Starting phenix.real_space_refine on Fri Mar 15 02:14:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shp_40491/03_2024/8shp_40491_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shp_40491/03_2024/8shp_40491.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/8shp_40491/03_2024/8shp_40491.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shp_40491/03_2024/8shp_40491.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shp_40491/03_2024/8shp_40491_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shp_40491/03_2024/8shp_40491_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= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Al 16 5.89 5 P 32 5.49 5 Mg 16 5.21 5 S 423 5.16 5 C 42515 2.51 5 N 11828 2.21 5 O 13171 1.98 5 F 48 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "N PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A ASP 529": "OD1" <-> "OD2" Residue "B TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 63": "OD1" <-> "OD2" Residue "D ASP 327": "OD1" <-> "OD2" Residue "D GLU 429": "OE1" <-> "OE2" Residue "E TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 532": "OD1" <-> "OD2" Residue "G GLU 293": "OE1" <-> "OE2" Residue "H GLU 243": "OE1" <-> "OE2" Residue "H ASP 251": "OD1" <-> "OD2" Residue "Q GLU 38": "OE1" <-> "OE2" Residue "Q PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 86": "OD1" <-> "OD2" Residue "Z GLU 201": "OE1" <-> "OE2" Residue "Z PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 51": "OD1" <-> "OD2" Residue "a TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 529": "OD1" <-> "OD2" Residue "b GLU 509": "OE1" <-> "OE2" Residue "e ASP 23": "OD1" <-> "OD2" Residue "e PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 110": "OE1" <-> "OE2" Residue "g TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 358": "OE1" <-> "OE2" Residue "P ASP 65": "OD1" <-> "OD2" Residue "P PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 68049 Number of models: 1 Model: "" Number of chains: 50 Chain: "N" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1408 Classifications: {'peptide': 186} Link IDs: {'PTRANS': 3, 'TRANS': 182} Chain breaks: 1 Chain: "A" Number of atoms: 4069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4069 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 14, 'TRANS': 521} Chain: "B" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3952 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 10, 'TRANS': 515} Chain: "D" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3923 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "E" Number of atoms: 4132 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} Conformer: "C" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} bond proxies already assigned to first conformer: 4158 Chain: "G" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4089 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "H" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4054 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 16, 'TRANS': 511} Chain: "Q" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4086 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 18, 'TRANS': 519} Chain: "Z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "a" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4041 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Chain: "b" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3943 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 10, 'TRANS': 514} Chain: "d" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3917 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 4169 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} Conformer: "B" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} bond proxies already assigned to first conformer: 4195 Chain: "g" Number of atoms: 4088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4088 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "h" Number of atoms: 4032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4032 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 16, 'TRANS': 508} Chain: "q" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4053 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 16, 'TRANS': 516} Chain: "z" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4033 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 512} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "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: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N BPHE E 9 " occ=0.38 ... (20 atoms not shown) pdb=" CZ CPHE E 9 " occ=0.62 residue: pdb=" N APHE e 9 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE e 9 " occ=0.50 Time building chain proxies: 28.33, per 1000 atoms: 0.42 Number of scatterers: 68049 At special positions: 0 Unit cell: (181.976, 176.686, 180.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 423 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 13171 8.00 N 11828 7.00 C 42515 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 "HETATM67956 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67572 O3A ADP B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67700 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67636 O3A ADP E 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67828 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67604 O3A ADP D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67892 O3A ADP e 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: 21.37 Conformation dependent library (CDL) restraints added in 10.4 seconds 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16458 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 319 helices and 114 sheets defined 50.1% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.28 Creating SS restraints... Processing helix chain 'A' and resid 15 through 35 removed outlier: 3.683A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N SER A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 5.638A 