Starting phenix.real_space_refine on Tue Apr 9 19:51:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sht_40494/04_2024/8sht_40494_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sht_40494/04_2024/8sht_40494.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/8sht_40494/04_2024/8sht_40494.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sht_40494/04_2024/8sht_40494.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sht_40494/04_2024/8sht_40494_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sht_40494/04_2024/8sht_40494_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 422 5.16 5 C 42658 2.51 5 N 11873 2.21 5 O 13207 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 GLU 68": "OE1" <-> "OE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A ASP 382": "OD1" <-> "OD2" Residue "A GLU 387": "OE1" <-> "OE2" Residue "A GLU 389": "OE1" <-> "OE2" Residue "B ASP 66": "OD1" <-> "OD2" Residue "B GLU 387": "OE1" <-> "OE2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "D ASP 67": "OD1" <-> "OD2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D GLU 101": "OE1" <-> "OE2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 329": "OE1" <-> "OE2" Residue "E ASP 532": "OD1" <-> "OD2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 415": "OE1" <-> "OE2" Residue "G GLU 497": "OE1" <-> "OE2" Residue "H GLU 11": "OE1" <-> "OE2" Residue "H ASP 46": "OD1" <-> "OD2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H GLU 413": "OE1" <-> "OE2" Residue "H PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 482": "OE1" <-> "OE2" Residue "Q ASP 200": "OD1" <-> "OD2" Residue "Q GLU 416": "OE1" <-> "OE2" Residue "Q ASP 499": "OD1" <-> "OD2" Residue "Q TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 86": "OD1" <-> "OD2" Residue "Z PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 529": "OD1" <-> "OD2" Residue "d ASP 26": "OD1" <-> "OD2" Residue "d GLU 93": "OE1" <-> "OE2" Residue "d GLU 524": "OE1" <-> "OE2" Residue "e GLU 207": "OE1" <-> "OE2" Residue "e PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 497": "OE1" <-> "OE2" Residue "h ASP 46": "OD1" <-> "OD2" Residue "h GLU 103": "OE1" <-> "OE2" Residue "h GLU 356": "OE1" <-> "OE2" Residue "h GLU 383": "OE1" <-> "OE2" Residue "h PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 141": "OE1" <-> "OE2" Residue "z ASP 32": "OD1" <-> "OD2" Residue "z GLU 415": "OE1" <-> "OE2" Residue "z ASP 519": "OD1" <-> "OD2" Residue "P GLU 208": "OE1" <-> "OE2" Residue "N GLU 182": "OE1" <-> "OE2" Residue "N PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 68272 Number of models: 1 Model: "" Number of chains: 50 Chain: "A" Number of atoms: 4069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4069 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 14, 'TRANS': 521} Chain: "B" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3952 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 10, 'TRANS': 515} Chain: "D" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3923 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "E" Number of atoms: 4132 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} Conformer: "C" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} bond proxies already assigned to first conformer: 4158 Chain: "G" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4089 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "H" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4054 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 16, 'TRANS': 511} Chain: "Q" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4086 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 18, 'TRANS': 519} Chain: "Z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "a" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4041 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Chain: "b" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3943 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 10, 'TRANS': 514} Chain: "d" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3917 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 4169 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} Conformer: "B" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} bond proxies already assigned to first conformer: 4195 Chain: "g" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4063 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 16, 'TRANS': 506} 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: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1507 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 3, 'TRANS': 182} Chain breaks: 9 Chain: "N" Number of atoms: 1656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1656 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 210} Chain breaks: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N BPHE E 9 " occ=0.38 ... (20 atoms not shown) pdb=" CZ CPHE E 9 " occ=0.62 residue: pdb=" N APHE e 9 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE e 9 " occ=0.50 Time building chain proxies: 29.06, per 1000 atoms: 0.43 Number of scatterers: 68272 At special positions: 0 Unit cell: (181.976, 176.686, 179.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 422 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 13207 8.00 N 11873 7.00 C 42658 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 "HETATM68179 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM68051 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67923 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67795 O3A ADP B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM68115 O3A ADP e 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67859 O3A ADP E 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67827 O3A ADP D 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 22.20 Conformation dependent library (CDL) restraints added in 10.4 seconds 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16508 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 319 helices and 115 sheets defined 49.8% alpha, 11.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.98 Creating SS restraints... Processing helix chain 'A' and resid 15 through 35 removed outlier: 3.653A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N SER A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 5.778A 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: 3.635A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 110 removed outlier: 3.620A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLN A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 135 Processing helix chain 'A' and resid 140 through 156 removed outlier: 6.687A pdb=" N ARG A 145 " --> pdb=" O ASP A 141 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N ASP A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N CYS A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 178 removed outlier: 4.146A pdb=" N ASP A 166 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ALA A 169 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 257 through 280 removed outlier: 4.457A pdb=" N ASP A 261 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 382 through 404 Processing helix chain 'A' and resid 414 through 426 Processing helix chain 'A' and resid 434 through 455 removed outlier: 3.748A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 5.093A 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: 3.604A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS A 484 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TRP A 485 " --> pdb=" O ASN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 525 Processing helix chain 'B' and resid 21 through 39 Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 99 through 119 Processing helix chain 'B' and resid 123 through 143 Processing helix chain 'B' and resid 152 through 169 removed outlier: 4.532A pdb=" N SER B 169 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 190 removed outlier: 3.651A pdb=" N LYS B 176 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ASP B 177 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 198 No H-bonds generated for 'chain 'B' and resid 196 through 198' Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 261 through 285 removed outlier: 4.085A pdb=" N HIS B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'B' and resid 317 through 327 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 380 through 402 Processing helix chain 'B' and resid 412 through 427 removed outlier: 3.769A 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: 3.744A 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: 4.385A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 5.455A 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: 4.122A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.924A 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: 3.693A 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: 4.141A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.984A 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: 4.008A 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 Processing helix chain 'D' and resid 447 through 469 removed outlier: 4.142A pdb=" N VAL D 460 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N ILE D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) Proline residue: D 462 - end of helix Processing helix chain 'D' and resid 473 through 486 Processing helix chain 'D' and resid 503 through 506 Processing helix chain 'D' and resid 512 through 530 Processing helix chain 'E' and resid 22 through 24 No H-bonds generated for 'chain 'E' and resid 22 through 24' Processing helix chain 'E' and resid 30 through 51 removed outlier: 3.641A pdb=" N ARG E 49 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR E 50 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 80 Processing helix chain 'E' and resid 86 through 101 Processing helix chain 'E' and resid 108 through 126 removed outlier: 3.631A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 150 Processing helix chain 'E' and resid 163 through 175 removed outlier: 4.777A pdb=" N SER E 175 " --> pdb=" O THR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 195 removed outlier: 3.947A pdb=" N SER E 180 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ARG E 183 " --> pdb=" O SER E 180 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR E 195 " --> pdb=" O ALA E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 219 through 221 No H-bonds generated for 'chain 'E' and resid 219 through 221' Processing helix chain 'E' and resid 271 through 295 removed outlier: 3.939A pdb=" N THR E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 316 Processing helix chain 'E' and resid 327 through 337 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 392 through 414 Processing helix chain 'E' and resid 424 through 439 removed outlier: 3.864A pdb=" N LYS E 439 " --> pdb=" O GLN E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 465 removed outlier: 3.777A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL E 457 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE E 458 " --> pdb=" O ALA E 454 " (cutoff:3.500A) Proline residue: E 459 - end of helix Processing helix chain 'E' and resid 470 through 483 Processing helix chain 'E' and resid 501 through 504 No H-bonds generated for 'chain 'E' and resid 501 through 504' Processing helix chain 'E' and resid 510 through 528 Processing helix chain 'G' and resid 20 through 37 removed outlier: 3.798A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 68 Processing helix chain 'G' and resid 75 through 90 Processing helix chain 'G' and resid 95 through 115 removed outlier: 3.773A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN G 115 " --> pdb=" O HIS G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 140 Processing helix chain 'G' and resid 149 through 160 Processing helix chain 'G' and resid 164 through 183 removed outlier: 3.885A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N SER G 170 " --> pdb=" O ARG G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 198 No H-bonds generated for 'chain 'G' and resid 195 through 198' Processing helix chain 'G' and resid 209 through 211 No H-bonds generated for 'chain 'G' and resid 209 through 211' Processing helix chain 'G' and resid 263 through 285 removed outlier: 4.260A pdb=" N LEU G 285 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 307 removed outlier: 