0.09), residues: 8670 helix: 1.79 (0.08), residues: 4460 sheet: -0.26 (0.16), residues: 1146 loop : -0.68 (0.11), residues: 3064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 266 HIS 0.015 0.001 HIS Z 161 PHE 0.020 0.001 PHE P 170 TYR 0.021 0.001 TYR z 498 ARG 0.007 0.000 ARG H 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 487 time to evaluate : 6.545 Fit side-chains revert: symmetry clash REVERT: N 211 LEU cc_start: 0.5968 (mp) cc_final: 0.5690 (mp) REVERT: N 243 LEU cc_start: 0.5449 (pp) cc_final: 0.5164 (pt) REVERT: A 430 MET cc_start: 0.8078 (pmm) cc_final: 0.7809 (pmm) REVERT: B 10 ASN cc_start: 0.8920 (OUTLIER) cc_final: 0.8541 (p0) REVERT: B 323 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9230 (mm) REVERT: B 387 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7753 (tt0) REVERT: D 24 TYR cc_start: 0.8981 (t80) cc_final: 0.8752 (t80) REVERT: D 93 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7843 (mt-10) REVERT: H 194 MET cc_start: 0.8848 (mmp) cc_final: 0.8475 (mmp) REVERT: H 524 ARG cc_start: 0.7738 (tmm-80) cc_final: 0.7381 (tmm-80) REVERT: Q 344 MET cc_start: 0.8493 (ttp) cc_final: 0.8292 (ttp) REVERT: Q 393 ASP cc_start: 0.8238 (t70) cc_final: 0.7959 (t0) REVERT: Z 32 ASP cc_start: 0.8236 (m-30) cc_final: 0.7755 (m-30) REVERT: Z 526 MET cc_start: 0.7827 (pmm) cc_final: 0.7531 (ptp) REVERT: a 156 MET cc_start: 0.8889 (OUTLIER) cc_final: 0.8625 (mtp) REVERT: b 10 ASN cc_start: 0.8984 (p0) cc_final: 0.8756 (p0) REVERT: b 87 MET cc_start: 0.9151 (ttp) cc_final: 0.8929 (ttp) REVERT: b 384 ASP cc_start: 0.8414 (m-30) cc_final: 0.8186 (m-30) REVERT: b 445 MET cc_start: 0.8874 (tpp) cc_final: 0.8584 (mmm) REVERT: e 21 ASP cc_start: 0.7684 (t70) cc_final: 0.7346 (OUTLIER) REVERT: e 121 GLU cc_start: 0.7908 (tp30) cc_final: 0.7560 (tm-30) REVERT: g 15 LYS cc_start: 0.8529 (mmtt) cc_final: 0.8326 (mmtm) REVERT: g 358 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8140 (mt-10) REVERT: h 70 ASP cc_start: 0.7454 (t0) cc_final: 0.7139 (t0) REVERT: h 324 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.7923 (mpp) REVERT: h 440 LYS cc_start: 0.9204 (OUTLIER) cc_final: 0.8626 (tppp) REVERT: h 524 ARG cc_start: 0.7768 (mmm160) cc_final: 0.7408 (tpt90) REVERT: z 207 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8883 (mm) REVERT: z 244 VAL cc_start: 0.8946 (OUTLIER) cc_final: 0.8631 (t) REVERT: z 272 LYS cc_start: 0.8708 (mtpt) cc_final: 0.8429 (mppt) REVERT: P 173 MET cc_start: 0.7985 (ttt) cc_final: 0.6889 (OUTLIER) outliers start: 90 outliers final: 58 residues processed: 541 average time/residue: 1.4542 time to fit residues: 1040.5767 Evaluate side-chains 546 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 481 time to evaluate : 5.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 332 VAL Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 497 MET Chi-restraints excluded: chain H residue 499 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 236 ASP Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Z residue 17 GLN Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 134 GLU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 320 VAL Chi-restraints excluded: chain b residue 413 SER Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 538 THR Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 307 ASP Chi-restraints excluded: chain e residue 522 GLN Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 283 HIS Chi-restraints excluded: chain h residue 324 MET Chi-restraints excluded: chain h residue 440 LYS Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 207 ILE Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 414 VAL Chi-restraints excluded: chain P residue 170 PHE Chi-restraints excluded: chain P residue 263 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 863 random chunks: chunk 508 optimal weight: 8.9990 chunk 819 optimal weight: 10.0000 chunk 500 optimal weight: 10.0000 chunk 388 optimal weight: 7.9990 chunk 569 optimal weight: 5.9990 chunk 859 optimal weight: 8.9990 chunk 791 optimal weight: 4.9990 chunk 684 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 528 optimal weight: 7.9990 chunk 419 optimal weight: 0.4980 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 12 GLN Z 161 HIS ** a 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 501 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.241 67915 Z= 0.414 Angle : 0.651 59.190 91690 Z= 0.334 Chirality : 0.044 0.421 10920 Planarity : 0.004 0.047 11702 Dihedral : 7.195 175.524 9422 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.04 % Favored : 95.95 % Rotamer: Outliers : 1.02 % Allowed : 13.72 % Favored : 85.26 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.09), residues: 8670 helix: 1.76 (0.08), residues: 4460 sheet: -0.26 (0.16), residues: 1146 loop : -0.69 (0.11), residues: 3064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 266 HIS 0.014 0.001 HIS Z 161 PHE 0.041 0.002 PHE P 271 TYR 0.020 0.001 TYR z 498 ARG 0.007 0.000 ARG H 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17340 Ramachandran restraints generated. 