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: 3.887A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 110 removed outlier: 3.675A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.641A 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: 4.418A pdb=" N ASP A 166 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 4.790A 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: 3.634A pdb=" N LEU A 260 " --> pdb=" O PRO A 257 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ASP A 261 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 5.036A 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: 4.782A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N SER A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 455 removed outlier: 3.805A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 5.139A 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: 3.943A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LYS A 484 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 3.831A 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 168 Processing helix chain 'B' and resid 171 through 190 removed outlier: 3.702A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS B 176 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N ASP B 177 " --> pdb=" O HIS B 174 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE B 179 " --> pdb=" O LYS B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 198 No H-bonds generated for 'chain 'B' and resid 196 through 198' Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 261 through 285 removed outlier: 3.979A pdb=" N HIS B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 317 through 327 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 380 through 402 Processing helix chain 'B' and resid 412 through 427 removed outlier: 3.801A 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: 3.639A 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: 4.445A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 5.578A 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 126 removed outlier: 4.114A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.945A 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: 3.703A 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: 3.921A pdb=" N THR D 293 " --> pdb=" O GLN D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 320 Processing helix chain 'D' and resid 330 through 340 removed outlier: 4.659A pdb=" N GLU D 334 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE D 340 " --> pdb=" O CYS D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 350 No H-bonds generated for 'chain 'D' and resid 348 through 350' Processing helix chain 'D' and resid 353 through 355 No H-bonds generated for 'chain 'D' and resid 353 through 355' Processing helix chain 'D' and resid 395 through 417 Processing helix chain 'D' and resid 427 through 441 Processing helix chain 'D' and resid 446 through 469 removed outlier: 4.026A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL D 460 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ILE D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) Proline residue: D 462 - end of helix Processing helix chain 'D' and resid 473 through 485 Processing helix chain 'D' and resid 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: 3.600A pdb=" N LEU E 34 " --> pdb=" O GLY E 30 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR E 50 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 5.045A 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: 3.830A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.564A 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: 4.654A pdb=" N SER E 175 " --> pdb=" O THR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 180 removed outlier: 3.916A pdb=" N SER E 180 " --> pdb=" O VAL E 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 177 through 180' Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 219 through 221 No H-bonds generated for 'chain 'E' and resid 219 through 221' Processing helix chain 'E' and resid 271 through 295 removed outlier: 3.826A pdb=" N THR E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 316 Processing helix chain 'E' and resid 327 through 337 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 392 through 414 Processing helix chain 'E' and resid 424 through 439 removed outlier: 3.951A pdb=" N LYS E 439 " --> pdb=" O GLN E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 466 removed outlier: 3.942A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL E 457 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N ILE E 458 " --> pdb=" O ALA E 454 " (cutoff:3.500A) Proline residue: E 459 - end of helix Processing helix chain 'E' and resid 470 through 483 Processing helix chain 'E' and resid 501 through 504 No H-bonds generated for 'chain 'E' and resid 501 through 504' Processing helix chain 'E' and resid 510 through 529 Processing helix chain 'G' and resid 19 through 40 removed outlier: 3.706A pdb=" N ARG G 38 " --> pdb=" O ASP G 35 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N THR G 39 " --> pdb=" O ILE G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 68 Processing helix chain 'G' and resid 75 through 90 Processing helix chain 'G' and resid 95 through 115 removed outlier: 3.755A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ILE G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 140 Processing helix chain 'G' and resid 149 through 160 Processing helix chain 'G' and resid 164 through 183 removed outlier: 4.218A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) removed outlier: 5.542A 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: 4.322A pdb=" N LEU G 285 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 307 removed outlier: 3.683A pdb=" N ALA G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 317 through 327 Processing helix chain 'G' and resid 335 through 337 No H-bonds generated for 'chain 'G' and resid 335 through 337' Processing