Starting phenix.real_space_refine on Sun Dec 10 16:15:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg8_40452/12_2023/8sg8_40452_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg8_40452/12_2023/8sg8_40452.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/8sg8_40452/12_2023/8sg8_40452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg8_40452/12_2023/8sg8_40452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg8_40452/12_2023/8sg8_40452_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sg8_40452/12_2023/8sg8_40452_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 412 5.16 5 C 41760 2.51 5 N 11628 2.21 5 O 12927 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 GLU 18": "OE1" <-> "OE2" Residue "B ASP 58": "OD1" <-> "OD2" Residue "B TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "D GLU 331": "OE1" <-> "OE2" Residue "D GLU 467": "OE1" <-> "OE2" Residue "E ASP 149": "OD1" <-> "OD2" Residue "E GLU 508": "OE1" <-> "OE2" Residue "G GLU 415": "OE1" <-> "OE2" Residue "H ASP 46": "OD1" <-> "OD2" Residue "H PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 413": "OE1" <-> "OE2" Residue "Q PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 368": "OE1" <-> "OE2" Residue "Q ASP 387": "OD1" <-> "OD2" Residue "Q GLU 473": "OE1" <-> "OE2" Residue "Q GLU 483": "OE1" <-> "OE2" Residue "Z ASP 220": "OD1" <-> "OD2" Residue "Z PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 415": "OE1" <-> "OE2" Residue "Z TYR 498": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 80": "OD1" <-> "OD2" Residue "a GLU 473": "OE1" <-> "OE2" Residue "b GLU 18": "OE1" <-> "OE2" Residue "b TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 32": "OE1" <-> "OE2" Residue "e ASP 58": "OD1" <-> "OD2" Residue "e GLU 118": "OE1" <-> "OE2" Residue "e TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 426": "OE1" <-> "OE2" Residue "g ASP 194": "OD1" <-> "OD2" Residue "g ASP 255": "OD1" <-> "OD2" Residue "g GLU 415": "OE1" <-> "OE2" Residue "g TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 70": "OD1" <-> "OD2" Residue "h GLU 103": "OE1" <-> "OE2" Residue "q GLU 117": "OE1" <-> "OE2" Residue "q GLU 443": "OE1" <-> "OE2" Residue "z ASP 342": "OD1" <-> "OD2" Residue "z GLU 352": "OE1" <-> "OE2" Residue "z TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 480": "OD1" <-> "OD2" Residue "P GLU 168": "OE1" <-> "OE2" Residue "P GLU 189": "OE1" <-> "OE2" Residue "P GLU 208": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 66839 Number of models: 1 Model: "" Number of chains: 50 Chain: "N" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 89 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} 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: 4121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} 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: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1627 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 6, 'TRANS': 198} 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: 1 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: 27.03, per 1000 atoms: 0.40 Number of scatterers: 66839 At special positions: 0 Unit cell: (179.86, 177.744, 180.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 412 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 12927 8.00 N 11628 7.00 C 41760 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 "HETATM66490 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66362 O3A ADP B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66746 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66394 O3A ADP D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66618 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66682 O3A ADP e 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66426 O3A ADP E 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.56 Conformation dependent library (CDL) restraints added in 9.8 seconds 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16166 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 323 helices and 108 sheets defined 50.8% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.33 Creating SS restraints... Processing helix chain 'A' and resid 15 through 35 removed outlier: 3.685A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 5.700A 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: 3.908A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 110 removed outlier: 3.568A pdb=" N GLN A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 135 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 146 through 156 Processing helix chain 'A' and resid 163 through 179 removed outlier: 4.595A pdb=" N ASP A 166 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 4.787A 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: 4.206A pdb=" N ASP A 261 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ILE A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 382 through 404 Processing helix chain 'A' and resid 414 through 429 removed outlier: 4.423A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N SER A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 455 removed outlier: 3.738A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 5.103A 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: 3.847A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TRP A 485 " --> pdb=" O ASN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 525 Processing helix chain 'B' and resid 21 through 39 Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 99 through 118 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: 3.578A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS B 176 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ASP B 177 " --> pdb=" O HIS B 174 " (cutoff:3.500A) removed outlier: 3.535A 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: 4.069A pdb=" N HIS B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 317 through 327 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 380 through 402 Processing helix chain 'B' and resid 412 through 427 removed outlier: 3.823A 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: 3.645A 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: 4.336A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N SER D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 80 Processing helix chain 'D' and resid 86 through 101 Processing helix chain 'D' and resid 106 through 125 removed outlier: 4.245A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 151 Processing helix chain 'D' and resid 160 through 172 Processing helix chain 'D' and resid 180 through 194 Proline residue: D 185 - end of helix removed outlier: 3.837A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 269 through 293 removed outlier: 4.222A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 4.054A 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: 4.505A pdb=" N GLU D 334 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 3.998A 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: 3.662A pdb=" N THR D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 468 removed outlier: 4.127A pdb=" N VAL D 460 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 5.001A 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 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: 3.601A pdb=" N LEU E 34 " --> pdb=" O GLY E 30 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N THR E 50 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N SER E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 79 Processing helix chain 'E' and resid 86 through 101 Processing helix chain 'E' and resid 108 through 126 removed outlier: 3.597A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 150 Processing helix chain 'E' and resid 163 through 173 Processing helix chain 'E' and resid 177 through 180 removed outlier: 3.939A 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: 3.942A pdb=" N THR E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 316 Processing helix chain 'E' and resid 327 through 337 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 392 through 414 Processing helix chain 'E' and resid 424 through 438 Processing helix chain 'E' and resid 442 through 465 removed outlier: 4.059A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.629A 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: 4.842A pdb=" N ILE E 458 " --> pdb=" O ALA E 454 " (cutoff:3.500A) Proline residue: E 459 - end of helix Processing helix chain 'E' and resid 470 through 483 Processing helix chain 'E' and resid 501 through 504 No H-bonds generated for 'chain 'E' and resid 501 through 504' Processing helix chain 'E' and resid 510 through 529 Processing helix chain 'G' and resid 19 through 37 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: 3.972A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.153A 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 169 through 183 Processing helix chain 'G' and resid 195 through 198 No H-bonds generated for 