3.767A 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: 3.593A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ALA G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 455 removed outlier: 3.745A pdb=" N TRP G 435 " --> pdb=" O VAL G 432 " (cutoff:3.500A) Proline residue: G 436 - end of helix removed outlier: 4.004A 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 460 through 470 Processing helix chain 'G' and resid 490 through 493 No H-bonds generated for 'chain 'G' and resid 490 through 493' Processing helix chain 'G' and resid 499 through 517 Processing helix chain 'H' and resid 19 through 34 Processing helix chain 'H' and resid 37 through 39 No H-bonds generated for 'chain 'H' and resid 37 through 39' Processing helix chain 'H' and resid 62 through 68 Processing helix chain 'H' and resid 76 through 89 removed outlier: 3.514A pdb=" N GLU H 89 " --> pdb=" O GLN H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 113 removed outlier: 4.141A 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: 3.858A pdb=" N MET H 185 " --> pdb=" O ASP H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'H' and resid 205 through 207 No H-bonds generated for 'chain 'H' and resid 205 through 207' Processing helix chain 'H' and resid 225 through 227 No H-bonds generated for 'chain 'H' and resid 225 through 227' Processing helix chain 'H' and resid 260 through 284 removed outlier: 3.581A pdb=" N SER H 284 " --> pdb=" O LYS H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 305 Processing helix chain 'H' and resid 316 through 326 Processing helix chain 'H' and resid 339 through 341 No H-bonds generated for 'chain 'H' and resid 339 through 341' Processing helix chain 'H' and resid 379 through 401 Processing helix chain 'H' and resid 411 through 426 removed outlier: 4.002A pdb=" N THR H 426 " --> pdb=" O ASP H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 453 removed outlier: 4.052A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE H 444 " --> pdb=" O LYS H 440 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ILE H 445 " --> pdb=" O ALA H 441 " (cutoff:3.500A) Proline residue: H 446 - end of helix Processing helix chain 'H' and resid 457 through 469 Processing helix chain 'H' and resid 496 through 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: 5.079A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) removed outlier: 5.765A 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 120 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: 4.148A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 177 through 189 Processing helix chain 'Q' and resid 212 through 214 No H-bonds generated for 'chain 'Q' and resid 212 through 214' Processing helix chain 'Q' and resid 262 through 286 removed outlier: 4.833A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) removed outlier: 3.888A 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: 3.925A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 434 through 456 removed outlier: 3.775A 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: 4.367A pdb=" N ALA Q 447 " --> pdb=" O GLU Q 443 " (cutoff:3.500A) removed outlier: 4.892A 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 'Q' and resid 536 through 538 No H-bonds generated for 'chain 'Q' and resid 536 through 538' Processing helix chain 'Z' and resid 3 through 7 Processing helix chain 'Z' and resid 17 through 37 removed outlier: 4.792A pdb=" N THR Z 36 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ASN Z 37 " --> pdb=" O VAL Z 33 " (cutoff:3.500A) Processing helix chain 'Z' and resid 60 through 66 Processing helix chain 'Z' and resid 72 through 87 Processing helix chain 'Z' and resid 92 through 112 removed outlier: 3.564A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) removed outlier: 5.058A 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: 4.295A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 162 through 179 removed outlier: 3.635A 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 263 Processing helix chain 'Z' and resid 265 through 281 removed outlier: 3.603A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 299 through 308 removed outlier: 3.823A pdb=" N GLU Z 308 " --> pdb=" O ALA Z 304 " (cutoff:3.500A) Processing helix chain 'Z' and resid 318 through 328 removed outlier: 4.295A 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: 4.047A pdb=" N GLN Z 434 " --> pdb=" O GLY Z 431 " (cutoff:3.500A) removed outlier: 3.666A 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: 3.689A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N SER a 34 " --> pdb=" O ASN a 30 " (cutoff:3.500A) removed outlier: 5.981A 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: 3.988A pdb=" N LEU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 110 removed outlier: 3.620A pdb=" N VAL a 94 " --> pdb=" O THR a 90 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN a 110 " --> pdb=" O GLU a 106 " (cutoff:3.500A) Processing helix chain 'a' and resid 114 through 135 Processing helix chain 'a' and resid 144 through 156 Processing helix chain 'a' and resid 163 through 179 removed outlier: 4.432A pdb=" N ASP a 166 " --> pdb=" O ILE a 163 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA a 169 " --> pdb=" O ASP a 166 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 186 No H-bonds generated for 'chain 'a' and resid 184 through 186' Processing helix chain 'a' and resid 205 through 207 No H-bonds generated for 'chain 'a' and resid 205 through 207' Processing helix chain 'a' and resid 257 through 280 removed outlier: 4.683A pdb=" N ASP a 261 " --> pdb=" O GLU a 258 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE a 270 " --> pdb=" O GLU a 267 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 303 Processing helix chain 'a' and resid 313 through 323 Processing helix chain 'a' and resid 342 through 344 No H-bonds generated for 'chain 'a' and resid 342 through 344' Processing helix chain 'a' and resid 382 through 404 Processing helix chain 'a' and resid 414 through 429 removed outlier: 4.361A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) Processing helix chain 'a' and resid 433 through 455 removed outlier: 3.785A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N ILE a 448 " --> pdb=" O SER a 444 " (cutoff:3.500A) Proline residue: a 449 - end of helix Processing helix chain 'a' and resid 460 through 476 Processing helix chain 'a' and resid 481 through 485 removed outlier: 3.946A pdb=" N TRP a 485 " --> pdb=" O ASN a 482 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 501 No H-bonds generated for 'chain 'a' and resid 498 through 501' Processing helix chain 'a' and resid 507 through 525 Processing helix chain 'b' and resid 21 through 39 Processing helix chain 'b' and resid 67 through 72 Processing helix chain 'b' and resid 79 through 94 Processing helix chain 'b' and resid 99 through 119 Processing helix chain 'b' and resid 123 through 144 Processing helix chain 'b' and resid 152 through 167 Processing helix chain 'b' and resid 171 through 190 removed outlier: 3.633A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS b 176 " --> pdb=" O THR b 173 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ASP b 177 " --> pdb=" O HIS b 174 " (cutoff:3.500A) Processing helix chain 'b' and resid 209 through 211 No H-bonds generated for 'chain 'b' and resid 209 through 211' Processing helix chain 'b' and resid 261 through 285 removed outlier: 3.951A 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 426 Processing helix chain 'b' and resid 431 through 454 Proline residue: b 447 - end of helix removed outlier: 3.849A pdb=" N ALA b 454 " --> pdb=" O ILE b 450 " (cutoff:3.500A) Processing helix chain 'b' and resid 458 through 471 Processing helix chain 'b' and resid 488 through 491 No H-bonds generated for 'chain 'b' and resid 488 through 491' Processing helix chain 'b' and resid 497 through 515 Processing helix chain 'd' and resid 29 through 49 Processing helix chain 'd' and resid 74 through 80 Processing helix chain 'd' and resid 86 through 101 Processing helix chain 'd' and resid 106 through 125 removed outlier: 3.737A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.894A 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 170 Processing helix chain 'd' and resid 175 through 192 removed outlier: 4.196A pdb=" N GLN d 178 " --> pdb=" O VAL d 175 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N SER d 181 " --> pdb=" O GLN d 178 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N SER d 184 " --> pdb=" O SER d 181 " (cutoff:3.500A) Proline residue: d 185 - end of helix Processing helix chain 'd' and resid 205 through 207 No H-bonds generated for 'chain 'd' and resid 205 through 207' Processing helix chain 'd' and resid 218 through 220 No H-bonds generated for 'chain 'd' and resid 218 through 220' Processing helix chain 'd' and resid 269 through 293 removed outlier: 3.661A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.915A 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: 4.531A pdb=" N GLU d 334 " --> pdb=" O GLU d 331 " (cutoff:3.500A) removed outlier: 3.808A 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: 3.767A pdb=" N THR d 442 " --> pdb=" O GLU d 438 " (cutoff:3.500A) Processing helix chain 'd' and resid 446 through 466 removed outlier: 3.988A pdb=" N VAL d 460 " --> pdb=" O ASP d 456 " (cutoff:3.500A) removed outlier: 4.958A 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 504 through 506 No H-bonds generated for 'chain 'd' and resid 504 through 506' Processing helix chain 'd' and resid 512 through 530 removed outlier: 4.969A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 51 removed outlier: 3.567A pdb=" N LEU e 34 " --> pdb=" O GLY e 30 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR e 50 " --> pdb=" O ASN e 46 " (cutoff:3.500A) removed outlier: 5.135A 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: 3.750A pdb=" N ARG e 126 " --> pdb=" O GLN e 122 " (cutoff:3.500A) Processing helix chain 'e' and resid 130 through 151 Processing helix chain 'e' and resid 163 through 175 removed outlier: 4.688A pdb=" N SER e 175 " --> pdb=" O THR e 171 " (cutoff:3.500A) Processing helix chain 'e' and resid 177 through 195 removed outlier: 4.098A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ARG e 183 " --> pdb=" O SER e 180 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU e 194 " --> pdb=" O ASN e 191 " (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 392 through 414 Processing helix chain 'e' and resid 424 through 437 Processing helix chain 'e' and resid 442 through 465 removed outlier: 3.877A 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: 3.633A pdb=" N VAL e 457 " --> pdb=" O ASP e 453 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ILE e 458 " --> pdb=" O ALA e 454 " (cutoff:3.500A) Proline residue: e 459 - end of helix Processing helix chain 'e' and resid 470 through 483 Processing helix chain 'e' and resid 510 through 528 Processing helix chain 'g' and resid 20 through 37 removed outlier: 3.853A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 68 Processing helix chain 'g' and resid 75 through 90 Processing helix chain 'g' and resid 95 through 114 removed outlier: 3.780A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.663A 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: 3.831A 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: 4.106A pdb=" N PHE g 264 " --> pdb=" O GLU g 261 " (cutoff:3.500A) Processing helix chain 'g' and resid 298 through 307 removed outlier: 3.719A 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: 3.631A pdb=" N LYS g 427 " --> pdb=" O THR g 423 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ALA g 428 " --> pdb=" O GLU g 424 " (cutoff:3.500A) Processing helix chain 'g' and resid 432 through 455 removed outlier: 3.974A pdb=" N TRP g 435 " --> pdb=" O VAL g 432 " (cutoff:3.500A) Proline residue: g 436 - end of helix removed outlier: 3.743A pdb=" N GLN g 442 " --> pdb=" O ALA g 439 " (cutoff:3.500A) Proline residue: g 448 - end of helix Processing helix chain 'g' and resid 459 through 470 Processing helix chain 'g' and resid 490 through 493 No H-bonds generated for 'chain 'g' and resid 490 through 493' Processing helix chain 'g' and resid 499 through 517 Processing helix chain 'h' and resid 19 through 34 Processing helix chain 'h' and resid 62 through 68 Processing helix chain 'h' and resid 76 through 89 