helix chain 'G' and resid 381 through 403 Processing helix chain 'G' and resid 413 through 428 removed outlier: 4.174A pdb=" N ALA G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 455 removed outlier: 3.552A pdb=" N TRP G 435 " --> pdb=" O VAL G 432 " (cutoff:3.500A) Proline residue: G 436 - end of helix removed outlier: 4.021A pdb=" N ILE G 447 " --> pdb=" O LEU G 444 " (cutoff:3.500A) Proline residue: G 448 - end of helix Processing helix chain 'G' and resid 459 through 471 Processing helix chain 'G' and resid 490 through 493 No H-bonds generated for 'chain 'G' and resid 490 through 493' Processing helix chain 'G' and resid 499 through 517 Processing helix chain 'H' and resid 19 through 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: 3.638A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 113 removed outlier: 4.117A 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: 3.694A 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: 3.529A 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 379 through 401 Processing helix chain 'H' and resid 411 through 426 removed outlier: 4.019A pdb=" N THR H 426 " --> pdb=" O ASP H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 453 removed outlier: 3.986A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE H 444 " --> pdb=" O LYS H 440 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N ILE H 445 " --> pdb=" O ALA H 441 " (cutoff:3.500A) Proline residue: H 446 - end of helix Processing helix chain 'H' and resid 457 through 470 Processing helix chain 'H' and resid 496 through 515 Processing helix chain 'Q' and resid 11 through 14 No H-bonds generated for 'chain 'Q' and resid 11 through 14' Processing helix chain 'Q' and resid 25 through 46 removed outlier: 4.378A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ALA Q 46 " --> pdb=" O THR Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 75 Processing helix chain 'Q' and resid 81 through 96 Processing helix chain 'Q' and resid 101 through 121 Processing helix chain 'Q' and resid 125 through 146 Proline residue: Q 144 - end of helix Processing helix chain 'Q' and resid 158 through 167 removed outlier: 4.338A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.199A 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: 4.884A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) removed outlier: 3.780A 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: 3.811A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 456 removed outlier: 3.637A 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 519 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: 4.831A pdb=" N THR Z 36 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 5.035A 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: 3.611A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) removed outlier: 4.614A 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: 4.037A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 162 through 179 removed outlier: 3.672A pdb=" N GLU Z 170 " --> pdb=" O ASP Z 166 " (cutoff:3.500A) removed outlier: 3.521A 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 281 removed outlier: 4.061A pdb=" N ARG Z 264 " --> pdb=" O VAL Z 260 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N LYS Z 265 " --> pdb=" O LYS Z 261 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N PHE Z 266 " --> pdb=" O ALA Z 262 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ILE Z 267 " --> pdb=" O GLU Z 263 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 299 through 308 removed outlier: 3.619A pdb=" N GLU Z 308 " --> pdb=" O ALA Z 304 " (cutoff:3.500A) Processing helix chain 'Z' and resid 318 through 327 removed outlier: 4.230A 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 454 removed outlier: 3.888A pdb=" N GLN Z 434 " --> pdb=" O GLY Z 431 " (cutoff:3.500A) removed outlier: 3.775A 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: 3.684A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N SER a 34 " --> pdb=" O ASN a 30 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N SER a 35 " --> pdb=" O ILE a 31 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 64 Processing helix chain 'a' and resid 70 through 85 Processing helix chain 'a' and resid 90 through 110 removed outlier: 3.870A pdb=" N VAL a 94 " --> pdb=" O THR a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 114 through 135 Processing helix chain 'a' and resid 144 through 156 Processing helix chain 'a' and resid 163 through 179 removed outlier: 4.037A pdb=" N ASP a 166 " --> pdb=" O ILE a 163 " (cutoff:3.500A) removed outlier: 4.565A 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: 4.568A pdb=" N ASP a 261 " --> pdb=" O GLU a 258 " (cutoff:3.500A) removed outlier: 4.865A 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: 4.389A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) Processing helix chain 'a' and resid 434 through 456 removed outlier: 3.719A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N VAL a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 5.202A 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: 3.815A pdb=" N TRP a 485 " --> pdb=" O ASN a 482 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 501 No H-bonds generated for 'chain 'a' and resid 498 through 501' Processing helix chain 'a' and resid 507 through 526 Processing helix chain 'b' and resid 21 through 39 Processing helix chain 'b' and resid 67 through 72 Processing helix chain 'b' and resid 79 through 94 Processing helix chain 'b' and resid 99 through 119 Processing helix chain 'b' and resid 123 through 144 Processing helix chain 'b' and resid 152 through 168 Processing helix chain 'b' and resid 171 through 190 removed outlier: 3.593A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS b 176 " --> pdb=" O THR b 173 " (cutoff:3.500A) removed outlier: 5.915A 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: 3.935A pdb=" N HIS b 285 " --> pdb=" O ARG b 281 " (cutoff:3.500A) Processing helix