'chain 'G' and resid 195 through 198' Processing helix chain 'G' and resid 209 through 211 No H-bonds generated for 'chain 'G' and resid 209 through 211' Processing helix chain 'G' and resid 263 through 285 removed outlier: 4.413A pdb=" N LEU G 285 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 307 removed outlier: 3.645A pdb=" N ALA G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 327 Processing helix chain 'G' and resid 335 through 337 No H-bonds generated for 'chain 'G' and resid 335 through 337' Processing helix chain 'G' and resid 381 through 403 Processing helix chain 'G' and resid 413 through 428 removed outlier: 3.603A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N ALA G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 455 removed outlier: 3.791A pdb=" N TRP G 435 " --> pdb=" O VAL G 432 " (cutoff:3.500A) Proline residue: G 436 - end of helix removed outlier: 4.173A 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 518 Processing helix chain 'H' and resid 19 through 35 removed outlier: 3.567A pdb=" N ALA H 35 " --> pdb=" O VAL H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 39 No H-bonds generated for 'chain 'H' and resid 37 through 39' Processing helix chain 'H' and resid 62 through 68 Processing helix chain 'H' and resid 76 through 89 removed outlier: 3.672A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 113 removed outlier: 4.018A pdb=" N THR H 98 " --> pdb=" O THR H 94 " (cutoff:3.500A) Proline residue: H 110 - end of helix Processing helix chain 'H' and resid 118 through 139 Processing helix chain 'H' and resid 148 through 163 Processing helix chain 'H' and resid 172 through 185 removed outlier: 3.770A pdb=" N MET H 185 " --> pdb=" O ASP H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'H' and resid 205 through 207 No H-bonds generated for 'chain 'H' and resid 205 through 207' Processing helix chain 'H' and resid 225 through 227 No H-bonds generated for 'chain 'H' and resid 225 through 227' Processing helix chain 'H' and resid 260 through 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: 4.130A pdb=" N THR H 426 " --> pdb=" O ASP H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 452 removed outlier: 4.147A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE H 444 " --> pdb=" O LYS H 440 " (cutoff:3.500A) removed outlier: 5.327A 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: 4.269A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ALA Q 46 " --> pdb=" O THR Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 75 Processing helix chain 'Q' and resid 81 through 96 Processing helix chain 'Q' and resid 101 through 121 Processing helix chain 'Q' and resid 125 through 146 Proline residue: Q 144 - end of helix Processing helix chain 'Q' and resid 158 through 167 removed outlier: 4.120A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.160A 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: 4.832A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) removed outlier: 3.840A 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: 3.664A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 434 through 456 removed outlier: 3.813A pdb=" N PHE Q 445 " --> pdb=" O PHE Q 441 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU Q 446 " --> pdb=" O ALA Q 442 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ALA Q 447 " --> pdb=" O GLU Q 443 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ILE Q 448 " --> pdb=" O ALA Q 444 " (cutoff:3.500A) Proline residue: Q 449 - end of helix Processing helix chain 'Q' and resid 460 through 473 Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'Z' and resid 3 through 7 Processing helix chain 'Z' and resid 16 through 37 removed outlier: 3.732A pdb=" N ARG Z 35 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 4.445A 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: 3.555A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLU Z 112 " --> pdb=" O LEU Z 108 " (cutoff:3.500A) Processing helix chain 'Z' and resid 116 through 137 Processing helix chain 'Z' and resid 145 through 159 removed outlier: 4.158A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 162 through 179 removed outlier: 3.634A pdb=" N GLU Z 170 " --> pdb=" O ASP Z 166 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 190 No H-bonds generated for 'chain 'Z' and resid 188 through 190' Processing helix chain 'Z' and resid 201 through 203 No H-bonds generated for 'chain 'Z' and resid 201 through 203' Processing helix chain 'Z' and resid 253 through 262 Processing helix chain 'Z' and resid 265 through 281 removed outlier: 3.572A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 299 through 308 removed outlier: 3.911A pdb=" N GLU Z 308 " --> pdb=" O ALA Z 304 " (cutoff:3.500A) Processing helix chain 'Z' and resid 318 through 327 removed outlier: 4.425A pdb=" N GLU Z 322 " --> pdb=" O ARG Z 318 " (cutoff:3.500A) Processing helix chain 'Z' and resid 341 through 343 No H-bonds generated for 'chain 'Z' and resid 341 through 343' Processing helix chain 'Z' and resid 381 through 403 Processing helix chain 'Z' and resid 413 through 428 Proline residue: Z 427 - end of helix Processing helix chain 'Z' and resid 431 through 455 removed outlier: 4.072A pdb=" N GLN Z 434 " --> pdb=" O GLY Z 431 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE Z 447 " --> pdb=" O LEU Z 444 " (cutoff:3.500A) Proline residue: Z 448 - end of helix Processing helix chain 'Z' and resid 459 through 473 Processing helix chain 'Z' and resid 489 through 492 No H-bonds generated for 'chain 'Z' and resid 489 through 492' Processing helix chain 'Z' and resid 498 through 516 Processing helix chain 'a' and resid 15 through 35 removed outlier: 3.674A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N SER a 34 " --> pdb=" O ASN a 30 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N SER a 35 " --> pdb=" O ILE a 31 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 64 Processing helix chain 'a' and resid 70 through 85 Processing helix chain 'a' and resid 90 through 109 removed outlier: 3.879A pdb=" N VAL a 94 " --> pdb=" O THR a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 114 through 135 Processing helix chain 'a' and resid 144 through 156 Processing helix chain 'a' and resid 163 through 178 removed outlier: 4.284A pdb=" N ASP a 166 " --> pdb=" O ILE a 163 " (cutoff:3.500A) removed outlier: 4.802A 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: 4.389A pdb=" N ASP a 261 " --> pdb=" O GLU a 258 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE a 270 " --> pdb=" O GLU a 267 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA a 280 " --> pdb=" O LYS a 277 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR a 281 " --> pdb=" O ILE a 278 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 302 Processing helix chain 'a' and resid 313 through 323 Processing helix chain 'a' and resid 342 through 344 No H-bonds generated for 'chain 'a' and resid 342 through 344' Processing helix chain 'a' and resid 382 through 404 Processing helix chain 'a' and resid 414 through 429 removed outlier: 4.464A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) Processing helix chain 'a' and resid 434 through 455 removed outlier: 3.728A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 5.180A 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: 3.913A pdb=" N LYS a 481 " --> pdb=" O PRO a 478 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ASN a 482 " --> pdb=" O GLU a 479 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TRP a 485 " --> pdb=" O ASN a 482 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 501 No H-bonds generated for 'chain 'a' and resid 498 through 501' Processing helix chain 'a' and resid 507 through 526 Processing helix chain 'b' and resid 21 through 39 Processing helix chain 'b' and resid 67 through 72 Processing helix chain 'b' and resid 79 through 94 Processing helix chain 'b' and resid 99 through 118 Processing helix chain 'b' and resid 123 through 144 Processing helix chain 'b' and resid 152 through 168 Processing helix chain 'b' and resid 171 through 174 removed outlier: 3.548A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 171 through 174' Processing helix chain 'b' and resid 176 through 190 removed outlier: 3.824A pdb=" N LEU b 190 " --> pdb=" O ALA b 186 " (cutoff:3.500A) Processing helix chain 'b' and resid 209 through 211 No H-bonds generated for 'chain 'b' and resid 209 through 211' Processing helix chain 'b' and resid 261 through 285 removed outlier: 3.959A 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 425 Processing helix chain 'b' and resid 431 through 454 Proline residue: b 447 - end of helix removed outlier: 3.776A pdb=" N ALA b 454 " --> pdb=" O ILE b 450 " (cutoff:3.500A) Processing helix chain 'b' and resid 458 through 471 Processing helix chain 'b' and resid 488 through 491 No H-bonds generated for 'chain 'b' and resid 488 through 491' Processing helix chain 'b' and resid 497 through 515 Processing helix