removed outlier: 3.675A pdb=" N GLU h 89 " --> pdb=" O GLN h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 113 removed outlier: 4.191A pdb=" N THR h 98 " --> pdb=" O THR h 94 " (cutoff:3.500A) Proline residue: h 110 - end of helix Processing helix chain 'h' and resid 118 through 139 Processing helix chain 'h' and resid 148 through 163 Processing helix chain 'h' and resid 169 through 185 removed outlier: 5.306A pdb=" N ALA h 173 " --> pdb=" O GLN h 170 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N MET h 184 " --> pdb=" O ASP h 181 " (cutoff:3.500A) Processing helix chain 'h' and resid 192 through 194 No H-bonds generated for 'chain 'h' and resid 192 through 194' Processing helix chain 'h' and resid 205 through 207 No H-bonds generated for 'chain 'h' and resid 205 through 207' Processing helix chain 'h' and resid 225 through 227 No H-bonds generated for 'chain 'h' and resid 225 through 227' Processing helix chain 'h' and resid 260 through 284 removed outlier: 3.561A pdb=" N SER h 284 " --> pdb=" O LYS h 280 " (cutoff:3.500A) Processing helix chain 'h' and resid 297 through 305 Processing helix chain 'h' and resid 316 through 326 Processing helix chain 'h' and resid 339 through 341 No H-bonds generated for 'chain 'h' and resid 339 through 341' Processing helix chain 'h' and resid 379 through 401 Processing helix chain 'h' and resid 411 through 426 removed outlier: 4.138A pdb=" N THR h 426 " --> pdb=" O ASP h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 430 through 453 removed outlier: 4.024A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU h 443 " --> pdb=" O ALA h 439 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE h 444 " --> pdb=" O LYS h 440 " (cutoff:3.500A) removed outlier: 5.332A 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: 4.175A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ALA q 46 " --> pdb=" O THR q 42 " (cutoff:3.500A) Processing helix chain 'q' and resid 69 through 75 Processing helix chain 'q' and resid 81 through 96 Processing helix chain 'q' and resid 101 through 121 Processing helix chain 'q' and resid 125 through 146 Proline residue: q 144 - end of helix Processing helix chain 'q' and resid 157 through 167 removed outlier: 4.191A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.324A 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: 4.730A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR q 286 " --> pdb=" O ALA q 282 " (cutoff:3.500A) Processing helix chain 'q' and resid 299 through 307 Processing helix chain 'q' and resid 318 through 328 Processing helix chain 'q' and resid 341 through 343 No H-bonds generated for 'chain 'q' and resid 341 through 343' Processing helix chain 'q' and resid 382 through 404 Processing helix chain 'q' and resid 414 through 429 removed outlier: 3.536A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 456 removed outlier: 3.846A pdb=" N TYR q 436 " --> pdb=" O LEU q 433 " (cutoff:3.500A) Proline residue: q 449 - end of helix Processing helix chain 'q' and resid 460 through 473 Processing helix chain 'q' and resid 492 through 495 No H-bonds generated for 'chain 'q' and resid 492 through 495' Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'z' and resid 17 through 37 removed outlier: 4.938A pdb=" N THR z 36 " --> pdb=" O ASP z 32 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ASN z 37 " --> pdb=" O VAL z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 60 through 66 Processing helix chain 'z' and resid 72 through 87 Processing helix chain 'z' and resid 92 through 112 removed outlier: 3.595A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) removed outlier: 5.133A 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: 4.080A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 162 through 179 removed outlier: 3.630A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE z 179 " --> pdb=" O SER z 175 " (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: 3.623A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 299 through 308 removed outlier: 3.895A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 318 through 327 removed outlier: 4.431A pdb=" N GLU z 322 " --> pdb=" O ARG z 318 " (cutoff:3.500A) Processing helix chain 'z' and resid 341 through 343 No H-bonds generated for 'chain 'z' and resid 341 through 343' Processing helix chain 'z' and resid 381 through 403 Processing helix chain 'z' and resid 413 through 428 Proline residue: z 427 - end of helix Processing helix chain 'z' and resid 432 through 455 removed outlier: 3.750A pdb=" N ILE z 447 " --> pdb=" O LEU z 444 " (cutoff:3.500A) Proline residue: z 448 - end of helix Processing helix chain 'z' and resid 459 through 473 Processing helix chain 'z' and resid 489 through 492 No H-bonds generated for 'chain 'z' and resid 489 through 492' Processing helix chain 'z' and resid 498 through 517 Processing helix chain 'P' and resid 58 through 61 No H-bonds generated for 'chain 'P' and resid 58 through 61' Processing helix chain 'P' and resid 63 through 84 removed outlier: 3.604A pdb=" N PHE P 69 " --> pdb=" O ASP P 65 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 139 No H-bonds generated for 'chain 'P' and resid 137 through 139' Processing helix chain 'P' and resid 141 through 151 removed outlier: 3.930A pdb=" N ARG P 144 " --> pdb=" O ARG P 141 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET P 145 " --> pdb=" O LYS P 142 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 175 removed outlier: 3.518A pdb=" N ILE P 174 " --> pdb=" O PHE P 170 " (cutoff:3.500A) Processing helix chain 'P' and resid 196 through 208 removed outlier: 3.719A pdb=" N ALA P 207 " --> pdb=" O ILE P 203 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU P 208 " --> pdb=" O CYS P 204 " (cutoff:3.500A) Processing helix chain 'P' and resid 227 through 230 No H-bonds generated for 'chain 'P' and resid 227 through 230' Processing helix chain 'P' and resid 261 through 271 removed outlier: 4.372A 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 180 through 182 removed outlier: 3.537A pdb=" N TYR A 181 " --> pdb=" O ARG A 189 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 196 through 201 removed outlier: 3.821A pdb=" N GLY A 379 " --> pdb=" O ALA A 200 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 213 through 216 Processing sheet with id= F, first strand: chain 'A' and resid 346 through 348 removed outlier: 6.595A pdb=" N VAL A 285 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N LEU A 237 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU A 287 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N MET A 306 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N THR A 288 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL A 308 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 408 through 410 Processing sheet with id= H, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.520A pdb=" N LYS A 494 " --> pdb=" O ASP A 489 " (cutoff:3.500A) 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 50 through 53 Processing sheet with id= K, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.420A pdb=" N CYS B 371 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N ILE B 202 " --> pdb=" O CYS B 371 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ILE B 373 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LYS B 204 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LEU B 375 " --> pdb=" O LYS B 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'B' and resid 218 through 220 Processing sheet with id= M, first strand: chain 'B' and resid 344 through 346 removed outlier: 3.506A pdb=" N CYS B 346 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N CYS B 289 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ALA B 240 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ILE B 291 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N MET B 310 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N ASN B 292 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ILE B 312 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 406 through 408 Processing sheet with id= O, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= P, first strand: chain 'D' and resid 59 through 62 removed outlier: 3.503A pdb=" N THR D 71 " --> pdb=" O LYS D 59 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.692A pdb=" N VAL D 386 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N VAL D 211 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ILE D 388 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LYS D 213 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL D 390 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 227 through 229 Processing sheet with id= S, first strand: chain 'D' and resid 357 through 359 removed outlier: 6.989A pdb=" N VAL D 297 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE D 249 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N LEU D 299 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N MET D 323 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N ILE D 300 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE D 325 " --> pdb=" O ILE D 300 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 421 through 423 Processing sheet with id= U, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.578A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 59 through 62 Processing sheet with id= W, first strand: chain 'E' and resid 209 through 215 removed outlier: 6.946A pdb=" N VAL E 383 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLU E 212 " --> pdb=" O VAL E 383 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N ILE E 385 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N LYS E 214 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE E 387 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 228 through 230 Processing sheet with id= Y, 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) Processing sheet with id= Z, first strand: chain 'E' and resid 418 through 420 Processing sheet with id= AA, first strand: chain 'G' and resid 48 through 51 Processing sheet with id= AB, first strand: chain 'G' and resid 185 through 187 Processing sheet with id= AC, first strand: chain 'G' and resid 199 through 203 removed outlier: 6.452A pdb=" N CYS G 372 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N GLU G 202 " --> pdb=" O CYS G 372 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE G 374 " --> pdb=" O GLU G 202 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'G' and resid 238 through 241 removed outlier: 6.529A pdb=" N VAL G 289 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N LEU G 241 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ILE G 291 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N THR G 310 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N THR G 292 " --> pdb=" O THR G 310 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE G 312 " --> pdb=" O THR G 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'G' and resid 351 through 355 Processing sheet with id= AF, first strand: chain 'G' and resid 407 through 409 Processing sheet with id= AG, first strand: chain 'G' and resid 478 through 480 Processing sheet with id= AH, first strand: chain 'H' and resid 14 through 17 Processing sheet with id= AI, first strand: chain 'H' and resid 47 through 50 Processing sheet with id= AJ, first strand: chain 'H' and resid 195 through 201 removed outlier: 6.372A pdb=" N CYS H 370 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LYS H 198 " --> pdb=" O CYS H 370 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N PHE H 372 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL H 200 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU H 374 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'H' and resid 214 through 217 Processing sheet with id= AL, first strand: chain 'H' and resid 237 through 240 removed outlier: 7.084A pdb=" N VAL H 288 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LEU H 240 " --> pdb=" O VAL H 288 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU H 290 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N PHE H 309 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N SER H 291 " --> pdb=" O PHE H 309 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA H 311 " --> pdb=" O SER H 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'H' and resid 405 through 407 Processing sheet with