chain 'b' and resid 298 through 306 Processing helix chain 'b' and resid 317 through 327 Processing helix chain 'b' and resid 338 through 340 No H-bonds generated for 'chain 'b' and resid 338 through 340' Processing helix chain 'b' and resid 380 through 402 Processing helix chain 'b' and resid 412 through 426 Processing helix chain 'b' and resid 431 through 454 Proline residue: b 447 - end of helix removed outlier: 3.832A pdb=" N ALA b 454 " --> pdb=" O ILE b 450 " (cutoff:3.500A) Processing helix chain 'b' and resid 458 through 471 Processing helix chain 'b' and resid 488 through 491 No H-bonds generated for 'chain 'b' and resid 488 through 491' Processing helix chain 'b' and resid 497 through 515 Processing helix chain 'd' and resid 29 through 49 Processing helix chain 'd' and resid 74 through 80 Processing helix chain 'd' and resid 86 through 102 Processing helix chain 'd' and resid 106 through 125 removed outlier: 3.727A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 132 through 151 Processing helix chain 'd' and resid 160 through 173 removed outlier: 4.545A pdb=" N SER d 173 " --> pdb=" O THR d 169 " (cutoff:3.500A) Processing helix chain 'd' and resid 175 through 192 removed outlier: 4.170A pdb=" N GLN d 178 " --> pdb=" O VAL d 175 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N SER d 181 " --> pdb=" O GLN d 178 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LEU d 182 " --> pdb=" O TYR d 179 " (cutoff:3.500A) removed outlier: 5.172A 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: 3.726A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.830A 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: 4.423A pdb=" N GLU d 334 " --> pdb=" O GLU d 331 " (cutoff:3.500A) removed outlier: 3.923A 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: 3.618A pdb=" N THR d 442 " --> pdb=" O GLU d 438 " (cutoff:3.500A) Processing helix chain 'd' and resid 446 through 466 removed outlier: 4.031A pdb=" N VAL d 460 " --> pdb=" O ASP d 456 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N ILE d 461 " --> pdb=" O ALA d 457 " (cutoff:3.500A) Proline residue: d 462 - end of helix Processing helix chain 'd' and resid 473 through 486 Processing helix chain 'd' and resid 512 through 530 removed outlier: 4.947A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 50 removed outlier: 3.533A pdb=" N LEU e 34 " --> pdb=" O GLY e 30 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THR e 50 " --> pdb=" O ASN e 46 " (cutoff:3.500A) Processing helix chain 'e' and resid 74 through 80 Processing helix chain 'e' and resid 86 through 101 Processing helix chain 'e' and resid 106 through 126 removed outlier: 3.868A pdb=" N VAL e 110 " --> pdb=" O THR e 106 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN e 122 " --> pdb=" O GLU e 118 " (cutoff:3.500A) removed outlier: 3.679A 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: 4.780A pdb=" N SER e 175 " --> pdb=" O THR e 171 " (cutoff:3.500A) Processing helix chain 'e' and resid 177 through 195 removed outlier: 3.881A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG e 183 " --> pdb=" O SER e 180 " (cutoff:3.500A) Processing helix chain 'e' and resid 206 through 208 No H-bonds generated for 'chain 'e' and resid 206 through 208' Processing helix chain 'e' and resid 219 through 221 No H-bonds generated for 'chain 'e' and resid 219 through 221' Processing helix chain 'e' and resid 271 through 294 Processing helix chain 'e' and resid 308 through 316 Processing helix chain 'e' and resid 327 through 337 Processing helix chain 'e' and resid 345 through 347 No H-bonds generated for 'chain 'e' and resid 345 through 347' Processing helix chain 'e' and resid 350 through 352 No H-bonds generated for 'chain 'e' and resid 350 through 352' Processing helix chain 'e' and resid 392 through 414 Processing helix chain 'e' and resid 424 through 439 removed outlier: 3.893A pdb=" N LYS e 439 " --> pdb=" O GLN e 435 " (cutoff:3.500A) Processing helix chain 'e' and resid 442 through 465 removed outlier: 3.840A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL e 457 " --> pdb=" O ASP e 453 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N ILE e 458 " --> pdb=" O ALA e 454 " (cutoff:3.500A) Proline residue: e 459 - end of helix Processing helix chain 'e' and resid 470 through 483 Processing helix chain 'e' and resid 501 through 504 No H-bonds generated for 'chain 'e' and resid 501 through 504' Processing helix chain 'e' and resid 510 through 528 Processing helix chain 'g' and resid 20 through 40 removed outlier: 3.899A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N THR g 39 " --> pdb=" O ASP g 35 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N CYS g 40 " --> pdb=" O ILE g 36 " (cutoff:3.500A) Processing helix chain 'g' and resid 63 through 68 Processing helix chain 'g' and resid 75 through 90 Processing helix chain 'g' and resid 95 through 114 removed outlier: 3.780A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE g 112 " --> pdb=" O VAL g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 119 through 140 Processing helix chain 'g' and resid 149 through 160 Processing helix chain 'g' and resid 164 through 167 removed outlier: 3.772A 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 263 through 285 removed outlier: 4.317A pdb=" N LEU g 285 " --> pdb=" O ASP g 281 " (cutoff:3.500A) Processing helix chain 'g' and resid 298 through 307 removed outlier: 3.697A 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: 3.633A pdb=" N LYS g 427 " --> pdb=" O THR g 423 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ALA g 428 " --> pdb=" O GLU g 424 " (cutoff:3.500A) Processing helix chain 'g' and resid 434 through 455 removed outlier: 3.927A pdb=" N LEU g 444 " --> pdb=" O VAL g 440 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU g 445 " --> pdb=" O ALA g 441 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL g 446 " --> pdb=" O GLN g 442 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ILE g 447 " --> pdb=" O ALA g 443 " (cutoff:3.500A) Proline residue: g 448 - end of helix Processing helix chain 'g' and resid 459 through 470 Processing helix chain 'g' and resid 490 through 493 No H-bonds generated for 'chain 'g' and resid 490 through 493' Processing helix chain 'g' and resid 499 through 518 Processing helix chain 'h' and resid 19 through 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: 3.522A pdb=" N GLU h 89 " --> pdb=" O GLN h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 96 through 113 Proline residue: h 110 - end of helix Processing helix chain 'h' and resid 118 through 139 Processing helix chain 'h' and resid 148 through 163 Processing helix chain 'h' and resid 172 through 185 removed outlier: 3.668A 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 260 through 284 removed outlier: 3.543A 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 379 through 401 Processing helix chain 'h' and resid 411 through 426 removed outlier: 4.131A pdb=" N THR h 426 " --> pdb=" O ASP h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 430 through 453 removed outlier: 4.089A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLU h 443 " --> pdb=" O ALA h 439 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE h 444 " --> pdb=" O LYS h 440 " (cutoff:3.500A) removed outlier: 5.360A 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: 4.158A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ALA q 46 " --> pdb=" O THR q 42 " (cutoff:3.500A) Processing helix chain 'q' and resid 69 through 75 Processing helix chain 'q' and resid 81 through 96 Processing helix chain 'q' and resid 101 through 121 Processing helix chain 'q' and resid 125 through 146 Proline residue: q 144 - end of helix Processing helix chain 'q' and resid 158 through 169 removed outlier: 4.156A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.255A 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: 4.758A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) removed outlier: 3.822A 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: 3.696A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 456 removed outlier: 3.633A 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 3 through 7 removed outlier: 3.766A pdb=" N LEU z 7 " --> pdb=" O ALA z 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'z' and resid 3 through 7' Processing helix chain 'z' and resid 17 through 37 removed outlier: 4.828A pdb=" N THR z 36 " --> pdb=" O ASP z 32 " (cutoff:3.500A) removed outlier: 4.979A 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: 3.627A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLU z 112 " --> pdb=" O LEU z 108 " (cutoff:3.500A) Processing helix chain 'z' and resid 116 through 137 Processing helix chain 'z' and resid 145 through 159 removed outlier: 3.987A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 162 through 179 removed outlier: 3.660A 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 253 through 262 Processing helix chain 'z' and resid 265 through 281 removed outlier: 3.687A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 299 through 308 removed outlier: 3.935A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 318 through 327 removed outlier: 4.208A 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: 3.675A pdb=" N ILE z 447 " --> pdb=" O LEU z 444 " (cutoff:3.500A) Proline residue: z 448 - end of helix Processing helix chain 'z' and resid 459 through 473 Processing helix chain 'z' and resid 489 through 492 No H-bonds generated for 'chain 'z' and resid 489 through 492' Processing helix chain 'z' and resid 498 through 516 Processing helix chain 'P' and resid 63 through 87 removed outlier: 3.817A pdb=" N LEU P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU P 85 " --> pdb=" O CYS P 81 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ARG P 86 " --> pdb=" O ARG P 82 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU P 87 " --> pdb=" O GLU P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 137 through 139 No H-bonds generated for 'chain 'P' and resid 137 through 139' Processing helix chain 'P' and resid 141 through 150 removed outlier: 4.426A pdb=" N MET P 145 " --> pdb=" O ARG P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 175 removed outlier: 3.617A pdb=" N ILE P 174 " --> pdb=" O PHE P 170 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 208 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 269 Processing sheet with id= A, first strand: chain 'N' and resid 200 through 203 removed outlier: 3.977A pdb=" N ALA N 200 " --> pdb=" O ALA N 213 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASP N 223 " --> pdb=" O LEU N 229 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LEU N 229 " --> pdb=" O ASP N 223 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'N' and resid 263 through 265 Processing sheet with id= C, first strand: chain 'N' and resid 284 through 289 removed outlier: 6.556A pdb=" N GLY N 299 " --> pdb=" O ASN N 285 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL N 287 " --> pdb=" O ALA N 297 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA N 297 " --> pdb=" O VAL N 287 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N TYR N 289 " --> pdb=" O ALA N 295 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA N 295 " --> pdb=" O TYR N 289 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N CYS N 305 " --> pdb=" O TYR N 319 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA N 317 " --> pdb=" O LEU N 307 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ASP N 309 " --> pdb=" O GLU N 315 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU N 315 " --> pdb=" O ASP N 309 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'N' and resid 348 through 353 removed outlier: 3.976A pdb=" N THR N 348 " --> pdb=" O TYR N 344 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 9 through 13 Processing sheet with id= F, first strand: chain 'A' and resid 43 through 46 Processing sheet with id= G, first