chain 'd' and resid 29 through 49 Processing helix chain 'd' and resid 74 through 80 Processing helix chain 'd' and resid 86 through 102 Processing helix chain 'd' and resid 108 through 125 removed outlier: 3.827A 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: 4.511A 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: 4.123A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.897A 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: 3.784A pdb=" N ILE d 333 " --> pdb=" O ARG d 330 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLU d 334 " --> pdb=" O GLU d 331 " (cutoff:3.500A) removed outlier: 4.110A 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: 3.630A pdb=" N THR d 442 " --> pdb=" O GLU d 438 " (cutoff:3.500A) Processing helix chain 'd' and resid 446 through 466 removed outlier: 4.045A pdb=" N VAL d 460 " --> pdb=" O ASP d 456 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N ILE d 461 " --> pdb=" O ALA d 457 " (cutoff:3.500A) Proline residue: d 462 - end of helix Processing helix chain 'd' and resid 473 through 486 Processing helix chain 'd' and resid 512 through 530 removed outlier: 4.982A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 51 removed outlier: 3.728A pdb=" N LEU e 34 " --> pdb=" O GLY e 30 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N THR e 50 " --> pdb=" O ASN e 46 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N SER e 51 " --> pdb=" O THR e 47 " (cutoff:3.500A) Processing helix chain 'e' and resid 74 through 80 Processing helix chain 'e' and resid 86 through 101 Processing helix chain 'e' and resid 108 through 125 removed outlier: 3.585A pdb=" N GLN e 122 " --> pdb=" O GLU e 118 " (cutoff:3.500A) Processing helix chain 'e' and resid 130 through 150 Processing helix chain 'e' and resid 163 through 173 Processing helix chain 'e' and resid 177 through 195 removed outlier: 3.910A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ARG e 183 " --> pdb=" O SER e 180 " (cutoff:3.500A) Processing helix chain 'e' and resid 206 through 208 No H-bonds generated for 'chain 'e' and resid 206 through 208' Processing helix chain 'e' and resid 219 through 221 No H-bonds generated for 'chain 'e' and resid 219 through 221' Processing helix chain 'e' and resid 271 through 294 Processing helix chain 'e' and resid 308 through 316 Processing helix chain 'e' and resid 327 through 337 Processing helix chain 'e' and resid 345 through 347 No H-bonds generated for 'chain 'e' and resid 345 through 347' Processing helix chain 'e' and resid 350 through 352 No H-bonds generated for 'chain 'e' and resid 350 through 352' Processing helix chain 'e' and resid 392 through 414 Processing helix chain 'e' and resid 424 through 437 Processing helix chain 'e' and resid 442 through 465 removed outlier: 3.929A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL e 457 " --> pdb=" O ASP e 453 " (cutoff:3.500A) removed outlier: 4.821A 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 63 through 69 removed outlier: 3.912A 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: 3.632A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.681A 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 167 removed outlier: 4.225A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 164 through 167' Processing helix chain 'g' and resid 169 through 183 Processing helix chain 'g' and resid 209 through 211 No H-bonds generated for 'chain 'g' and resid 209 through 211' Processing helix chain 'g' and resid 261 through 285 removed outlier: 4.280A pdb=" N PHE g 264 " --> pdb=" O GLU g 261 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN g 284 " --> pdb=" O ASP g 281 " (cutoff:3.500A) Processing helix chain 'g' and resid 298 through 307 removed outlier: 3.804A pdb=" N ALA g 307 " --> pdb=" O TYR g 303 " (cutoff:3.500A) Processing helix chain 'g' and resid 317 through 327 Processing helix chain 'g' and resid 335 through 337 No H-bonds generated for 'chain 'g' and resid 335 through 337' Processing helix chain 'g' and resid 381 through 403 Processing helix chain 'g' and resid 413 through 428 removed outlier: 4.272A pdb=" N ALA g 428 " --> pdb=" O GLU g 424 " (cutoff:3.500A) Processing helix chain 'g' and resid 434 through 455 removed outlier: 3.933A pdb=" N LEU g 444 " --> pdb=" O VAL g 440 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N GLU g 445 " --> pdb=" O ALA g 441 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N VAL g 446 " --> pdb=" O GLN g 442 " (cutoff:3.500A) removed outlier: 5.335A 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: 3.900A 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: 3.661A pdb=" N GLU h 89 " --> pdb=" O GLN h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 96 through 113 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: 5.831A pdb=" N ALA h 173 " --> pdb=" O GLN h 170 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE h 175 " --> pdb=" O LYS h 172 " (cutoff:3.500A) Processing helix chain 'h' and resid 192 through 194 No H-bonds generated for 'chain 'h' and resid 192 through 194' Processing helix chain 'h' and resid 205 through 207 No H-bonds generated for 'chain 'h' and resid 205 through 207' Processing helix chain 'h' and resid 260 through 283 Processing helix chain 'h' and resid 297 through 305 Processing helix chain 'h' and resid 316 through 326 Processing helix chain 'h' and resid 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: 4.148A pdb=" N THR h 426 " --> pdb=" O ASP h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 430 through 453 removed outlier: 4.082A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N GLU h 443 " --> pdb=" O ALA h 439 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE h 444 " --> pdb=" O LYS h 440 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ILE h 445 " --> pdb=" O ALA h 441 " (cutoff:3.500A) Proline residue: h 446 - end of helix Processing helix chain 'h' and resid 457 through 470 Processing helix chain 'h' and resid 496 through 514 Processing helix chain 'q' and resid 11 through 14 No H-bonds generated for 'chain 'q' and resid 11 through 14' Processing helix chain 'q' and resid 25 through 46 removed outlier: 4.607A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ALA q 46 " --> pdb=" O THR q 42 " (cutoff:3.500A) Processing helix chain 'q' and resid 69 through 74 Processing helix chain 'q' and resid 81 through 96 Processing helix chain 'q' and resid 101 through 121 Processing helix chain 'q' and resid 125 through 146 Proline residue: q 144 - end of helix Processing helix chain 'q' and resid 157 through 167 removed outlier: 4.331A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.543A 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: 4.825A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) removed outlier: 3.832A 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: 3.984A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 434 through 456 removed outlier: 3.788A pdb=" N PHE q 445 " --> pdb=" O PHE q 441 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU q 446 " --> pdb=" O ALA q 442 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ALA q 447 " --> pdb=" O GLU q 443 " (cutoff:3.500A) removed outlier: 4.977A 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: 3.732A pdb=" N ARG z 35 " --> pdb=" O ASP z 32 " (cutoff:3.500A) removed outlier: 4.029A 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: 3.554A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N GLU z 112 " --> pdb=" O LEU z 108 " (cutoff:3.500A) Processing helix chain 'z' and resid 116 through 137 Processing helix chain 'z' and resid 145 through 159 removed outlier: 3.982A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 162 through 179 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: 4.374A pdb=" N ARG z 264 " --> pdb=" O VAL z 260 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LYS z 265 " --> pdb=" O LYS z 261 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N PHE z 266 " --> pdb=" O ALA z 262 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE z 267 " --> pdb=" O GLU z 263 " (cutoff:3.500A) Processing helix chain 'z' and resid 299 through 308 removed outlier: 3.762A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 318 through 328 removed outlier: 4.352A pdb=" N GLU z 322 " --> pdb=" O ARG z 318 " (cutoff:3.500A) Processing helix chain 'z' and resid 341 through 343 No H-bonds generated for 'chain 'z' and resid 341 through 343' Processing helix chain 'z' and resid 381 through 403 Processing helix chain 'z' and resid 413 through 428 Proline residue: z 427 - end of helix Processing helix chain 'z' and resid 431 through 455 removed outlier: 4.187A pdb=" N GLN z 434 " --> pdb=" O GLY z 431 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE z 447 " --> pdb=" O LEU z 444 " (cutoff:3.500A) Proline residue: z 448 - end of helix Processing helix chain 'z' and resid 459 through 473 Processing helix chain 'z' and resid 489 through 492 No H-bonds generated for 'chain 'z' and resid 