id= AN, first strand: chain 'H' and resid 475 through 478 removed outlier: 3.532A pdb=" N ALA H 485 " --> pdb=" O GLY H 476 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'Q' and resid 20 through 23 Processing sheet with id= AP, first strand: chain 'Q' and resid 54 through 57 Processing sheet with id= AQ, first strand: chain 'Q' and resid 202 through 206 removed outlier: 6.471A pdb=" N SER Q 373 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N CYS Q 205 " --> pdb=" O SER Q 373 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ILE Q 375 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'Q' and resid 220 through 223 Processing sheet with id= AS, first strand: chain 'Q' and resid 240 through 242 removed outlier: 6.056A pdb=" N MET Q 311 " --> pdb=" O VAL Q 291 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N THR Q 293 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N VAL Q 313 " --> pdb=" O THR Q 293 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Q' and resid 498 through 500 removed outlier: 3.954A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N VAL Q 147 " --> pdb=" O PRO Q 410 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id= AV, first strand: chain 'Z' and resid 12 through 15 removed outlier: 3.557A pdb=" N GLU Z 12 " --> pdb=" O ARG Z 523 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'Z' and resid 45 through 48 Processing sheet with id= AX, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.908A pdb=" N VAL Z 372 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N MET Z 194 " --> pdb=" O VAL Z 372 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LEU Z 374 " --> pdb=" O MET Z 194 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N MET Z 196 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N ILE Z 376 " --> pdb=" O MET Z 196 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id= AZ, first strand: chain 'Z' and resid 345 through 347 removed outlier: 7.062A pdb=" N GLY Z 288 " --> pdb=" O TYR Z 229 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N LEU Z 231 " --> pdb=" O GLY Z 288 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL Z 290 " --> pdb=" O LEU Z 231 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N CYS Z 233 " --> pdb=" O VAL Z 290 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ILE Z 292 " --> pdb=" O CYS Z 233 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'Z' and resid 407 through 409 Processing sheet with id= BB, first strand: chain 'Z' and resid 477 through 479 removed outlier: 3.519A pdb=" N MET Z 487 " --> pdb=" O GLY Z 478 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'a' and resid 9 through 13 Processing sheet with id= BD, first strand: chain 'a' and resid 43 through 46 Processing sheet with id= BE, first strand: chain 'a' and resid 180 through 182 Processing sheet with id= BF, first strand: chain 'a' and resid 196 through 201 removed outlier: 3.840A pdb=" N ASN a 196 " --> pdb=" O ALA a 373 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLY a 379 " --> pdb=" O ALA a 200 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'a' and resid 213 through 216 Processing sheet with id= BH, first strand: chain 'a' and resid 346 through 348 removed outlier: 3.545A pdb=" N ALA a 348 " --> pdb=" O ALA a 232 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL a 285 " --> pdb=" O ALA a 235 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU a 237 " --> pdb=" O VAL a 285 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU a 287 " --> pdb=" O LEU a 237 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N MET a 306 " --> pdb=" O ILE a 286 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N THR a 288 " --> pdb=" O MET a 306 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL a 308 " --> pdb=" O THR a 288 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'a' and resid 408 through 410 Processing sheet with id= BJ, first strand: chain 'a' and resid 486 through 489 Processing sheet with id= BK, first strand: chain 'b' and resid 17 through 19 Processing sheet with id= BL, first strand: chain 'b' and resid 50 through 53 Processing sheet with id= BM, first strand: chain 'b' and resid 199 through 205 removed outlier: 6.225A pdb=" N CYS b 371 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ILE b 202 " --> pdb=" O CYS b 371 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ILE b 373 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LYS b 204 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU b 375 " --> pdb=" O LYS b 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= BM Processing sheet with id= BN, first strand: chain 'b' and resid 218 through 220 Processing sheet with id= BO, first strand: chain 'b' and resid 344 through 346 removed outlier: 6.625A pdb=" N CYS b 289 " --> pdb=" O LEU b 238 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N ALA b 240 " --> pdb=" O CYS b 289 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ILE b 291 " --> pdb=" O ALA b 240 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N MET b 310 " --> pdb=" O PHE b 290 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N ASN b 292 " --> pdb=" O MET b 310 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE b 312 " --> pdb=" O ASN b 292 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'b' and resid 406 through 408 Processing sheet with id= BQ, first strand: chain 'b' and resid 476 through 479 Processing sheet with id= BR, first strand: chain 'd' and resid 59 through 62 Processing sheet with id= BS, first strand: chain 'd' and resid 208 through 214 removed outlier: 6.797A pdb=" N VAL d 386 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VAL d 211 " --> pdb=" O VAL d 386 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE d 388 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N LYS d 213 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N VAL d 390 " --> pdb=" O LYS d 213 " (cutoff:3.500A) No H-bonds generated for sheet with id= BS Processing sheet with id= BT, first strand: chain 'd' and resid 227 through 229 Processing sheet with id= BU, first strand: chain 'd' and resid 357 through 359 removed outlier: 6.515A pdb=" N VAL d 297 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ILE d 249 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N LEU d 299 " --> pdb=" O ILE d 249 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N MET d 323 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ILE d 300 " --> pdb=" O MET d 323 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE d 325 " --> pdb=" O ILE d 300 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 'd' and resid 421 through 423 Processing sheet with id= BW, first strand: chain 'd' and resid 491 through 494 Processing sheet with id= BX, first strand: chain 'e' and resid 26 through 29 Processing sheet with id= BY, first strand: chain 'e' and resid 59 through 62 Processing sheet with id= BZ, first strand: chain 'e' and resid 209 through 215 removed outlier: 6.801A pdb=" N VAL e 383 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLU e 212 " --> pdb=" O VAL e 383 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ILE e 385 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LYS e 214 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE e 387 " --> pdb=" O LYS e 214 " (cutoff:3.500A) Processing sheet with id= CA, first strand: chain 'e' and resid 228 through 230 Processing sheet with id= CB, first strand: chain 'e' and resid 354 through 356 removed outlier: 6.985A pdb=" N LEU e 299 " --> pdb=" O ALA e 249 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'e' and resid 418 through 420 Processing sheet with id= CD, first strand: chain 'g' and resid 15 through 18 Processing sheet with id= CE, first strand: chain 'g' and resid 48 through 51 Processing sheet with id= CF, first strand: chain 'g' and resid 185 through 187 Processing sheet with id= CG, first strand: chain 'g' and resid 200 through 205 removed outlier: 3.877A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) Processing sheet with id= CH, first strand: chain 'g' and resid 218 through 220 Processing sheet with id= CI, first strand: chain 'g' and resid 238 through 241 removed outlier: 6.575A pdb=" N VAL g 289 " --> pdb=" O VAL g 239 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LEU g 241 " --> pdb=" O VAL g 289 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE g 291 " --> pdb=" O LEU g 241 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N THR g 310 " --> pdb=" O VAL g 290 " (cutoff:3.500A) removed outlier: 7.980A pdb=" N THR g 292 " --> pdb=" O THR g 310 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE g 312 " --> pdb=" O THR g 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= CI Processing sheet with id= CJ, first strand: chain 'g' and resid 407 through 409 Processing sheet with id= CK, first strand: chain 'g' and resid 478 through 480 Processing sheet with id= CL, first strand: chain 'h' and resid 14 through 17 Processing sheet with id= CM, first strand: chain 'h' and resid 47 through 50 Processing sheet with id= CN, first strand: chain 'h' and resid 195 through 201 removed outlier: 6.671A pdb=" N CYS h 370 " --> pdb=" O GLY h 196 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LYS h 198 " --> pdb=" O CYS h 370 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE h 372 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N VAL h 200 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N LEU h 374 " --> pdb=" O VAL h 200 " (cutoff:3.500A) Processing sheet with id= CO, first strand: chain 'h' and resid 214 through 217 Processing sheet with id= CP, first strand: chain 'h' and resid 237 through 240 removed outlier: 7.176A pdb=" N VAL h 288 " --> pdb=" O ALA h 238 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU h 240 " --> pdb=" O VAL h 288 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU h 290 " --> pdb=" O LEU h 240 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE h 309 " --> pdb=" O VAL h 289 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N SER h 291 " --> pdb=" O PHE h 309 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA h 311 " --> pdb=" O SER h 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= CP Processing sheet with id= CQ, first strand: chain 'h' and resid 405 through 407 Processing sheet with id= CR, first strand: chain 'h' and resid 475 through 478 Processing sheet with id= CS, first strand: chain 'q' and resid 20 through 23 Processing sheet with id= CT, first strand: chain 'q' and resid 54 through 57 Processing sheet with id= CU, first strand: chain 'q' and resid 202 through 208 removed outlier: 6.618A pdb=" N SER q 373 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N CYS q 205 " --> pdb=" O SER q 373 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE q 375 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ILE q 207 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LEU q 377 " --> pdb=" O ILE q 207 " (cutoff:3.500A) Processing sheet with id= CV, first strand: chain 'q' and resid 220 through 223 Processing sheet with id= CW, first strand: chain 'q' and resid 240 through 242 removed outlier: 6.019A pdb=" N MET q 311 " --> pdb=" O VAL q 291 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR q 293 " --> pdb=" O MET q 311 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL q 313 " --> pdb=" O THR q 293 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain 'q' and resid 498 through 500 removed outlier: 3.855A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N VAL q 147 " --> pdb=" O PRO q 410 " (cutoff:3.500A) Processing sheet with id= CY, first strand: chain 'q' and resid 478 through 480 Processing sheet with id= CZ, first strand: chain 'z' and resid 12 through 15 removed outlier: 3.549A pdb=" N GLU z 12 " --> pdb=" O ARG z 523 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'z' and resid 45 through 48 Processing sheet with id= DB, first strand: chain 'z' and resid 191 through 196 removed outlier: 6.962A pdb=" N VAL z 372 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N MET z 194 " --> pdb=" O VAL z 372 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N LEU z 374 " --> pdb=" O MET z 194 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N MET z 196 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ILE z 376 " --> pdb=" O MET z 196 " (cutoff:3.500A) Processing sheet with id= DC, first strand: chain 'z' and resid 