strand: chain 'A' and resid 180 through 182 removed outlier: 3.537A pdb=" N TYR A 181 " --> pdb=" O ARG A 189 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG A 189 " --> pdb=" O TYR A 181 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'A' and resid 196 through 199 Processing sheet with id= I, first strand: chain 'A' and resid 213 through 216 removed outlier: 3.502A pdb=" N GLU A 350 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 346 through 348 removed outlier: 6.446A pdb=" N VAL A 285 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU A 237 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N LEU A 287 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N MET A 306 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N THR A 288 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL A 308 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 408 through 410 Processing sheet with id= L, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.504A pdb=" N LYS A 494 " --> pdb=" O ASP A 489 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 17 through 19 Processing sheet with id= N, first strand: chain 'B' and resid 50 through 53 Processing sheet with id= O, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.329A pdb=" N CYS B 371 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ILE B 202 " --> pdb=" O CYS B 371 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE B 373 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LYS B 204 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU B 375 " --> pdb=" O LYS B 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'B' and resid 218 through 220 Processing sheet with id= Q, first strand: chain 'B' and resid 344 through 346 removed outlier: 3.528A pdb=" N CYS B 346 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N CYS B 289 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ALA B 240 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE B 291 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N MET B 310 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASN B 292 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE B 312 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 406 through 408 Processing sheet with id= S, first strand: chain 'B' and resid 476 through 479 removed outlier: 3.507A pdb=" N THR B 484 " --> pdb=" O ASP B 479 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 59 through 62 Processing sheet with id= U, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.872A pdb=" N VAL D 386 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N VAL D 211 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE D 388 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LYS D 213 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL D 390 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 227 through 229 Processing sheet with id= W, first strand: chain 'D' and resid 357 through 359 removed outlier: 6.595A pdb=" N VAL D 297 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N ILE D 249 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU D 299 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N MET D 323 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N ILE D 300 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE D 325 " --> pdb=" O ILE D 300 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 421 through 423 Processing sheet with id= Y, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.613A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 59 through 62 Processing sheet with id= AA, first strand: chain 'E' and resid 209 through 215 removed outlier: 6.892A pdb=" N VAL E 383 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N GLU E 212 " --> pdb=" O VAL E 383 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ILE E 385 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LYS E 214 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ILE E 387 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 228 through 230 removed outlier: 3.554A pdb=" N LEU E 358 " --> pdb=" O GLU E 375 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 354 through 356 removed outlier: 6.976A pdb=" N LEU E 299 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU E 251 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ILE E 301 " --> pdb=" O LEU E 251 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N CYS E 302 " --> pdb=" O PRO E 320 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL E 322 " --> pdb=" O CYS E 302 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 418 through 420 Processing sheet with id= AE, first strand: chain 'G' and resid 48 through 51 Processing sheet with id= AF, first strand: chain 'G' and resid 185 through 187 Processing sheet with id= AG, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.494A pdb=" N CYS G 372 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLU G 202 " --> pdb=" O CYS G 372 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ILE G 374 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ILE G 204 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU G 376 " --> pdb=" O ILE G 204 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N THR G 373 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 238 through 241 removed outlier: 6.506A pdb=" N VAL G 289 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N LEU G 241 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE G 291 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR G 310 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N THR G 292 " --> pdb=" O THR G 310 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE G 312 " --> pdb=" O THR G 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'G' and resid 351 through 355 Processing sheet with id= AJ, first strand: chain 'G' and resid 407 through 409 Processing sheet with id= AK, first strand: chain 'G' and resid 478 through 480 Processing sheet with id= AL, first strand: chain 'H' and resid 14 through 17 