489 through 492' Processing helix chain 'z' and resid 498 through 516 Processing helix chain 'P' and resid 57 through 61 removed outlier: 3.631A pdb=" N GLY P 61 " --> pdb=" O THR P 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 57 through 61' Processing helix chain 'P' and resid 63 through 87 removed outlier: 3.725A pdb=" N LEU P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLU P 79 " --> pdb=" O GLU P 75 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU P 85 " --> pdb=" O CYS P 81 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG P 86 " --> pdb=" O ARG P 82 " (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: 4.028A pdb=" N MET P 145 " --> pdb=" O ARG P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 174 Processing helix chain 'P' and resid 196 through 208 Processing helix chain 'P' and resid 219 through 222 No H-bonds generated for 'chain 'P' and resid 219 through 222' Processing helix chain 'P' and resid 226 through 231 Processing helix chain 'P' and resid 252 through 255 No H-bonds generated for 'chain 'P' and resid 252 through 255' Processing helix chain 'P' and resid 261 through 271 removed outlier: 4.293A pdb=" N PHE P 271 " --> pdb=" O PHE P 267 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 9 through 13 Processing sheet with id= B, first strand: chain 'A' and resid 43 through 46 Processing sheet with id= C, first strand: chain 'A' and resid 137 through 139 Processing sheet with id= D, first strand: chain 'A' and resid 180 through 182 removed outlier: 3.587A pdb=" N TYR A 181 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 196 through 199 Processing sheet with id= F, first strand: chain 'A' and resid 213 through 216 Processing sheet with id= G, first strand: chain 'A' and resid 346 through 348 removed outlier: 6.560A pdb=" N VAL A 285 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU A 237 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N LEU A 287 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N MET A 306 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR A 288 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N VAL A 308 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 486 through 489 Processing sheet with id= I, first strand: chain 'B' and resid 17 through 19 Processing sheet with id= J, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.399A pdb=" N CYS B 371 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE B 202 " --> pdb=" O CYS B 371 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ILE B 373 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N LYS B 204 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N LEU B 375 " --> pdb=" O LYS B 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 218 through 220 Processing sheet with id= L, first strand: chain 'B' and resid 344 through 346 removed outlier: 6.831A pdb=" N CYS B 289 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ALA B 240 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ILE B 291 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N MET B 310 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N ASN B 292 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE B 312 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 406 through 408 Processing sheet with id= N, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= O, first strand: chain 'D' and resid 59 through 62 Processing sheet with id= P, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.800A pdb=" N VAL D 386 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N VAL D 211 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ILE D 388 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LYS D 213 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL D 390 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 227 through 229 Processing sheet with id= R, first strand: chain 'D' and resid 357 through 359 removed outlier: 6.854A pdb=" N VAL D 297 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.782A pdb=" N ILE D 249 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU D 299 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N MET D 323 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE D 300 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE D 325 " --> pdb=" O ILE D 300 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 421 through 423 Processing sheet with id= T, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.626A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 59 through 62 Processing sheet with id= V, first strand: chain 'E' and resid 209 through 215 removed outlier: 7.226A pdb=" N VAL E 383 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N GLU E 212 " --> pdb=" O VAL E 383 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE E 385 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LYS E 214 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ILE E 387 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 228 through 230 Processing sheet with id= X, first strand: chain 'E' and resid 354 through 356 removed outlier: 6.904A pdb=" N LEU E 299 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N LEU E 251 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ILE E 301 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N CYS E 302 " --> pdb=" O PRO E 320 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N VAL E 322 " --> pdb=" O CYS E 302 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 418 through 420 Processing sheet with id= Z, first strand: chain 'G' and resid 48 through 51 Processing sheet with id= AA, first strand: chain 'G' and resid 185 through 187 Processing sheet with id= AB, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.602A pdb=" N CYS G 372 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N GLU G 202 " --> pdb=" O CYS G 372 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE G 374 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N ILE G 204 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU G 376 " --> pdb=" O ILE G 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'G' and resid 238 through 241 removed outlier: 6.466A pdb=" N VAL G 289 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LEU G 241 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE G 291 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N THR G 310 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N THR G 292 " --> pdb=" O THR G 310 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE G 312 " --> pdb=" O THR G 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'G' and resid 351 through 355 Processing sheet with id= AE, first strand: chain 'G' and resid 407 through 409 Processing sheet with id= AF, first strand: chain 'G' and resid 478 through 480 Processing sheet with id= AG, first strand: chain 'H' and resid 14 through 17 Processing sheet with id= AH, first strand: chain 'H' and resid 47 through 50 Processing sheet with id= AI, first strand: chain 'H' and resid 195 through 201 removed outlier: 6.332A pdb=" N CYS H 370 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N LYS H 198 " --> pdb=" O CYS H 370 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N PHE H 372 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL H 200 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LEU H 374 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR H 371 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 214 through 217 Processing sheet with id= AK, first strand: chain 'H' and resid 237 through 240 removed outlier: 6.999A pdb=" N VAL H 288 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LEU H 240 " --> pdb=" O VAL H 288 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N LEU H 290 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N PHE H 309 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N SER H 291 " --> pdb=" O PHE H 309 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA H 311 " --> pdb=" O SER H 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'H' and resid 405 through 407 Processing sheet with id= AM, first strand: chain 'H' and resid 475 through 478 Processing sheet with id= AN, first strand: chain 'Q' and resid 20 through 23 Processing sheet with id= AO, first strand: chain 'Q' and resid 54 through 57 Processing sheet with id= AP, first strand: chain 'Q' and resid 202 through 208 removed outlier: 6.609A pdb=" N SER Q 373 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N CYS Q 205 " --> pdb=" O SER Q 373 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE Q 375 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N ILE Q 207 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N LEU Q 377 " --> pdb=" O ILE Q 207 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'Q' and resid 220 through 223 Processing sheet with id= AR, first strand: chain 'Q' and resid 240 through 242 removed outlier: 6.193A pdb=" N MET Q 311 " --> pdb=" O VAL Q 291 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N THR