210 through 212 Processing sheet with id= DD, first strand: chain 'z' and resid 345 through 347 Processing sheet with id= DE, first strand: chain 'z' and resid 407 through 409 Processing sheet with id= DF, first strand: chain 'z' and resid 477 through 479 Processing sheet with id= DG, first strand: chain 'P' and resid 213 through 218 removed outlier: 3.760A pdb=" N MET P 184 " --> pdb=" O LYS P 213 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N HIS P 186 " --> pdb=" O CYS P 215 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY P 246 " --> pdb=" O ILE P 238 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LYS P 240 " --> pdb=" O LEU P 244 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N LEU P 244 " --> pdb=" O LYS P 240 " (cutoff:3.500A) Processing sheet with id= DH, first strand: chain 'N' and resid 198 through 203 removed outlier: 6.808A pdb=" N ALA N 213 " --> pdb=" O SER N 199 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N CYS N 201 " --> pdb=" O LEU N 211 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU N 211 " --> pdb=" O CYS N 201 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N PHE N 203 " --> pdb=" O GLN N 209 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N GLN N 209 " --> pdb=" O PHE N 203 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN N 231 " --> pdb=" O LEU N 221 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ASP N 223 " --> pdb=" O LEU N 229 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU N 229 " --> pdb=" O ASP N 223 " (cutoff:3.500A) Processing sheet with id= DI, first strand: chain 'N' and resid 255 through 257 removed outlier: 7.177A pdb=" N ASP N 267 " --> pdb=" O CYS N 273 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N CYS N 273 " --> pdb=" O ASP N 267 " (cutoff:3.500A) Processing sheet with id= DJ, first strand: chain 'N' and resid 287 through 289 removed outlier: 3.751A pdb=" N ARG N 306 " --> pdb=" O SER N 298 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA N 317 " --> pdb=" O LEU N 307 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N ASP N 309 " --> pdb=" O GLU N 315 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLU N 315 " --> pdb=" O ASP N 309 " (cutoff:3.500A) Processing sheet with id= DK, first strand: chain 'N' and resid 349 through 351 removed outlier: 4.107A pdb=" N SER N 361 " --> pdb=" O VAL N 351 " (cutoff:3.500A) 3461 hydrogen bonds defined for protein. 9090 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: 27.25 Time building geometry restraints manager: 24.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 23029 1.35 - 1.46: 13251 1.46 - 1.58: 31982 1.58 - 1.70: 48 1.70 - 1.82: 744 Bond restraints: 69054 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 6.52e+01 bond pdb=" F2 AF3 g 603 " pdb="AL AF3 g 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.39e+01 bond pdb=" F2 AF3 G 603 " pdb="AL AF3 G 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.36e+01 bond pdb=" F2 AF3 A 603 " pdb="AL AF3 A 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.36e+01 bond pdb=" F2 AF3 Z 603 " pdb="AL AF3 Z 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.34e+01 ... (remaining 69049 not shown) Histogram of bond angle deviations from ideal: 97.80 - 105.56: 1121 105.56 - 113.33: 40131 113.33 - 121.09: 33980 121.09 - 128.85: 17689 128.85 - 136.61: 304 Bond angle restraints: 93225 Sorted by residual: angle pdb=" CA MET N 193 " pdb=" CB MET N 193 " pdb=" CG MET N 193 " ideal model delta sigma weight residual 114.10 121.08 -6.98 2.00e+00 2.50e-01 1.22e+01 angle pdb=" N GLY Q 209 " pdb=" CA GLY Q 209 " pdb=" C GLY Q 209 " ideal model delta sigma weight residual 113.18 120.96 -7.78 2.37e+00 1.78e-01 1.08e+01 angle pdb=" CB LYS z 430 " pdb=" CG LYS z 430 " pdb=" CD LYS z 430 " ideal model delta sigma weight residual 111.30 118.65 -7.35 2.30e+00 1.89e-01 1.02e+01 angle pdb=" C ALA q 151 " pdb=" N LYS q 152 " pdb=" CA LYS q 152 " ideal model delta sigma weight residual 121.54 127.52 -5.98 1.91e+00 2.74e-01 9.80e+00 angle pdb=" N GLU P 78 " pdb=" CA GLU P 78 " pdb=" CB GLU P 78 " ideal model delta sigma weight residual 110.16 114.59 -4.43 1.48e+00 4.57e-01 8.97e+00 ... (remaining 93220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 41914 35.98 - 71.96: 664 71.96 - 107.94: 53 107.94 - 143.92: 10 143.92 - 179.90: 6 Dihedral angle restraints: 42647 sinusoidal: 17162 harmonic: 25485 Sorted by residual: dihedral pdb=" O2A ADP q 601 " pdb=" O3A ADP q 601 " pdb=" PA ADP q 601 " pdb=" PB ADP q 601 " ideal model delta sinusoidal sigma weight residual -60.00 119.90 -179.90 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP g 601 " pdb=" O3A ADP g 601 " pdb=" PA ADP g 601 " pdb=" PB ADP g 601 " ideal model delta sinusoidal sigma weight residual -60.00 117.00 -177.00 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP q 601 " pdb=" O5' ADP q 601 " pdb=" PA ADP q 601 " pdb=" O2A ADP q 601 " ideal model delta sinusoidal sigma weight residual 300.00 132.01 167.99 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 42644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 8171 0.040 - 0.079: 2034 0.079 - 0.119: 799 0.119 - 0.158: 78 0.158 - 0.198: 3 Chirality restraints: 11085 Sorted by residual: chirality pdb=" CB VAL h 36 " pdb=" CA VAL h 36 " pdb=" CG1 VAL h 36 " pdb=" CG2 VAL h 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.81e-01 chirality pdb=" CB VAL H 36 " pdb=" CA VAL H 36 " pdb=" CG1 VAL H 36 " pdb=" CG2 VAL H 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 9.62e-01 chirality pdb=" CA ILE g 363 " pdb=" N ILE g 363 " pdb=" C ILE g 363 " pdb=" CB ILE g 363 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.25e-01 ... (remaining 11082 not shown) Planarity restraints: 11897 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.032 5.00e-02 4.00e+02 4.85e-02 3.77e+00 pdb=" N PRO e 441 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE b 11 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.45e+00 pdb=" C ILE b 11 " 0.032 2.00e-02 2.50e+03 pdb=" O ILE b 11 " -0.012 2.00e-02 2.50e+03 pdb=" N PHE b 12 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS z 161 " -0.011 2.00e-02 2.50e+03 1.45e-02 3.17e+00 pdb=" CG HIS z 161 " 0.031 2.00e-02 2.50e+03 pdb=" ND1 HIS z 161 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 HIS z 161 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 HIS z 161 " 0.000 2.00e-02 2.50e+03 pdb=" NE2 HIS z 161 " -0.001 2.00e-02 2.50e+03 ... (remaining 11894 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 620 2.55 - 3.14: 54168 3.14 - 3.72: 107802 3.72 - 4.31: 150724 4.31 - 4.90: 256690 Nonbonded interactions: 570004 Sorted by model distance: nonbonded pdb=" O1A ADP q 601 " pdb="MG MG q 602 " model vdw 1.962 2.170 nonbonded pdb="MG MG D 602 " pdb=" F2 AF3 D 603 " model vdw 1.963 2.120 nonbonded pdb="MG MG H 602 " pdb=" F2 AF3 H 603 " model vdw 1.970 2.120 nonbonded pdb=" O3A ADP h 601 " pdb="MG MG h 602 " model vdw 1.988 2.170 nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.990 2.120 ... (remaining 569999 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 8 through 528 or resid 601 through 603)) selection = (chain 'g' and (resid 8 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: 1.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 8.520 Check model and map are aligned: 0.790 Set scattering table: 0.490 Process input model: 149.400 Find NCS groups from input model: 6.390 Set up NCS constraints: 0.600 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 180.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 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 69054 Z= 0.279 Angle : 0.531 8.795 93225 Z= 0.259 Chirality : 0.041 0.198 11085 Planarity : 0.003 0.049 11897 Dihedral : 14.546 179.902 26139 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.01 % Allowed : 0.20 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.09), residues: 8805 helix: 2.32 (0.08), residues: 4428 sheet: 0.30 (0.16), residues: 1166 loop : -0.54 (0.11), residues: 3211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP g 168 HIS 0.018 0.001 HIS z 161 PHE 0.021 0.001 PHE P 136 TYR 0.019 0.001 TYR G 437 ARG 0.009 0.000 ARG z 15 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 594 time to evaluate : 5.990 Fit side-chains REVERT: A 171 MET cc_start: 0.8778 (ttp) cc_final: 0.8346 (ttm) REVERT: A 359 ASP cc_start: 0.7698 (t0) cc_final: 0.7370 (t0) REVERT: B 49 ASP cc_start: 0.8023 (m-30) cc_final: 0.7810 (m-30) REVERT: D 257 LYS cc_start: 0.9126 (tttt) cc_final: 0.8922 (ttmt) REVERT: E 4 MET cc_start: 0.2976 (ptt) cc_final: 0.2295 (tmm) REVERT: G 527 LYS cc_start: 0.8910 (tppt) cc_final: 0.8588 (tttm) REVERT: H 293 LEU cc_start: 0.9118 (mt) cc_final: 0.8797 (mt) REVERT: Z 496 ASP cc_start: 0.7726 (t70) cc_final: 0.7331 (t0) REVERT: a 51 ASP cc_start: 0.8090 (m-30) cc_final: 0.7839 (m-30) REVERT: e 39 MET cc_start: 0.8439 (ttp) cc_final: 0.8212 (ttm) REVERT: e 93 GLU cc_start: 0.8338 (mm-30) cc_final: 0.8010 (mm-30) REVERT: g 46 MET cc_start: 0.9079 (mmm) cc_final: 0.8857 (mmm) REVERT: h 524 ARG cc_start: 0.7767 (mtp-110) cc_final: 0.7229 (mmm160) REVERT: q 319 TRP cc_start: 0.7930 (m-90) cc_final: 0.7642 (m-90) REVERT: P 260 PHE cc_start: 0.6029 (p90) cc_final: 0.5372 (p90) outliers start: 1 outliers final: 3 residues processed: 595 average time/residue: 1.4748 time to fit residues: 1147.9199 Evaluate side-chains 490 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 487 time to evaluate : 6.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain d residue 503 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 741 optimal weight: 0.6980 chunk 665 optimal weight: 10.0000 chunk 369 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 448 optimal weight: 0.8980 chunk 355 optimal weight: 8.9990 chunk 688 optimal weight: 3.9990 chunk 266 optimal weight: 7.9990 chunk 418 optimal weight: 4.9990 chunk 512 optimal weight: 6.9990 chunk 797 optimal weight: 10.0000 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN G 390 ASN ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 103 ASN ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 95 ASN z 161 HIS ** N 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.0611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 69054 Z= 0.268 Angle : 0.551 8.317 93225 Z= 0.274 Chirality : 0.042 0.167 11085 Planarity : 0.004 0.050 11897 Dihedral : 7.469 178.881 9585 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 0.78 % Allowed : 6.44 % Favored : 92.78 % 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: 8805 helix: 2.08 (0.08), residues: 4435 sheet: 0.20 (0.16), residues: 1169 loop : -0.56 (0.11), residues: 3201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 266 HIS 0.010 0.001 HIS z 161 PHE 0.020 0.001 PHE N 333 TYR 0.014 0.001 TYR G 437 ARG 0.011 0.000 ARG z 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 514 time to evaluate : 6.100 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7692 (t70) cc_final: 0.6946 (t0) REVERT: A 171 MET cc_start: 0.8642 (ttp) cc_final: 0.8316 (ttm) REVERT: A 358 ASP cc_start: 0.8047 (OUTLIER) cc_final: 0.7759 (m-30) REVERT: A 359 ASP cc_start: 0.7737 (t0) cc_final: 0.7427 (t0) REVERT: A 382 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8203 (m-30) REVERT: D 257 LYS cc_start: 0.9131 (tttt) cc_final: 0.8921 (ttmt) REVERT: D 320 MET cc_start: 0.8864 (OUTLIER) cc_final: 0.8561 (mtp) REVERT: E 4 MET cc_start: 0.3024 (ptt) cc_final: 0.2305 (tmm) REVERT: E 196 VAL cc_start: 0.8861 (OUTLIER) cc_final: 0.8645 (m) REVERT: G 527 LYS cc_start: 0.8949 (tppt) cc_final: 0.8561 (tttm) REVERT: H 293 LEU cc_start: 0.9144 (mt) cc_final: 0.8834 (mt) REVERT: Z 244 VAL cc_start: 0.9133 (OUTLIER) cc_final: 0.8865 (t) REVERT: Z 496 ASP cc_start: 0.7768 (t70) cc_final: 0.7331 (t0) REVERT: a 51 ASP cc_start: 0.8071 (m-30) cc_final: 0.7815 (m-30) REVERT: e 93 GLU cc_start: 0.8347 (mm-30) cc_final: 0.8005 (mm-30) REVERT: g 46 MET cc_start: 0.9086 (mmm) cc_final: 0.8833 (mmm) REVERT: h 7 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8407 (pp) REVERT: h 356 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7804 (mm-30) REVERT: h 383 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7380 (mm-30) REVERT: h 401 LYS cc_start: 0.8626 (tppt) cc_final: 0.8184 (pptt) REVERT: q 319 TRP cc_start: 0.7957 (m-90) cc_final: 0.7672 (m-90) REVERT: z 522 MET cc_start: 0.8175 (mtm) cc_final: 0.7660 (mtm) REVERT: P 184 MET cc_start: 0.6011 (mpp) cc_final: 0.5738 (mmt) REVERT: P 202 MET cc_start: 0.8750 (ptp) cc_final: 0.8428 (ptp) REVERT: N 225 GLU cc_start: 0.8668 (tp30) cc_final: 0.8178 (mm-30) REVERT: N 290 TYR cc_start: 0.7737 (t80) cc_final: 0.7341 (t80) REVERT: N 307 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8041 (tp) REVERT: N 333 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.8035 (m-10) outliers start: 58 outliers final: 15 residues processed: 538 average time/residue: 1.5341 time to fit residues: 1076.3529 Evaluate side-chains 507 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 483 time to evaluate : 5.