8670 Oldfield, 0 Emsley, 8670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 483 time to evaluate : 6.269 Fit side-chains revert: symmetry clash REVERT: N 211 LEU cc_start: 0.5971 (mp) cc_final: 0.5694 (mp) REVERT: N 243 LEU cc_start: 0.5454 (pp) cc_final: 0.5164 (pt) REVERT: A 430 MET cc_start: 0.8078 (pmm) cc_final: 0.7820 (pmm) REVERT: B 10 ASN cc_start: 0.8922 (OUTLIER) cc_final: 0.8544 (p0) REVERT: B 247 ASP cc_start: 0.8184 (t0) cc_final: 0.7313 (p0) REVERT: B 323 LEU cc_start: 0.9479 (OUTLIER) cc_final: 0.9232 (mm) REVERT: B 387 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7757 (tt0) REVERT: D 24 TYR cc_start: 0.8982 (t80) cc_final: 0.8755 (t80) REVERT: D 93 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7845 (mt-10) REVERT: H 194 MET cc_start: 0.8849 (mmp) cc_final: 0.8478 (mmp) REVERT: H 524 ARG cc_start: 0.7739 (tmm-80) cc_final: 0.7374 (tmm-80) REVERT: Q 85 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.7755 (mmm) REVERT: Q 393 ASP cc_start: 0.8241 (t70) cc_final: 0.7962 (t0) REVERT: Z 32 ASP cc_start: 0.8237 (m-30) cc_final: 0.7757 (m-30) REVERT: Z 526 MET cc_start: 0.7829 (pmm) cc_final: 0.7530 (ptp) REVERT: a 156 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8628 (mtp) REVERT: b 10 ASN cc_start: 0.8985 (p0) cc_final: 0.8755 (p0) REVERT: b 87 MET cc_start: 0.9152 (ttp) cc_final: 0.8932 (ttp) REVERT: b 384 ASP cc_start: 0.8416 (m-30) cc_final: 0.8188 (m-30) REVERT: b 445 MET cc_start: 0.8877 (tpp) cc_final: 0.8587 (mmm) REVERT: e 21 ASP cc_start: 0.7684 (t70) cc_final: 0.7347 (OUTLIER) REVERT: e 121 GLU cc_start: 0.7914 (tp30) cc_final: 0.7564 (tm-30) REVERT: g 15 LYS cc_start: 0.8530 (mmtt) cc_final: 0.8315 (mmtm) REVERT: g 358 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8143 (mt-10) REVERT: h 70 ASP cc_start: 0.7457 (t0) cc_final: 0.7142 (t0) REVERT: h 324 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.7925 (mpp) REVERT: h 440 LYS cc_start: 0.9206 (OUTLIER) cc_final: 0.8628 (tppp) REVERT: h 524 ARG cc_start: 0.7770 (mmm160) cc_final: 0.7410 (tpt90) REVERT: z 207 ILE cc_start: 0.9130 (OUTLIER) cc_final: 0.8887 (mm) REVERT: z 244 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8634 (t) REVERT: z 272 LYS cc_start: 0.8710 (mtpt) cc_final: 0.8432 (mppt) outliers start: 74 outliers final: 62 residues processed: 524 average time/residue: 1.4644 time to fit residues: 1015.0667 Evaluate side-chains 547 residues out of total 7272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 476 time to evaluate : 5.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 221 LEU Chi-restraints excluded: chain N residue 266 TRP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain B residue 10 ASN Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 387 GLU Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain D residue 60 MET Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 332 VAL Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 319 LEU Chi-restraints excluded: chain H residue 497 MET Chi-restraints excluded: chain H residue 499 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 85 MET Chi-restraints excluded: chain Q residue 236 ASP Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Z residue 17 GLN Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 134 GLU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 320 VAL Chi-restraints excluded: chain b residue 413 SER Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 538 THR Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 307 ASP Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 283 HIS Chi-restraints excluded: chain h residue 324 MET Chi-restraints excluded: chain h residue 440 LYS Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 85 MET Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 207 ILE Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 414 VAL Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 170 PHE Chi-restraints excluded: chain P residue 263 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 863 random chunks: chunk 543 optimal weight: 7.9990 chunk 729 optimal weight: 0.8980 chunk 209 optimal weight: 0.6980 chunk 631 optimal weight: 0.9980 chunk 101 optimal weight: 0.9990 chunk 190 optimal weight: 10.0000 chunk 685 optimal weight: 0.8980 chunk 286 optimal weight: 7.9990 chunk 704 optimal weight: 0.0030 chunk 86 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 12 GLN Z 161 HIS ** a 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 537 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 501 ASN P 287 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.075288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.061409 restraints weight = 201517.652| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 3.00 r_work: 0.2594 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.241 67915 Z= 0.414 Angle : 0.651 59.190 91690 Z= 0.334 Chirality : 0.044 0.421 10920 Planarity : 0.004 0.047 11702 Dihedral : 7.195 175.524 9422 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.04 % Favored : 95.95 % Rotamer: Outliers : 0.99 % Allowed : 13.75 % Favored : 85.26 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.09), residues: 8670 helix: 1.76 (0.08), residues: 4460 sheet: -0.26 (0.16), residues: 1146 loop : -0.69 (0.11), residues: 3064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 266 HIS 0.014 0.001 HIS Z 161 PHE 0.041 0.002 PHE P 271 TYR 0.020 0.001 TYR z 498 ARG 0.007 0.000 ARG H 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16384.80 seconds wall clock time: 288 minutes 46.74 seconds (17326.74 seconds total)