Q 293 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N VAL Q 313 " --> pdb=" O THR Q 293 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'Q' and resid 498 through 500 removed outlier: 3.907A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N VAL Q 147 " --> pdb=" O PRO Q 410 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id= AU, first strand: chain 'Z' and resid 12 through 15 removed outlier: 3.630A pdb=" N GLU Z 12 " --> pdb=" O ARG Z 523 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'Z' and resid 45 through 48 Processing sheet with id= AW, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.899A pdb=" N VAL Z 372 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N MET Z 194 " --> pdb=" O VAL Z 372 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LEU Z 374 " --> pdb=" O MET Z 194 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N MET Z 196 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ILE Z 376 " --> pdb=" O MET Z 196 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id= AY, first strand: chain 'Z' and resid 345 through 347 Processing sheet with id= AZ, first strand: chain 'Z' and resid 477 through 479 removed outlier: 3.534A pdb=" N MET Z 487 " --> pdb=" O GLY Z 478 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'a' and resid 9 through 13 Processing sheet with id= BB, first strand: chain 'a' and resid 43 through 46 Processing sheet with id= BC, first strand: chain 'a' and resid 137 through 139 Processing sheet with id= BD, first strand: chain 'a' and resid 180 through 183 removed outlier: 3.858A pdb=" N GLN a 187 " --> pdb=" O ASP a 183 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'a' and resid 196 through 201 removed outlier: 3.595A pdb=" N GLY a 379 " --> pdb=" O ALA a 200 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'a' and resid 213 through 216 Processing sheet with id= BG, first strand: chain 'a' and resid 346 through 348 removed outlier: 6.601A pdb=" N VAL a 285 " --> pdb=" O ALA a 235 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N LEU a 237 " --> pdb=" O VAL a 285 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N LEU a 287 " --> pdb=" O LEU a 237 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N MET a 306 " --> pdb=" O ILE a 286 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N THR a 288 " --> pdb=" O MET a 306 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL a 308 " --> pdb=" O THR a 288 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'a' and resid 486 through 489 removed outlier: 3.532A pdb=" N ARG a 496 " --> pdb=" O GLY a 487 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'b' and resid 17 through 19 Processing sheet with id= BJ, first strand: chain 'b' and resid 50 through 53 Processing sheet with id= BK, first strand: chain 'b' and resid 199 through 205 removed outlier: 6.286A pdb=" N CYS b 371 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ILE b 202 " --> pdb=" O CYS b 371 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE b 373 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LYS b 204 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N LEU b 375 " --> pdb=" O LYS b 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= BK Processing sheet with id= BL, first strand: chain 'b' and resid 218 through 220 Processing sheet with id= BM, first strand: chain 'b' and resid 344 through 346 removed outlier: 3.586A pdb=" N CYS b 346 " --> pdb=" O ALA b 235 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N CYS b 289 " --> pdb=" O LEU b 238 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ALA b 240 " --> pdb=" O CYS b 289 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE b 291 " --> pdb=" O ALA b 240 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N MET b 310 " --> pdb=" O PHE b 290 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ASN b 292 " --> pdb=" O MET b 310 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE b 312 " --> pdb=" O ASN b 292 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'b' and resid 406 through 408 Processing sheet with id= BO, first strand: chain 'b' and resid 476 through 479 Processing sheet with id= BP, first strand: chain 'd' and resid 59 through 62 Processing sheet with id= BQ, first strand: chain 'd' and resid 208 through 214 removed outlier: 6.691A pdb=" N VAL d 386 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N VAL d 211 " --> pdb=" O VAL d 386 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE d 388 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LYS d 213 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL d 390 " --> pdb=" O LYS d 213 " (cutoff:3.500A) No H-bonds generated for sheet with id= BQ Processing sheet with id= BR, first strand: chain 'd' and resid 227 through 229 Processing sheet with id= BS, first strand: chain 'd' and resid 246 through 249 removed outlier: 6.530A pdb=" N VAL d 297 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ILE d 249 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU d 299 " --> pdb=" O ILE d 249 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N MET d 323 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 7.664A pdb=" N ILE d 300 " --> pdb=" O MET d 323 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE d 325 " --> pdb=" O ILE d 300 " (cutoff:3.500A) No H-bonds generated for sheet with id= BS Processing sheet with id= BT, first strand: chain 'd' and resid 421 through 423 Processing sheet with id= BU, first strand: chain 'd' and resid 491 through 494 Processing sheet with id= BV, first strand: chain 'e' and resid 26 through 29 Processing sheet with id= BW, first strand: chain 'e' and resid 59 through 62 Processing sheet with id= BX, first strand: chain 'e' and resid 209 through 215 removed outlier: 6.820A pdb=" N VAL e 383 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N GLU e 212 " --> pdb=" O VAL e 383 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ILE e 385 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N LYS e 214 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ILE e 387 " --> pdb=" O LYS e 214 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'e' and resid 228 through 230 Processing sheet with id= BZ, first strand: chain 'e' and resid 354 through 356 removed outlier: 7.048A pdb=" N LEU e 299 " --> pdb=" O ALA e 249 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU e 251 " --> pdb=" O LEU e 299 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE e 301 " --> pdb=" O LEU e 251 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N CYS e 302 " --> pdb=" O PRO e 320 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL e 322 " --> pdb=" O CYS e 302 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'e' and resid 418 through 420 Processing sheet with id= CB, first strand: chain 'g' and resid 15 through 18 Processing sheet with id= CC, first strand: chain 'g' and resid 48 through 51 Processing sheet with id= CD, first strand: chain 'g' and resid 185 through 187 Processing sheet with id= CE, first strand: chain 'g' and resid 200 through 205 removed outlier: 3.838A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'g' and resid 218 through 220 Processing sheet with id= CG, first strand: chain 'g' and resid 238 through 241 removed outlier: 6.408A pdb=" N VAL g 289 " --> pdb=" O VAL g 239 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N LEU g 241 " --> pdb=" O VAL g 289 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE g 291 " --> pdb=" O LEU g 241 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N THR g 310 " --> pdb=" O VAL g 290 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N THR g 292 " --> pdb=" O THR g 310 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE g 312 " --> pdb=" O THR g 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= CG Processing sheet with id= CH, first strand: chain 'g' and resid 407 through 409 Processing sheet with id= CI, first strand: chain 'g' and resid 478 through 480 Processing sheet with id= CJ, first strand: chain 'h' and resid 14 through 17 Processing sheet with id= CK, first strand: chain 'h' and resid 47 through 50 Processing sheet with id= CL, first strand: chain 'h' and resid 195 through 201 removed outlier: 6.701A pdb=" N CYS h 370 " --> pdb=" O GLY h 196 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N LYS h 198 " --> pdb=" O CYS h 370 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N PHE h 372 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N VAL h 200 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N LEU h 374 " --> pdb=" O VAL h 200 " (cutoff:3.500A) Processing sheet with id= CM, first strand: chain 'h' and resid 214 through 217 Processing sheet with id= CN, first strand: chain 'h' and resid 342 through 344 removed outlier: 6.768A pdb=" N VAL h 288 " --> pdb=" O ALA h 238 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU h 240 " --> pdb=" O VAL h 288 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU h 290 " --> pdb=" O LEU h 240 