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain Q residue 473 GLU Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 503 ILE Chi-restraints excluded: chain e residue 501 MET Chi-restraints excluded: chain g residue 255 ASP Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 356 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain N residue 307 LEU Chi-restraints excluded: chain N residue 333 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 443 optimal weight: 9.9990 chunk 247 optimal weight: 8.9990 chunk 663 optimal weight: 5.9990 chunk 542 optimal weight: 10.0000 chunk 219 optimal weight: 0.9990 chunk 798 optimal weight: 7.9990 chunk 862 optimal weight: 5.9990 chunk 711 optimal weight: 6.9990 chunk 792 optimal weight: 2.9990 chunk 272 optimal weight: 1.9990 chunk 640 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS P 199 ASN N 275 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.0771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 69054 Z= 0.301 Angle : 0.555 8.840 93225 Z= 0.274 Chirality : 0.042 0.169 11085 Planarity : 0.004 0.048 11897 Dihedral : 7.344 179.556 9580 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.08 % Allowed : 8.60 % Favored : 90.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.09), residues: 8805 helix: 1.93 (0.08), residues: 4442 sheet: 0.14 (0.16), residues: 1160 loop : -0.60 (0.11), residues: 3203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP z 495 HIS 0.013 0.001 HIS z 161 PHE 0.018 0.001 PHE e 306 TYR 0.013 0.001 TYR E 420 ARG 0.008 0.000 ARG E 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 510 time to evaluate : 5.997 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7715 (t70) cc_final: 0.7160 (t0) REVERT: A 48 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8401 (p0) REVERT: A 171 MET cc_start: 0.8473 (ttp) cc_final: 0.8181 (ttm) REVERT: A 246 MET cc_start: 0.9081 (mmm) cc_final: 0.8745 (mmp) REVERT: A 358 ASP cc_start: 0.7994 (OUTLIER) cc_final: 0.7777 (m-30) REVERT: A 359 ASP cc_start: 0.7773 (t0) cc_final: 0.7476 (t0) REVERT: A 382 ASP cc_start: 0.8540 (OUTLIER) cc_final: 0.8171 (m-30) REVERT: D 63 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8175 (t0) REVERT: D 257 LYS cc_start: 0.9132 (tttt) cc_final: 0.8917 (ttmt) REVERT: D 320 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8566 (mtp) REVERT: E 4 MET cc_start: 0.3022 (ptt) cc_final: 0.2342 (tmm) REVERT: E 196 VAL cc_start: 0.8901 (OUTLIER) cc_final: 0.8693 (m) REVERT: H 7 ILE cc_start: 0.9049 (tp) cc_final: 0.8758 (tt) REVERT: H 293 LEU cc_start: 0.9179 (mt) cc_final: 0.8880 (mt) REVERT: Z 244 VAL cc_start: 0.9127 (OUTLIER) cc_final: 0.8861 (t) REVERT: Z 496 ASP cc_start: 0.7753 (t70) cc_final: 0.7306 (t0) REVERT: a 51 ASP cc_start: 0.8060 (m-30) cc_final: 0.7843 (m-30) REVERT: e 93 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8030 (mm-30) REVERT: e 212 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7244 (tt0) REVERT: g 46 MET cc_start: 0.9084 (mmm) cc_final: 0.8834 (mmm) REVERT: h 7 ILE cc_start: 0.8777 (OUTLIER) cc_final: 0.8419 (pp) REVERT: h 356 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7772 (mm-30) REVERT: h 401 LYS cc_start: 0.8608 (tppt) cc_final: 0.8194 (pptt) REVERT: q 319 TRP cc_start: 0.7970 (m-90) cc_final: 0.7685 (m-90) REVERT: P 183 ILE cc_start: 0.6744 (mm) cc_final: 0.6526 (mp) REVERT: P 184 MET cc_start: 0.6249 (mpp) cc_final: 0.5951 (mmt) REVERT: P 202 MET cc_start: 0.8693 (ptp) cc_final: 0.8409 (ptp) REVERT: N 225 GLU cc_start: 0.8661 (tp30) cc_final: 0.8183 (mm-30) REVERT: N 288 ARG cc_start: 0.7749 (ttm-80) cc_final: 0.7060 (ttm110) REVERT: N 290 TYR cc_start: 0.7745 (t80) cc_final: 0.7334 (t80) REVERT: N 307 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8039 (tp) REVERT: N 333 PHE cc_start: 0.8498 (m-10) cc_final: 0.7864 (m-10) outliers start: 80 outliers final: 25 residues processed: 546 average time/residue: 1.4990 time to fit residues: 1072.6833 Evaluate side-chains 529 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 493 time to evaluate : 5.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain Q residue 473 GLU Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain Z residue 404 ASP Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain e residue 212 GLU Chi-restraints excluded: chain g residue 255 ASP Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 227 MET Chi-restraints excluded: chain h residue 356 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain N residue 305 CYS Chi-restraints excluded: chain N residue 307 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 789 optimal weight: 0.9990 chunk 600 optimal weight: 10.0000 chunk 414 optimal weight: 6.9990 chunk 88 optimal weight: 0.0170 chunk 381 optimal weight: 1.9990 chunk 536 optimal weight: 5.9990 chunk 801 optimal weight: 5.9990 chunk 848 optimal weight: 30.0000 chunk 418 optimal weight: 3.9990 chunk 759 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 overall best weight: 2.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 23 ASN ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 103 ASN ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 481 ASN h 501 ASN z 161 HIS P 199 ASN N 231 GLN N 275 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 69054 Z= 0.198 Angle : 0.520 8.416 93225 Z= 0.256 Chirality : 0.041 0.223 11085 Planarity : 0.003 0.069 11897 Dihedral : 7.046 173.686 9578 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.08 % Allowed : 10.36 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.09), residues: 8805 helix: 1.99 (0.08), residues: 4426 sheet: 0.10 (0.16), residues: 1165 loop : -0.54 (0.11), residues: 3214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 435 HIS 0.013 0.001 HIS z 161 PHE 0.035 0.001 PHE P 158 TYR 0.020 0.001 TYR z 351 ARG 0.012 0.000 ARG z 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 526 time to evaluate : 5.985 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.7564 (OUTLIER) cc_final: 0.6743 (tmt) REVERT: A 47 ASP cc_start: 0.7710 (t70) cc_final: 0.7255 (t0) REVERT: A 171 MET cc_start: 0.8436 (ttp) cc_final: 0.8225 (ttm) REVERT: A 358 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7710 (m-30) REVERT: A 359 ASP cc_start: 0.7748 (t0) cc_final: 0.7448 (t0) REVERT: A 382 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.8156 (m-30) REVERT: B 49 ASP cc_start: 0.7788 (m-30) cc_final: 0.7561 (m-30) REVERT: D 257 LYS cc_start: 0.9123 (tttt) cc_final: 0.8914 (ttmt) REVERT: D 320 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8514 (mtp) REVERT: E 4 MET cc_start: 0.3097 (ptt) cc_final: 0.2388 (tmm) REVERT: E 196 VAL cc_start: 0.8886 (OUTLIER) cc_final: 0.8667 (m) REVERT: E 288 MET cc_start: 0.8976 (ptp) cc_final: 0.8734 (ptp) REVERT: H 7 ILE cc_start: 0.9041 (tp) cc_final: 0.8759 (tt) REVERT: H 293 LEU cc_start: 0.9177 (mt) cc_final: 0.8861 (mt) REVERT: Z 244 VAL cc_start: 0.9123 (OUTLIER) cc_final: 0.8857 (t) REVERT: Z 496 ASP cc_start: 0.7770 (t70) cc_final: 0.7332 (t0) REVERT: a 51 ASP cc_start: 0.8093 (m-30) cc_final: 0.7883 (m-30) REVERT: e 93 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8017 (mm-30) REVERT: h 7 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8417 (pp) REVERT: h 401 LYS cc_start: 0.8560 (tppt) cc_final: 0.8160 (pptt) REVERT: q 319 TRP cc_start: 0.7943 (m-90) cc_final: 0.7662 (m-90) REVERT: P 184 MET cc_start: 0.6584 (mpp) cc_final: 0.6294 (mmt) REVERT: P 202 MET cc_start: 0.8610 (ptp) cc_final: 0.8280 (ptt) REVERT: P 260 PHE cc_start: 0.6279 (p90) cc_final: 0.5767 (p90) REVERT: N 225 GLU cc_start: 0.8621 (tp30) cc_final: 0.8194 (mm-30) REVERT: N 288 ARG cc_start: 0.7769 (ttm-80) cc_final: 0.7153 (ttm110) REVERT: N 333 PHE cc_start: 0.8506 (m-10) cc_final: 0.8038 (m-10) outliers start: 80 outliers final: 29 residues processed: 563 average time/residue: 1.4662 time to fit residues: 1083.0863 Evaluate side-chains 528 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 492 time to evaluate : 5.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain b residue 445 MET Chi-restraints excluded: chain e residue 371 MET Chi-restraints excluded: chain e residue 485 MET Chi-restraints excluded: chain e residue 501 MET Chi-restraints excluded: chain g residue 255 ASP Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 227 MET Chi-restraints excluded: chain h residue 482 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain N residue 305 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 706 optimal weight: 0.6980 chunk 481 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 631 optimal weight: 6.9990 chunk 350 optimal weight: 6.9990 chunk 724 optimal weight: 3.9990 chunk 586 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 433 optimal weight: 0.9980 chunk 761 optimal weight: 10.0000 chunk 214 optimal weight: 10.0000 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 23 ASN ** Z 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 103 ASN ** e 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS P 199 ASN N 275 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 69054 Z= 0.224 Angle : 0.529 9.437 93225 Z= 0.259 Chirality : 0.041 0.162 11085 Planarity : 0.003 0.051 11897 Dihedral : 6.919 172.634 9578 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.15 % Allowed : 11.27 % Favored : 87.58 % 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: 1.22 (0.09), residues: 8805 helix: 1.99 (0.08), residues: 4424 sheet: 0.07 (0.16), residues: 1171 loop : -0.54 (0.11), residues: 3210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP z 495 HIS 0.008 0.001 HIS z 161 PHE 0.021 0.001 PHE P 136 TYR 0.013 0.001 TYR N 347 ARG 0.011 0.000 ARG E 201 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 514 time to evaluate : 6.110 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.7610 (OUTLIER) cc_final: 0.6833 (tmt) REVERT: A 47 ASP cc_start: 0.7749 (t70) cc_final: 0.7206 (t0) REVERT: A 246 MET cc_start: 0.9051 (mmm) cc_final: 0.8719 (mmp) REVERT: A 358 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7705 (m-30) REVERT: A 359 ASP cc_start: 0.7753 (t0) cc_final: 0.7461 (t0) REVERT: A 382 ASP cc_start: 0.8509 (OUTLIER) cc_final: 0.8146 (m-30) REVERT: D 257 LYS cc_start: 0.9127 (tttt) cc_final: 0.8922 (ttmt) REVERT: D 320 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8555 (mtp) REVERT: E 4 MET cc_start: 0.2941 (ptt) cc_final: 0.2255 (tmm) REVERT: E 196 VAL cc_start: 0.8847 (OUTLIER) cc_final: 0.8619 (m) REVERT: E 288 MET cc_start: 0.8995 (ptp) cc_final: 0.8747 (ptp) REVERT: E 443 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8556 (tp) REVERT: G 527 LYS cc_start: 0.8854 (tppt) cc_final: 0.8498 (tttm) REVERT: H 7 ILE cc_start: 0.9070 (tp) cc_final: 0.8783 (tt) REVERT: H 293 LEU cc_start: 0.9172 (mt) cc_final: 0.8858 (mt) REVERT: Z 244 VAL cc_start: 0.9103 (OUTLIER) cc_final: 0.8839 (t) REVERT: Z 496 ASP cc_start: 0.7741 (t70) cc_final: 0.7297 (t0) REVERT: e 93 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8014 (mm-30) REVERT: e 212 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.7291 (tt0) REVERT: h 7 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8433 (pp) REVERT: h 356 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7735 (mm-30) REVERT: h 401 LYS cc_start: 0.8564 (tppt) cc_final: 0.8171 (pptt) REVERT: P 184 MET cc_start: 0.6287 (mpp) cc_final: 0.5954 (mmt) REVERT: P 202 MET cc_start: 0.8585 (ptp) cc_final: 0.8311 (ptt) REVERT: P 260 PHE cc_start: 0.6344 (p90) cc_final: 0.5824 (p90) REVERT: N 225 GLU cc_start: 0.8625 (tp30) cc_final: 0.8210 (mm-30) REVERT: N 307 LEU cc_start: 0.8486 (tp) cc_final: 0.8184 (tp) REVERT: N 333 PHE cc_start: 0.8490 (m-10) cc_final: 0.8131 (m-10) outliers start: 85 outliers final: 35 residues processed: 565 average time/residue: 1.4611 time to fit residues: 1088.6467 Evaluate side-chains 538 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 493 time to evaluate : 5.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain Z residue 404 ASP Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 346 CYS Chi-restraints excluded: chain e residue 212 GLU Chi-restraints excluded: chain e residue 371 MET Chi-restraints excluded: chain e residue 485 MET Chi-restraints excluded: chain e residue 501 MET Chi-restraints excluded: chain g residue 255 ASP Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 227 MET Chi-restraints excluded: chain h residue 356 GLU Chi-restraints excluded: chain h residue 482 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain N residue 250 THR Chi-restraints excluded: chain N residue 305 CYS Chi-restraints excluded: chain N residue 340 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 285 optimal weight: 8.9990 chunk 764 optimal weight: 10.0000 chunk 167 optimal weight: 8.9990 chunk 498 optimal weight: 0.7980 chunk 209 optimal weight: 1.9990 chunk 849 optimal weight: 20.0000 chunk 705 optimal weight: 7.9990 chunk 393 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 281 optimal weight: 6.9990 chunk 445 optimal weight: 0.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 103 ASN ** e 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 501 ASN z 115 HIS P 199 ASN N 275 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.0956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 69054 Z= 0.226 Angle : 0.534 15.447 93225 Z= 0.260 Chirality : 0.041 0.162 11085 Planarity : 0.003 0.071 11897 Dihedral : 6.837 170.525 9578 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.16 % Allowed : 11.97 % Favored : 86.87 % 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: 8805 helix: 2.00 (0.08), residues: 4420 sheet: 0.06 (0.16), residues: 1181 loop : -0.53 (0.11), residues: 3204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP z 495 HIS 0.004 0.001 HIS D 347 PHE 0.037 0.001 PHE P 158 TYR 0.024 0.001 TYR z 351 ARG 0.016 0.000 ARG z 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 516 time to evaluate : 6.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.6883 (tmt) REVERT: A 47 ASP cc_start: 0.7685 (t70) cc_final: 0.7194 (t0) REVERT: A 246 MET cc_start: 0.9091 (mmm) cc_final: 0.8756 (mmp) REVERT: A 358 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7787 (m-30) REVERT: A 359 ASP cc_start: 0.7821 (t0) cc_final: 0.7527 (t0) REVERT: A 382 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8117 (m-30) REVERT: D 63 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8142 (t0) REVERT: D 257 LYS cc_start: 0.9127 (tttt) cc_final: 0.8923 (ttmt) REVERT: D 320 MET cc_start: 0.8876 (OUTLIER) cc_final: 0.8556 (mtp) REVERT: E 4 MET cc_start: 0.2933 (ptt) cc_final: 0.2263 (tmm) REVERT: E 288 MET cc_start: 0.8993 (ptp) cc_final: 0.8738 (ptp) REVERT: E 443 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8531 (tp) REVERT: G 52 ASP cc_start: 0.8313 (t70) cc_final: 0.8083 (t0) REVERT: G 527 LYS cc_start: 0.8855 (tppt) cc_final: 0.8497 (tttm) REVERT: H 7 ILE cc_start: 0.9047 (tp) cc_final: 0.8767 (tt) REVERT: H 293 LEU cc_start: 0.9176 (mt) cc_final: 0.8862 (mt) REVERT: Q 17 GLU cc_start: 0.8152 (pm20) cc_final: 0.7873 (tm-30) REVERT: Z 244 VAL cc_start: 0.9105 (OUTLIER) cc_final: 0.8835 (t) REVERT: Z 496 ASP cc_start: 0.7742 (t70) cc_final: 0.7289 (t0) REVERT: e 93 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8008 (mm-30) REVERT: e 212 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7298 (tt0) REVERT: h 401 LYS cc_start: 0.8548 (tppt) cc_final: 0.8143 (pptt) REVERT: z 359 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8170 (tppp) REVERT: P 184 MET cc_start: 0.6077 (tpp) cc_final: 0.5840 (mmt) REVERT: P 202 MET cc_start: 0.8554 (ptp) cc_final: 0.8256 (ptt) REVERT: P 260 PHE cc_start: 0.6331 (p90) cc_final: 0.5663 (p90) REVERT: N 225 GLU cc_start: 0.8624 (tp30) cc_final: 0.8214 (mm-30) REVERT: N 307 LEU cc_start: 0.8421 (tp) cc_final: 0.8107 (tp) REVERT: N 333 PHE cc_start: 0.8479 (m-10) cc_final: 0.8170 (m-10) outliers start: 86 outliers final: 42 residues processed: 564 average time/residue: 1.4988 time to fit residues: 1109.8522 Evaluate side-chains 543 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 492 time to evaluate : 5.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain Z residue 404 ASP Chi-restraints excluded: chain a residue 49 ILE Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 346 CYS Chi-restraints excluded: chain b residue 445 MET Chi-restraints excluded: chain d residue 186 MET Chi-restraints excluded: chain e residue 212 GLU Chi-restraints excluded: chain e residue 371 MET Chi-restraints excluded: chain e residue 485 MET Chi-restraints excluded: chain e residue 501 MET Chi-restraints excluded: chain g residue 255 ASP Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 227 MET Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain z residue 70 GLN Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 359 LYS Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain N residue 194 HIS Chi-restraints excluded: chain N residue 250 THR Chi-restraints excluded: chain N residue 305 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 819 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 484 optimal weight: 1.9990 chunk 620 optimal weight: 6.9990 chunk 480 optimal weight: 8.9990 chunk 715 optimal weight: 0.9990 chunk 474 optimal weight: 6.9990 chunk 846 optimal weight: 9.9990 chunk 529 optimal weight: 6.9990 chunk 515 optimal weight: 0.9990 chunk 390 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 103 ASN ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 501 ASN z 161 HIS P 199 ASN N 275 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 69054 Z= 0.229 Angle : 0.535 13.271 93225 Z= 0.261 Chirality : 0.041 0.162 11085 Planarity : 0.003 0.053 11897 Dihedral : 6.779 168.265 9578 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.14 % Allowed : 12.46 % Favored : 86.41 % 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: 8805 helix: 2.00 (0.08), residues: 4417 sheet: 0.09 (0.16), residues: 1170 loop : -0.54 (0.11), residues: 3218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP z 495 HIS 0.006 0.001 HIS z 161 PHE 0.015 0.001 PHE P 228 TYR 0.026 0.001 TYR z 351 ARG 0.013 0.000 ARG E 201 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 501 time to evaluate : 6.082 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.6887 (tmt) REVERT: A 47 ASP cc_start: 0.7579 (t70) cc_final: 0.7131 (t0) REVERT: A 358 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7769 (m-30) REVERT: A 359 ASP cc_start: 0.7821 (t0) cc_final: 0.7531 (t0) REVERT: A 382 ASP cc_start: 0.8508 (OUTLIER) cc_final: 0.8127 (m-30) REVERT: B 244 MET cc_start: 0.9095 (mmm) cc_final: 0.8894 (mmm) REVERT: D 63 ASP cc_start: 0.8427 (OUTLIER) cc_final: 0.8148 (t0) REVERT: D 257 LYS cc_start: 0.9126 (tttt) cc_final: 0.8924 (ttmt) REVERT: D 320 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8531 (mtp) REVERT: E 4 MET cc_start: 0.2941 (ptt) cc_final: 0.2267 (tmm) REVERT: E 288 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8732 (ptp) REVERT: E 443 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8522 (tp) REVERT: G 345 THR cc_start: 0.9149 (OUTLIER) cc_final: 0.8856 (p) REVERT: G 527 LYS cc_start: 0.8850 (tppt) cc_final: 0.8482 (tttm) REVERT: H 293 LEU cc_start: 0.9179 (mt) cc_final: 0.8866 (mt) REVERT: Z 244 VAL cc_start: 0.9105 (OUTLIER) cc_final: 0.8841 (t) REVERT: Z 496 ASP cc_start: 0.7748 (t70) cc_final: 0.7291 (t0) REVERT: e 93 GLU cc_start: 0.8364 (mm-30) cc_final: 0.8027 (mm-30) REVERT: h 53 ARG cc_start: 0.8461 (OUTLIER) cc_final: 0.7877 (mpp-170) REVERT: h 401 LYS cc_start: 0.8549 (tppt) cc_final: 0.8145 (pptt) REVERT: z 270 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.6544 (mtp180) REVERT: z 359 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8241 (ttmp) REVERT: P 184 MET cc_start: 0.6204 (tpp) cc_final: 0.5906 (mmt) REVERT: P 202 MET cc_start: 0.8537 (ptp) cc_final: 0.8238 (ptt) REVERT: P 260 PHE cc_start: 0.6370 (p90) cc_final: 0.5682 (p90) REVERT: N 225 GLU cc_start: 0.8622 (tp30) cc_final: 0.8215 (mm-30) REVERT: N 307 LEU cc_start: 0.8392 (tp) cc_final: 0.8084 (tp) REVERT: N 333 PHE cc_start: 0.8452 (m-10) cc_final: 0.8134 (m-10) outliers start: 84 outliers final: 48 residues processed: 549 average time/residue: 1.5348 time to fit residues: 1115.8653 Evaluate side-chains 549 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 489 time to evaluate : 5.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain Q residue 473 GLU Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain Z residue 286 ASP Chi-restraints excluded: chain Z residue 404 ASP Chi-restraints excluded: chain a residue 49 ILE Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain a residue 182 THR Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 346 CYS Chi-restraints excluded: chain b residue 445 MET Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 186 MET Chi-restraints excluded: chain e residue 371 MET Chi-restraints excluded: chain e residue 485 MET Chi-restraints excluded: chain e residue 501 MET Chi-restraints excluded: chain g residue 255 ASP Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 53 ARG Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 227 MET Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain z residue 70 GLN Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 270 ARG Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 359 LYS Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain N residue 250 THR Chi-restraints excluded: chain N residue 305 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 523 optimal weight: 1.9990 chunk 337 optimal weight: 8.9990 chunk 505 optimal weight: 7.9990 chunk 254 optimal weight: 0.9990 chunk 166 optimal weight: 9.9990 chunk 163 optimal weight: 3.9990 chunk 538 optimal weight: 0.9980 chunk 576 optimal weight: 5.9990 chunk 418 optimal weight: 5.9990 chunk 78 optimal weight: 0.0270 chunk 665 optimal weight: 7.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 103 ASN ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 426 ASN ** e 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS P 199 ASN N 275 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 69054 Z= 0.178 Angle : 0.527 12.573 93225 Z= 0.255 Chirality : 0.040 0.164 11085 Planarity : 0.003 0.083 11897 Dihedral : 6.650 166.297 9578 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.95 % Allowed : 12.93 % Favored : 86.12 % 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: 1.30 (0.09), residues: 8805 helix: 2.05 (0.08), residues: 4410 sheet: 0.17 (0.16), residues: 1157 loop : -0.51 (0.11), residues: 3238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 266 HIS 0.006 0.001 HIS z 161 PHE 0.042 0.001 PHE P 158 TYR 0.025 0.001 TYR z 351 ARG 0.020 0.000 ARG z 15 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 521 time to evaluate : 6.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7554 (t70) cc_final: 0.7107 (t0) REVERT: A 246 MET cc_start: 0.9018 (mmm) cc_final: 0.8734 (mmp) REVERT: A 358 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7682 (m-30) REVERT: A 359 ASP cc_start: 0.7820 (t0) cc_final: 0.7531 (t0) REVERT: A 382 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.8090 (m-30) REVERT: B 221 ASP cc_start: 0.8412 (t0) cc_final: 0.7820 (t0) REVERT: D 63 ASP cc_start: 0.8414 (OUTLIER) cc_final: 0.8129 (t0) REVERT: D 320 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8533 (mtp) REVERT: E 4 MET cc_start: 0.2932 (ptt) cc_final: 0.2265 (tmm) REVERT: E 288 MET cc_start: 0.8988 (OUTLIER) cc_final: 0.8737 (ptp) REVERT: E 443 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8534 (tp) REVERT: G 52 ASP cc_start: 0.8293 (t70) cc_final: 0.8062 (t0) REVERT: G 251 GLU cc_start: 0.8700 (mp0) cc_final: 0.8375 (mp0) REVERT: G 345 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8809 (p) REVERT: G 527 LYS cc_start: 0.8838 (tppt) cc_final: 0.8468 (tttm) REVERT: H 7 ILE cc_start: 0.8984 (tp) cc_final: 0.8754 (tt) REVERT: H 293 LEU cc_start: 0.9170 (mt) cc_final: 0.8847 (mt) REVERT: Q 17 GLU cc_start: 0.8163 (pm20) cc_final: 0.7821 (tm-30) REVERT: Z 244 VAL cc_start: 0.9120 (OUTLIER) cc_final: 0.8861 (t) REVERT: Z 496 ASP cc_start: 0.7726 (t70) cc_final: 0.7277 (t0) REVERT: e 84 ASP cc_start: 0.8604 (m-30) cc_final: 0.8355 (m-30) REVERT: e 93 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8021 (mm-30) REVERT: g 437 TYR cc_start: 0.8910 (t80) cc_final: 0.8657 (t80) REVERT: h 401 LYS cc_start: 0.8528 (tppt) cc_final: 0.8055 (pptt) REVERT: z 124 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7522 (mm-30) REVERT: z 359 LYS cc_start: 0.8634 (OUTLIER) cc_final: 0.8302 (ttmp) REVERT: P 184 MET cc_start: 0.6073 (tpp) cc_final: 0.5838 (mmt) REVERT: P 202 MET cc_start: 0.8541 (ptp) cc_final: 0.8232 (ptt) REVERT: P 260 PHE cc_start: 0.6470 (p90) cc_final: 0.5776 (p90) REVERT: N 225 GLU cc_start: 0.8615 (tp30) cc_final: 0.8207 (mm-30) REVERT: N 307 LEU cc_start: 0.8329 (tp) cc_final: 0.8037 (tp) REVERT: N 333 PHE cc_start: 0.8430 (m-10) cc_final: 0.8085 (m-10) outliers start: 70 outliers final: 36 residues processed: 560 average time/residue: 1.4640 time to fit residues: 1085.0436 Evaluate side-chains 547 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 502 time to evaluate : 5.