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N PHE h 309 " --> pdb=" O VAL h 289 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N SER h 291 " --> pdb=" O PHE h 309 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA h 311 " --> pdb=" O SER h 291 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'h' and resid 405 through 407 Processing sheet with id= CP, first strand: chain 'h' and resid 475 through 478 Processing sheet with id= CQ, first strand: chain 'q' and resid 20 through 23 Processing sheet with id= CR, first strand: chain 'q' and resid 54 through 57 Processing sheet with id= CS, first strand: chain 'q' and resid 202 through 208 removed outlier: 6.392A pdb=" N SER q 373 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N CYS q 205 " --> pdb=" O SER q 373 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N ILE q 375 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE q 207 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LEU q 377 " --> pdb=" O ILE q 207 " (cutoff:3.500A) Processing sheet with id= CT, first strand: chain 'q' and resid 220 through 223 Processing sheet with id= CU, first strand: chain 'q' and resid 240 through 242 removed outlier: 6.092A pdb=" N MET q 311 " --> pdb=" O VAL q 291 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N THR q 293 " --> pdb=" O MET q 311 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL q 313 " --> pdb=" O THR q 293 " (cutoff:3.500A) Processing sheet with id= CV, first strand: chain 'q' and resid 498 through 500 removed outlier: 3.846A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N VAL q 147 " --> pdb=" O PRO q 410 " (cutoff:3.500A) Processing sheet with id= CW, first strand: chain 'q' and resid 478 through 480 Processing sheet with id= CX, first strand: chain 'z' and resid 12 through 15 removed outlier: 3.537A pdb=" N GLU z 12 " --> pdb=" O ARG z 523 " (cutoff:3.500A) Processing sheet with id= CY, first strand: chain 'z' and resid 45 through 48 Processing sheet with id= CZ, first strand: chain 'z' and resid 191 through 196 removed outlier: 6.855A pdb=" N VAL z 372 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N MET z 194 " --> pdb=" O VAL z 372 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU z 374 " --> pdb=" O MET z 194 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N MET z 196 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ILE z 376 " --> pdb=" O MET z 196 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'z' and resid 210 through 212 Processing sheet with id= DB, first strand: chain 'z' and resid 345 through 347 Processing sheet with id= DC, first strand: chain 'z' and resid 477 through 479 Processing sheet with id= DD, first strand: chain 'P' and resid 162 through 164 removed outlier: 4.526A pdb=" N LYS P 218 " --> pdb=" O ILE P 164 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA P 235 " --> pdb=" O ILE P 187 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY P 246 " --> pdb=" O ILE P 238 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N LYS P 240 " --> pdb=" O LEU P 244 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N LEU P 244 " --> pdb=" O LYS P 240 " (cutoff:3.500A) 3436 hydrogen bonds defined for protein. 9237 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 28.79 Time building geometry restraints manager: 22.65 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: 22496 1.34 - 1.46: 11757 1.46 - 1.58: 32563 1.58 - 1.70: 49 1.70 - 1.81: 731 Bond restraints: 67596 Sorted by residual: bond pdb=" F2 AF3 z 603 " pdb="AL AF3 z 603 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.46e+01 bond pdb=" F2 AF3 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 6.44e+01 bond pdb=" F2 AF3 g 603 " pdb="AL AF3 g 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.34e+01 bond pdb=" F2 AF3 G 603 " pdb="AL AF3 G 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.33e+01 bond pdb=" F2 AF3 q 603 " pdb="AL AF3 q 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.33e+01 ... (remaining 67591 not shown) Histogram of bond angle deviations from ideal: 97.18 - 105.00: 979 105.00 - 112.81: 38597 112.81 - 120.63: 29309 120.63 - 128.45: 22080 128.45 - 136.27: 298 Bond angle restraints: 91263 Sorted by residual: angle pdb=" CA PRO G 6 " pdb=" N PRO G 6 " pdb=" CD PRO G 6 " ideal model delta sigma weight residual 112.00 100.17 11.83 1.40e+00 5.10e-01 7.14e+01 angle pdb=" N PRO G 6 " pdb=" CD PRO G 6 " pdb=" CG PRO G 6 " ideal model delta sigma weight residual 103.20 97.18 6.02 1.50e+00 4.44e-01 1.61e+01 angle pdb=" C ILE A 184 " pdb=" N ARG A 185 " pdb=" CA ARG A 185 " ideal model delta sigma weight residual 121.54 128.78 -7.24 1.91e+00 2.74e-01 1.44e+01 angle pdb=" N GLY Q 209 " pdb=" CA GLY Q 209 " pdb=" C GLY Q 209 " ideal model delta sigma weight residual 113.18 121.13 -7.95 2.37e+00 1.78e-01 1.12e+01 angle pdb=" C ALA q 151 " pdb=" N LYS q 152 " pdb=" CA LYS q 152 " ideal model delta sigma weight residual 121.54 127.63 -6.09 1.91e+00 2.74e-01 1.02e+01 ... (remaining 91258 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.52: 41068 35.52 - 71.04: 665 71.04 - 106.56: 60 106.56 - 142.08: 12 142.08 - 177.60: 6 Dihedral angle restraints: 41811 sinusoidal: 16850 harmonic: 24961 Sorted by residual: dihedral pdb=" O2A ADP q 601 " pdb=" O3A ADP q 601 " pdb=" PA ADP q 601 " pdb=" PB ADP q 601 " ideal model delta sinusoidal sigma weight residual -60.00 117.60 -177.60 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP z 601 " pdb=" O3A ADP z 601 " pdb=" PA ADP z 601 " pdb=" PB ADP z 601 " ideal model delta sinusoidal sigma weight residual -60.00 110.53 -170.52 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O2A ADP g 601 " pdb=" O3A ADP g 601 " pdb=" PA ADP g 601 " pdb=" PB ADP g 601 " ideal model delta sinusoidal sigma weight residual 300.00 135.09 164.91 1 2.00e+01 2.50e-03 4.72e+01 ... (remaining 41808 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 8582 0.046 - 0.093: 1661 0.093 - 0.139: 617 0.139 - 0.186: 6 0.186 - 0.232: 1 Chirality restraints: 10867 Sorted by residual: chirality pdb=" CA PRO G 6 " pdb=" N PRO G 6 " pdb=" C PRO G 6 " pdb=" CB PRO G 6 " both_signs ideal model delta sigma weight residual False 2.72 2.49 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE g 83 " pdb=" CA ILE g 83 " pdb=" CG1 ILE g 83 " pdb=" CG2 ILE g 83 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.42e-01 chirality pdb=" CB ILE G 363 " pdb=" CA ILE G 363 " pdb=" CG1 ILE G 363 " pdb=" CG2 ILE G 363 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.11e-01 ... (remaining 10864 not shown) Planarity restraints: 11652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN a 477 " 0.065 5.00e-02 4.00e+02 9.82e-02 1.54e+01 pdb=" N PRO a 478 " -0.170 5.00e-02 4.00e+02 pdb=" CA PRO a 478 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO a 478 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG G 5 " 0.057 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO G 6 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO G 6 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO G 6 " 0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG e 14 " -0.034 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO e 15 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO e 15 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO e 15 " -0.029 5.00e-02 4.00e+02 ... (remaining 11649 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 577 2.53 - 3.13: 51453 3.13 - 3.72: 105525 3.72 - 4.31: 147725 4.31 - 4.90: 252901 Nonbonded interactions: 558181 Sorted by model distance: nonbonded pdb=" OD1 ASP b 97 " pdb="MG MG b 602 " model vdw 1.943 2.170 nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.949 2.120 nonbonded pdb="MG MG e 602 " pdb=" F1 AF3 e 603 " model vdw 1.950 2.120 nonbonded pdb="MG MG H 602 " pdb=" F2 AF3 H 603 " model vdw 1.957 2.120 nonbonded pdb=" O2A ADP Z 601 " pdb="MG MG Z 602 " model vdw 1.966 2.170 ... (remaining 558176 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 535 or resid 601 through 603)) selection = chain 'a' } ncs_group { reference = (chain 'B' and (resid 2 through 526 or resid 601 through 603)) selection = chain 'b' } ncs_group { reference = (chain 'D' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 538 or resid 601 through 603)) selection = chain 'd' } ncs_group { reference = (chain 'E' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) selection = (chain 'e' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) } ncs_group { reference = (chain 'G' and (resid 5 through 528 or resid 601 through 603)) selection = (chain 'g' and (resid 5 through 528 or resid 601 through 603)) } ncs_group { reference = (chain 'H' and (resid 1 through 525 or resid 601 through 603)) selection = chain 'h' } ncs_group { reference = (chain 'Q' and (resid 2 through 534 or resid 601 through 603)) selection = chain 'q' } ncs_group { reference = chain 'Z' selection = (chain 'z' and (resid 2 through 526 or resid 601 through 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 8.580 Check model and map are aligned: 0.740 Set scattering table: 0.450 Process input model: 143.210 Find NCS groups from input model: 6.530 Set up NCS constraints: 0.640 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:11.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 172.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.161 67596 Z= 0.290 Angle : 0.537 11.832 91263 Z= 0.264 Chirality : 0.041 0.232 10867 Planarity : 0.003 0.098 11652 Dihedral : 14.663 177.595 25645 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: 1.72 (0.09), residues: 8639 helix: 2.43 (0.08), residues: 4433 sheet: 0.26 (0.16), residues: 1116 loop : -0.44 (0.11), residues: 3090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP q 319 HIS 0.006 0.001 HIS a 201 PHE 0.029 0.001 PHE e 386 TYR 0.015 0.001 TYR G 437 ARG 0.014 0.000 ARG h 53 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 612 time to evaluate : 5.952 Fit side-chains outliers start: 0 outliers final: 1 residues processed: 612 average time/residue: 1.4465 time to fit residues: 1167.8993 Evaluate side-chains 489 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 488 time to evaluate : 5.926 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 1.9168 time to fit residues: 10.2163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 726 optimal weight: 8.9990 chunk 651 optimal weight: 9.9990 chunk 361 optimal weight: 2.9990 chunk 222 optimal weight: 10.0000 chunk 439 optimal weight: 10.0000 chunk 348 optimal weight: 3.9990 chunk 674 optimal weight: 2.9990 chunk 260 optimal weight: 6.9990 chunk 409 optimal weight: 9.9990 chunk 501 optimal weight: 7.9990 chunk 780 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 288 ASN B 380 GLN ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 352 GLN Z 386 GLN ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 534 HIS b 361 HIS ** d 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN ** g 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 182 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 67596 Z= 0.428 Angle : 0.626 11.085 91263 Z= 0.311 Chirality : 0.044 0.167 10867 Planarity : 0.004 0.072 11652 Dihedral : 7.684 177.865 9386 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.06 % Allowed : 7.27 % Favored : 91.67 % 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: 1.26 (0.09), residues: 8639 helix: 2.03 (0.08), residues: 4441 sheet: 0.02 (0.16), residues: 1130 loop : -0.61 (0.11), residues: 3068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP e 304 HIS 0.010 0.001 HIS a 201 PHE 0.029 0.002 PHE e 386 TYR 0.019 0.002 TYR z 351 ARG 0.006 0.000 ARG h 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 498 time to evaluate : 5.904 Fit side-chains outliers start: 77 outliers final: 31 residues processed: 530 average time/residue: 1.5234 time to fit residues: 1065.2364 Evaluate side-chains 503 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 472 time to evaluate : 5.821 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 18 residues processed: 14 average time/residue: 0.8771 time to fit residues: 26.5827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 434 optimal weight: 0.9990 chunk 242 optimal weight: 8.9990 chunk 649 optimal weight: 6.9990 chunk 531 optimal weight: 0.9990 chunk 215 optimal weight: 0.8980 chunk 782 optimal weight: 0.0060 chunk 845 optimal weight: 20.0000 chunk 696 optimal weight: 0.9980 chunk 775 optimal weight: 0.8980 chunk 266 optimal weight: 0.8980 chunk 627 optimal weight: 1.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 4 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN ** Z 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 534 HIS ** d 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN g 390 ASN ** z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 386 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.0789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 67596 Z= 0.136 Angle : 0.513 8.190 91263 Z= 0.252 Chirality : 0.040 0.152 10867 Planarity : 0.003 0.059 11652 Dihedral : 7.350 177.352 9386 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.99 % Allowed : 8.90 % Favored : 90.11 % 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: 1.41 (0.09), residues: 8639 helix: 2.13 (0.08), residues: 4435 sheet: 0.10 (0.16), residues: 1111 loop : -0.48 (0.11), residues: 3093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 168 HIS 0.005 0.001 HIS G 4 PHE 0.015 0.001 PHE e 386 TYR 0.021 0.001 TYR z 351 ARG 0.005 0.000 ARG h 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 535 time to evaluate : 6.047 Fit side-chains outliers start: 72 outliers final: 27 residues processed: 569 average time/residue: 1.4693 time to fit residues: 1111.8309 Evaluate side-chains 518 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 491 time to evaluate : 5.842 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 19 residues processed: 9 average time/residue: 0.8327 time to fit residues: 19.5112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 773 optimal weight: 8.9990 chunk 588 optimal weight: 0.9990 chunk 406 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 373 optimal weight: 9.9990 chunk 525 optimal weight: 9.9990 chunk 785 optimal weight: 8.9990 chunk 831 optimal weight: 1.9990 chunk 410 optimal weight: 0.0270 chunk 744 optimal weight: 6.9990 chunk 224 optimal weight: 2.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 4 HIS G 61 ASN ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 534 HIS ** d 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 GLN ** g 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 67596 Z= 0.248 Angle : 0.537 9.669 91263 Z= 0.263 Chirality : 0.041 0.152 10867 Planarity : 0.003 0.054 11652 Dihedral : 7.260 177.092 9386 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.19 % Allowed : 10.29 % Favored : 88.52 % 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: 1.38 (0.09), residues: 8639 helix: 2.10 (0.08), residues: 4442 sheet: 0.07 (0.16), residues: 1133 loop : -0.50 (0.11), residues: 3064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.006 0.001 HIS a 201 PHE 0.018 0.001 PHE e 386 TYR 0.021 0.001 TYR z 351 ARG 0.009 0.000 ARG H 524 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 507 time to evaluate : 6.090 Fit side-chains outliers start: 86 outliers final: 38 residues processed: 553 average time/residue: 1.4980 time to fit residues: 1100.6803 Evaluate side-chains 521 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 483 time to evaluate : 5.891 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 26 residues processed: 13 average time/residue: 0.7780 time to fit residues: 24.1274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 692 optimal weight: 5.9990 chunk 471 optimal weight: 8.9990 chunk 12 optimal weight: 2.9990 chunk 618 optimal weight: 9.9990 chunk 342 optimal weight: 4.9990 chunk 709 optimal weight: 4.9990 chunk 574 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 424 optimal weight: 2.9990 chunk 746 optimal weight: 0.9990 chunk 209 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 534 HIS ** d 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 390 ASN ** h 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 67596 Z= 0.258 Angle : 0.542 9.803 91263 Z= 0.264 Chirality : 0.041 0.166 10867 Planarity : 0.003 0.054 11652 Dihedral : 7.193 173.827 9386 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.22 % Allowed : 11.41 % Favored : 87.37 % 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: 8639 helix: 2.07 (0.08), residues: 4443 sheet: 0.07 (0.16), residues: 1131 loop : -0.51 (0.11), residues: 3065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 435 HIS 0.006 0.001 HIS a 201 PHE 0.017 0.001 PHE P 267 TYR 0.021 0.001 TYR z 351 ARG 0.010 0.000 ARG e 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 504 time to evaluate : 5.983 Fit side-chains outliers start: 88 outliers final: 47 residues processed: 555 average time/residue: 1.5465 time to fit residues: 1141.3800 Evaluate side-chains 527 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 480 time to evaluate : 5.853 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 34 residues processed: 14 average time/residue: 0.8324 time to fit residues: 26.3946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 279 optimal weight: 6.9990 chunk 748 optimal weight: 0.9990 chunk 164 optimal weight: 10.0000 chunk 488 optimal weight: 9.9990 chunk 205 optimal weight: 6.9990 chunk 832 optimal weight: 6.9990 chunk 690 optimal weight: 4.9990 chunk 385 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 275 optimal weight: 7.9990 chunk 436 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 GLN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 534 HIS ** d 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 390 ASN ** h 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 80 GLN ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 67596 Z= 0.336 Angle : 0.575 10.198 91263 Z= 0.282 