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain B residue 495 GLU Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain Z residue 404 ASP Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 171 MET Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 346 CYS Chi-restraints excluded: chain b residue 445 MET Chi-restraints excluded: chain e residue 371 MET Chi-restraints excluded: chain e residue 485 MET Chi-restraints excluded: chain e residue 501 MET Chi-restraints excluded: chain g residue 255 ASP Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 227 MET Chi-restraints excluded: chain z residue 70 GLN Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 359 LYS Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain N residue 250 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 769 optimal weight: 0.1980 chunk 810 optimal weight: 10.0000 chunk 739 optimal weight: 8.9990 chunk 788 optimal weight: 10.0000 chunk 474 optimal weight: 7.9990 chunk 343 optimal weight: 2.9990 chunk 619 optimal weight: 0.0770 chunk 242 optimal weight: 0.9990 chunk 712 optimal weight: 8.9990 chunk 745 optimal weight: 7.9990 chunk 785 optimal weight: 1.9990 overall best weight: 1.2544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 501 ASN P 199 ASN N 275 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 69054 Z= 0.159 Angle : 0.524 12.295 93225 Z= 0.254 Chirality : 0.040 0.164 11085 Planarity : 0.003 0.049 11897 Dihedral : 6.483 165.258 9578 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.81 % Allowed : 13.47 % Favored : 85.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.09), residues: 8805 helix: 2.11 (0.08), residues: 4402 sheet: 0.20 (0.16), residues: 1161 loop : -0.49 (0.11), residues: 3242 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP g 496 HIS 0.003 0.001 HIS N 236 PHE 0.014 0.001 PHE P 260 TYR 0.025 0.001 TYR z 351 ARG 0.011 0.000 ARG E 201 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 523 time to evaluate : 6.243 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7493 (t70) cc_final: 0.7079 (t0) REVERT: A 358 ASP cc_start: 0.7958 (OUTLIER) cc_final: 0.7675 (m-30) REVERT: A 359 ASP cc_start: 0.7816 (t0) cc_final: 0.7522 (t0) REVERT: A 382 ASP cc_start: 0.8465 (OUTLIER) cc_final: 0.8084 (m-30) REVERT: B 49 ASP cc_start: 0.7764 (m-30) cc_final: 0.7537 (m-30) REVERT: D 63 ASP cc_start: 0.8352 (OUTLIER) cc_final: 0.8061 (t0) REVERT: D 320 MET cc_start: 0.8849 (OUTLIER) cc_final: 0.8544 (mtp) REVERT: E 4 MET cc_start: 0.2936 (ptt) cc_final: 0.2266 (tmm) REVERT: E 288 MET cc_start: 0.8987 (OUTLIER) cc_final: 0.8749 (ptp) REVERT: G 52 ASP cc_start: 0.8231 (t70) cc_final: 0.7980 (t0) REVERT: G 198 TYR cc_start: 0.9325 (m-80) cc_final: 0.9061 (m-80) REVERT: G 251 GLU cc_start: 0.8686 (mp0) cc_final: 0.8374 (mp0) REVERT: G 345 THR cc_start: 0.9091 (OUTLIER) cc_final: 0.8752 (p) REVERT: G 527 LYS cc_start: 0.8854 (tppt) cc_final: 0.8488 (tttm) REVERT: H 7 ILE cc_start: 0.8971 (tp) cc_final: 0.8728 (tt) REVERT: H 293 LEU cc_start: 0.9142 (mt) cc_final: 0.8789 (mt) REVERT: Q 17 GLU cc_start: 0.8140 (pm20) cc_final: 0.7770 (tm-30) REVERT: Z 244 VAL cc_start: 0.9097 (OUTLIER) cc_final: 0.8844 (t) REVERT: Z 496 ASP cc_start: 0.7726 (t70) cc_final: 0.7285 (t0) REVERT: e 29 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6980 (mtt) REVERT: e 84 ASP cc_start: 0.8612 (m-30) cc_final: 0.8354 (m-30) REVERT: e 93 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8008 (mm-30) REVERT: g 437 TYR cc_start: 0.8878 (t80) cc_final: 0.8606 (t80) REVERT: q 92 MET cc_start: 0.9270 (tpp) cc_final: 0.8999 (tpt) REVERT: z 124 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7536 (mm-30) REVERT: z 270 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.6577 (mtp180) REVERT: z 359 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8331 (ttmp) REVERT: P 184 MET cc_start: 0.6004 (tpp) cc_final: 0.5745 (mmt) REVERT: P 202 MET cc_start: 0.8485 (ptp) cc_final: 0.8169 (ptt) REVERT: P 260 PHE cc_start: 0.6460 (p90) cc_final: 0.5742 (p90) REVERT: N 225 GLU cc_start: 0.8610 (tp30) cc_final: 0.8214 (mm-30) REVERT: N 307 LEU cc_start: 0.8283 (tp) cc_final: 0.8030 (tp) REVERT: N 333 PHE cc_start: 0.8408 (m-10) cc_final: 0.8039 (m-10) outliers start: 60 outliers final: 37 residues processed: 559 average time/residue: 1.4775 time to fit residues: 1094.8774 Evaluate side-chains 554 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 507 time to evaluate : 5.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Q residue 473 GLU Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain Z residue 404 ASP Chi-restraints excluded: chain a residue 49 ILE Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 346 CYS Chi-restraints excluded: chain d residue 186 MET Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 485 MET Chi-restraints excluded: chain e residue 501 MET Chi-restraints excluded: chain g residue 255 ASP Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 227 MET Chi-restraints excluded: chain q residue 266 MET Chi-restraints excluded: chain z residue 70 GLN Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 270 ARG Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 359 LYS Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain N residue 250 THR Chi-restraints excluded: chain N residue 340 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 517 optimal weight: 8.9990 chunk 833 optimal weight: 4.9990 chunk 508 optimal weight: 6.9990 chunk 395 optimal weight: 0.9980 chunk 579 optimal weight: 10.0000 chunk 874 optimal weight: 8.9990 chunk 805 optimal weight: 4.9990 chunk 696 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 538 optimal weight: 0.9990 chunk 427 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 103 ASN ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 501 ASN P 199 ASN N 275 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 69054 Z= 0.260 Angle : 0.566 15.573 93225 Z= 0.273 Chirality : 0.042 0.180 11085 Planarity : 0.004 0.093 11897 Dihedral : 6.485 168.381 9578 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.74 % Allowed : 13.66 % Favored : 85.60 % 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: 1.27 (0.09), residues: 8805 helix: 2.02 (0.08), residues: 4412 sheet: 0.14 (0.16), residues: 1177 loop : -0.53 (0.11), residues: 3216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP e 304 HIS 0.004 0.001 HIS D 347 PHE 0.045 0.001 PHE P 158 TYR 0.026 0.001 TYR z 351 ARG 0.021 0.000 ARG z 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17610 Ramachandran restraints generated. 8805 Oldfield, 0 Emsley, 8805 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 504 time to evaluate : 6.071 Fit side-chains REVERT: A 47 ASP cc_start: 0.7591 (t70) cc_final: 0.7133 (t0) REVERT: A 358 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7760 (m-30) REVERT: A 359 ASP cc_start: 0.7840 (t0) cc_final: 0.7556 (t0) REVERT: A 382 ASP cc_start: 0.8510 (OUTLIER) cc_final: 0.8110 (m-30) REVERT: D 63 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8151 (t0) REVERT: D 320 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8549 (mtp) REVERT: E 4 MET cc_start: 0.2945 (ptt) cc_final: 0.2276 (tmm) REVERT: E 288 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8756 (ptp) REVERT: G 251 GLU cc_start: 0.8698 (mp0) cc_final: 0.8365 (mp0) REVERT: G 345 THR cc_start: 0.9155 (OUTLIER) cc_final: 0.8837 (p) REVERT: G 527 LYS cc_start: 0.8870 (tppt) cc_final: 0.8502 (tttm) REVERT: H 7 ILE cc_start: 0.8987 (tp) cc_final: 0.8730 (tt) REVERT: H 293 LEU cc_start: 0.9183 (mt) cc_final: 0.8864 (mt) REVERT: Z 244 VAL cc_start: 0.9113 (OUTLIER) cc_final: 0.8848 (t) REVERT: Z 496 ASP cc_start: 0.7755 (t70) cc_final: 0.7289 (t0) REVERT: d 496 ARG cc_start: 0.8136 (tmm160) cc_final: 0.7919 (tmm-80) REVERT: e 84 ASP cc_start: 0.8610 (m-30) cc_final: 0.8362 (m-30) REVERT: e 93 GLU cc_start: 0.8362 (mm-30) cc_final: 0.8024 (mm-30) REVERT: z 124 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7579 (mm-30) REVERT: z 270 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.6704 (mtp180) REVERT: z 359 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8330 (ttmp) REVERT: P 173 MET cc_start: 0.6705 (tmt) cc_final: 0.6272 (ppp) REVERT: P 184 MET cc_start: 0.6107 (tpp) cc_final: 0.5859 (mmt) REVERT: P 202 MET cc_start: 0.8509 (ptp) cc_final: 0.8180 (ptt) REVERT: P 260 PHE cc_start: 0.6463 (p90) cc_final: 0.6125 (p90) REVERT: N 225 GLU cc_start: 0.8627 (tp30) cc_final: 0.8237 (mm-30) REVERT: N 288 ARG cc_start: 0.7589 (ttm170) cc_final: 0.7249 (ttm-80) REVERT: N 307 LEU cc_start: 0.8356 (tp) cc_final: 0.8060 (tp) REVERT: N 333 PHE cc_start: 0.8426 (m-10) cc_final: 0.8057 (m-10) outliers start: 55 outliers final: 38 residues processed: 540 average time/residue: 1.4850 time to fit residues: 1059.8362 Evaluate side-chains 541 residues out of total 7392 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 494 time to evaluate : 5.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 371 CYS Chi-restraints excluded: chain D residue 63 ASP Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain E residue 231 ASP Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Q residue 473 GLU Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain Z residue 404 ASP Chi-restraints excluded: chain a residue 49 ILE Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain b residue 6 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 346 CYS Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 485 MET Chi-restraints excluded: chain e residue 501 MET Chi-restraints excluded: chain g residue 255 ASP Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 227 MET Chi-restraints excluded: chain z residue 70 GLN Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 270 ARG Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 359 LYS Chi-restraints excluded: chain P residue 145 MET Chi-restraints excluded: chain P residue 183 ILE Chi-restraints excluded: chain P residue 198 MET Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain N residue 250 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 878 random chunks: chunk 553 optimal weight: 0.9990 chunk 741 optimal weight: 1.9990 chunk 213 optimal weight: 6.9990 chunk 642 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 193 optimal weight: 0.2980 chunk 697 optimal weight: 0.9990 chunk 291 optimal weight: 2.9990 chunk 716 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 103 ASN ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 501 ASN z 161 HIS P 199 ASN N 275 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.082012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.066462 restraints weight = 172505.566| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.89 r_work: 0.2686 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 69054 Z= 0.151 Angle : 0.536 14.991 93225 Z= 0.258 Chirality : 0.040 0.166 11085 Planarity : 0.003 0.056 11897 Dihedral : 6.332 165.693 9578 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.72 % Allowed : 13.86 % Favored : 85.42 % 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: 1.35 (0.09), residues: 8805 helix: 2.08 (0.08), residues: 4410 sheet: 0.20 (0.16), residues: 1176 loop : -0.48 (0.11), residues: 3219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP g 496 HIS 0.007 0.001 HIS z 161 PHE 0.039 0.001 PHE P 158 TYR 0.025 0.001 TYR z 351 ARG 0.013 0.000 ARG z 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17275.94 seconds wall clock time: 303 minutes 8.44 seconds (18188.44 seconds total)