Chirality : 0.043 0.181 10867 Planarity : 0.004 0.053 11652 Dihedral : 7.164 168.233 9386 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.20 % Allowed : 12.37 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.09), residues: 8639 helix: 1.99 (0.08), residues: 4440 sheet: 0.02 (0.16), residues: 1133 loop : -0.57 (0.11), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.008 0.001 HIS a 201 PHE 0.019 0.001 PHE P 267 TYR 0.023 0.001 TYR z 351 ARG 0.011 0.000 ARG h 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 489 time to evaluate : 5.872 Fit side-chains outliers start: 87 outliers final: 51 residues processed: 546 average time/residue: 1.4846 time to fit residues: 1081.2004 Evaluate side-chains 518 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 467 time to evaluate : 5.849 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 40 residues processed: 11 average time/residue: 0.7600 time to fit residues: 21.4203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 802 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 474 optimal weight: 9.9990 chunk 607 optimal weight: 10.0000 chunk 470 optimal weight: 0.9990 chunk 700 optimal weight: 6.9990 chunk 464 optimal weight: 1.9990 chunk 828 optimal weight: 3.9990 chunk 518 optimal weight: 10.0000 chunk 505 optimal weight: 0.7980 chunk 382 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 53 ASN a 534 HIS ** d 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 80 GLN ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 67596 Z= 0.229 Angle : 0.550 11.851 91263 Z= 0.268 Chirality : 0.041 0.168 10867 Planarity : 0.003 0.055 11652 Dihedral : 6.984 157.996 9386 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.12 % Allowed : 13.06 % Favored : 85.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.09), residues: 8639 helix: 2.03 (0.08), residues: 4434 sheet: 0.06 (0.16), residues: 1129 loop : -0.55 (0.11), residues: 3076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.006 0.001 HIS a 201 PHE 0.028 0.001 PHE P 267 TYR 0.023 0.001 TYR z 351 ARG 0.010 0.000 ARG h 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 494 time to evaluate : 5.956 Fit side-chains outliers start: 81 outliers final: 56 residues processed: 543 average time/residue: 1.5018 time to fit residues: 1080.3964 Evaluate side-chains 534 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 478 time to evaluate : 5.867 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 44 residues processed: 14 average time/residue: 0.7302 time to fit residues: 24.6846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 512 optimal weight: 5.9990 chunk 331 optimal weight: 10.0000 chunk 495 optimal weight: 1.9990 chunk 249 optimal weight: 4.9990 chunk 162 optimal weight: 9.9990 chunk 160 optimal weight: 6.9990 chunk 526 optimal weight: 3.9990 chunk 564 optimal weight: 3.9990 chunk 409 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 651 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN a 20 GLN a 534 HIS ** d 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 80 GLN ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 67596 Z= 0.335 Angle : 0.585 11.006 91263 Z= 0.286 Chirality : 0.043 0.199 10867 Planarity : 0.004 0.052 11652 Dihedral : 6.948 153.701 9386 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.12 % Allowed : 13.62 % Favored : 85.26 % 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: 1.19 (0.09), residues: 8639 helix: 1.95 (0.08), residues: 4438 sheet: -0.00 (0.16), residues: 1119 loop : -0.60 (0.11), residues: 3082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 168 HIS 0.008 0.001 HIS a 201 PHE 0.032 0.001 PHE P 267 TYR 0.024 0.001 TYR z 351 ARG 0.011 0.000 ARG h 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 478 time to evaluate : 6.006 Fit side-chains outliers start: 81 outliers final: 60 residues processed: 531 average time/residue: 1.5042 time to fit residues: 1066.4234 Evaluate side-chains 528 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 468 time to evaluate : 5.845 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 47 residues processed: 14 average time/residue: 0.7513 time to fit residues: 25.0953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 754 optimal weight: 5.9990 chunk 794 optimal weight: 6.9990 chunk 724 optimal weight: 3.9990 chunk 772 optimal weight: 8.9990 chunk 793 optimal weight: 0.9990 chunk 464 optimal weight: 0.7980 chunk 336 optimal weight: 9.9990 chunk 606 optimal weight: 7.9990 chunk 237 optimal weight: 1.9990 chunk 698 optimal weight: 8.9990 chunk 730 optimal weight: 9.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 534 HIS ** d 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 67596 Z= 0.258 Angle : 0.567 11.858 91263 Z= 0.275 Chirality : 0.042 0.160 10867 Planarity : 0.003 0.052 11652 Dihedral : 6.831 147.259 9386 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.88 % Allowed : 14.15 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.09), residues: 8639 helix: 2.00 (0.08), residues: 4435 sheet: 0.02 (0.16), residues: 1122 loop : -0.57 (0.11), residues: 3082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.006 0.001 HIS a 201 PHE 0.015 0.001 PHE P 259 TYR 0.024 0.001 TYR z 351 ARG 0.012 0.000 ARG h 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 486 time to evaluate : 6.037 Fit side-chains outliers start: 64 outliers final: 52 residues processed: 534 average time/residue: 1.5392 time to fit residues: 1097.5722 Evaluate side-chains 522 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 470 time to evaluate : 5.857 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 46 residues processed: 7 average time/residue: 0.7080 time to fit residues: 16.1314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 769 optimal weight: 10.0000 chunk 507 optimal weight: 1.9990 chunk 816 optimal weight: 7.9990 chunk 498 optimal weight: 7.9990 chunk 387 optimal weight: 0.9990 chunk 567 optimal weight: 1.9990 chunk 856 optimal weight: 9.9990 chunk 788 optimal weight: 7.9990 chunk 682 optimal weight: 0.1980 chunk 70 optimal weight: 7.9990 chunk 526 optimal weight: 3.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 217 ASN a 534 HIS ** d 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 12 GLN ** q 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 67596 Z= 0.197 Angle : 0.550 13.121 91263 Z= 0.266 Chirality : 0.041 0.165 10867 Planarity : 0.003 0.054 11652 Dihedral : 6.630 139.831 9386 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.82 % Allowed : 14.26 % Favored : 84.93 % 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: 1.32 (0.09), residues: 8639 helix: 2.05 (0.08), residues: 4435 sheet: 0.05 (0.16), residues: 1128 loop : -0.52 (0.11), residues: 3076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 168 HIS 0.005 0.001 HIS a 201 PHE 0.014 0.001 PHE P 259 TYR 0.031 0.001 TYR D 24 ARG 0.014 0.000 ARG h 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17278 Ramachandran restraints generated. 8639 Oldfield, 0 Emsley, 8639 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 503 time to evaluate : 6.108 Fit side-chains outliers start: 59 outliers final: 50 residues processed: 553 average time/residue: 1.4905 time to fit residues: 1104.5080 Evaluate side-chains 531 residues out of total 7238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 481 time to evaluate : 5.867 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 44 residues processed: 7 average time/residue: 0.9962 time to fit residues: 18.2336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 860 random chunks: chunk 418 optimal weight: 0.9990 chunk 541 optimal weight: 5.9990 chunk 726 optimal weight: 10.0000 chunk 209 optimal weight: 0.7980 chunk 629 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 683 optimal weight: 8.9990 chunk 285 optimal weight: 7.9990 chunk 701 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 381 GLN ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 25 ASN ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 534 HIS ** d 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.078661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.065828 restraints weight = 144929.439| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.52 r_work: 0.2724 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 67596 Z= 0.335 Angle : 0.597 11.101 91263 Z= 0.290 Chirality : 0.043 0.214 10867 Planarity : 0.004 0.055 11652 Dihedral : 6.699 143.056 9386 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.84 % Allowed : 14.47 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.09), residues: 8639 helix: 1.95 (0.08), residues: 4432 sheet: 0.02 (0.16), residues: 1125 loop : -0.60 (0.11), residues: 3082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.007 0.001 HIS a 201 PHE 0.016 0.001 PHE P 259 TYR 0.024 0.001 TYR z 351 ARG 0.014 0.000 ARG h 53 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17797.35 seconds wall clock time: 312 minutes 55.45 seconds (18775.45 seconds total)