Processing sheet with id= AM, first strand: chain 'H' and resid 47 through 50 Processing sheet with id= AN, first strand: chain 'H' and resid 195 through 201 removed outlier: 6.507A pdb=" N CYS H 370 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N LYS H 198 " --> pdb=" O CYS H 370 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N PHE H 372 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL H 200 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N LEU H 374 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'H' and resid 214 through 217 Processing sheet with id= AP, first strand: chain 'H' and resid 237 through 240 removed outlier: 6.842A pdb=" N VAL H 288 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N LEU H 240 " --> pdb=" O VAL H 288 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU H 290 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N PHE H 309 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 8.414A pdb=" N SER H 291 " --> pdb=" O PHE H 309 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA H 311 " --> pdb=" O SER H 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'H' and resid 405 through 407 Processing sheet with id= AR, first strand: chain 'H' and resid 475 through 478 Processing sheet with id= AS, first strand: chain 'Q' and resid 20 through 23 Processing sheet with id= AT, first strand: chain 'Q' and resid 54 through 57 Processing sheet with id= AU, first strand: chain 'Q' and resid 202 through 206 removed outlier: 6.563A pdb=" N SER Q 373 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N CYS Q 205 " --> pdb=" O SER Q 373 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ILE Q 375 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'Q' and resid 220 through 223 Processing sheet with id= AW, first strand: chain 'Q' and resid 240 through 242 removed outlier: 6.125A pdb=" N MET Q 311 " --> pdb=" O VAL Q 291 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N THR Q 293 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL Q 313 " --> pdb=" O THR Q 293 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'Q' and resid 498 through 500 removed outlier: 3.969A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N VAL Q 147 " --> pdb=" O PRO Q 410 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id= AZ, first strand: chain 'Z' and resid 12 through 15 Processing sheet with id= BA, first strand: chain 'Z' and resid 45 through 48 Processing sheet with id= BB, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.816A pdb=" N VAL Z 372 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N MET Z 194 " --> pdb=" O VAL Z 372 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU Z 374 " --> pdb=" O MET Z 194 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N MET Z 196 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILE Z 376 " --> pdb=" O MET Z 196 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id= BD, first strand: chain 'Z' and resid 345 through 347 removed outlier: 6.452A pdb=" N VAL Z 311 " --> pdb=" O VAL Z 291 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ASN Z 293 " --> pdb=" O VAL Z 311 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU Z 313 " --> pdb=" O ASN Z 293 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'Z' and resid 407 through 409 Processing sheet with id= BF, first strand: chain 'Z' and resid 477 through 479 removed outlier: 3.636A pdb=" N MET Z 487 " --> pdb=" O GLY Z 478 " (cutoff:3.500A) Processing sheet with id= BG, first strand: chain 'a' and resid 9 through 13 Processing sheet with id= BH, first strand: chain 'a' and resid 43 through 46 Processing sheet with id= BI, first strand: chain 'a' and resid 180 through 182 Processing sheet with id= BJ, first strand: chain 'a' and resid 196 through 201 removed outlier: 3.798A pdb=" N GLY a 379 " --> pdb=" O ALA a 200 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'a' and resid 213 through 216 Processing sheet with id= BL, first strand: chain 'a' and resid 346 through 348 removed outlier: 6.622A pdb=" N VAL a 285 " --> pdb=" O ALA a 235 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N LEU a 237 " --> pdb=" O VAL a 285 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU a 287 " --> pdb=" O LEU a 237 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N MET a 306 " --> pdb=" O ILE a 286 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N THR a 288 " --> pdb=" O MET a 306 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL a 308 " --> pdb=" O THR a 288 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'a' and resid 408 through 410 Processing sheet with id= BN, first strand: chain 'a' and resid 486 through 489 removed outlier: 3.526A pdb=" N LYS a 494 " --> pdb=" O ASP a 489 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'b' and resid 17 through 19 Processing sheet with id= BP, first strand: chain 'b' and resid 50 through 53 Processing sheet with id= BQ, first strand: chain 'b' and resid 199 through 205 removed outlier: 6.315A pdb=" N CYS b 371 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N ILE b 202 " --> pdb=" O CYS b 371 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE b 373 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N LYS b 204 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LEU b 375 " --> pdb=" O LYS b 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= BQ Processing sheet with id= BR, first strand: chain 'b' and resid 218 through 220 Processing sheet with id= BS, first strand: chain 'b' and resid 344 through 346 removed outlier: 6.980A pdb=" N CYS b 289 " --> pdb=" O LEU b 238 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N ALA b 240 " --> pdb=" O CYS b 289 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE b 291 " --> pdb=" O ALA b 240 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N MET b 310 " --> pdb=" O PHE b 290 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N ASN b 292 " --> pdb=" O MET b 310 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE b 312 " --> pdb=" O ASN b 292 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'b' and resid 406 through 408 Processing sheet with id= BU, first strand: chain 'b' and resid 476 through 479 Processing sheet with id= BV, first strand: chain 'd' and resid 59 through 62 Processing sheet with id= BW, first strand: chain 'd' and resid 208 through 214 removed outlier: 6.637A pdb=" N VAL d 386 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N VAL d 211 " --> pdb=" O VAL d 386 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE d 388 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LYS d 213 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL d 390 " --> pdb=" O LYS d 213 " (cutoff:3.500A) No H-bonds generated for sheet with id= BW Processing sheet with id= BX, first strand: chain 'd' and resid 227 through 229 Processing sheet with id= BY, first strand: chain 'd' and resid 357 through 359 removed outlier: 6.471A pdb=" N VAL d 297 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ILE d 249 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU d 299 " --> pdb=" O ILE d 249 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N MET d 323 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE d 300 " --> pdb=" O MET d 323 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE d 325 " --> pdb=" O ILE d 300 " (cutoff:3.500A) Processing sheet with id= BZ, first strand: chain 'd' and resid 421 through 423 Processing sheet with id= CA, first strand: chain 'd' and resid 491 through 494 Processing sheet with id= CB, first strand: chain 'e' and resid 26 through 29 Processing sheet with id= CC, first strand: chain 'e' and resid 59 through 62 Processing sheet with id= CD, first strand: chain 'e' and resid 209 through 215 removed outlier: 7.128A pdb=" N VAL e 383 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N GLU e 212 " --> pdb=" O VAL e 383 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N ILE e 385 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N LYS e 214 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ILE e 387 " --> pdb=" O LYS e 214 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'e' and resid 228 through 230 Processing sheet with id= CF, first strand: chain 'e' and resid 354 through 356 removed outlier: 7.176A pdb=" N LEU e 299 " --> pdb=" O ALA e 249 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LEU e 251 " --> pdb=" O LEU e 299 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILE e 301 " --> pdb=" O LEU e 251 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N CYS e 302 " --> pdb=" O PRO e 320 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL e 322 " --> pdb=" O CYS e 302 " (cutoff:3.500A) Processing sheet with id= CG, first strand: chain 'e' and resid 418 through 420 Processing sheet with id= CH, first strand: chain 'g' and resid 15 through 18 Processing sheet with id= CI, first strand: chain 'g' and resid 48 through 51 Processing sheet with id= CJ, first strand: chain 'g' and resid 185 through 187 Processing sheet with id= CK, first strand: chain 'g' and resid 200 through 205 removed outlier: 3.953A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) Processing sheet with id= CL, first strand: chain 'g' and resid 218 through 220 Processing sheet with id= CM, first strand: chain 'g' and resid 238 through 241 removed outlier: 6.360A pdb=" N VAL g 289 " --> pdb=" O VAL g 239 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N LEU g 241 " --> pdb=" O VAL g 289 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE g 291 " --> pdb=" O LEU g 241 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N THR g 310 " --> pdb=" O VAL g 290 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N THR g 292 " --> pdb=" O THR g 310 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE g 312 " --> pdb=" O THR g 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= CM Processing sheet with id= CN, first strand: chain 'g' and resid 407 through 409 Processing sheet with id= CO, first strand: chain 'g' and resid 478 through 481 removed outlier: 3.582A pdb=" N VAL g 488 " --> pdb=" O GLY g 479 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR g 486 " --> pdb=" O ASN g 481 " (cutoff:3.500A) Processing sheet with id= CP, first strand: chain 'h' and resid 14 through 17 Processing sheet with id= CQ, first strand: chain 'h' and resid 47 through 50 Processing sheet with id= CR, first strand: chain 'h' and resid 195 through 201 removed outlier: 6.594A pdb=" N CYS h 370 " --> pdb=" O GLY h 196 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LYS h 198 " --> pdb=" O CYS h 370 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N PHE h 372 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL h 200 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N LEU h 374 " --> pdb=" O VAL h 200 " (cutoff:3.500A) Processing sheet with id= CS, first strand: chain 'h' and resid 214 through 217 Processing sheet with id= CT, first strand: chain 'h' and resid 237 through 240 removed outlier: 7.053A pdb=" N VAL h 288 " --> pdb=" O ALA h 238 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU h 240 " --> pdb=" O VAL h 288 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LEU h 290 " --> pdb=" O LEU h 240 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N PHE h 309 " --> pdb=" O VAL h 289 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N SER h 291 " --> pdb=" O PHE h 309 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ALA h 311 " --> pdb=" O SER h 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= CT Processing sheet with id= CU, first strand: chain 'h' and resid 405 through 407 Processing sheet with id= CV, first strand: chain 'h' and resid 475 through 478 Processing sheet with id= CW, first strand: chain 'q' and resid 20 through 23 Processing sheet with id= CX, first strand: chain 'q' and resid 54 through 57 Processing sheet with id= CY, first strand: chain 'q' and resid 202 through 206 removed outlier: 6.593A pdb=" N SER q 373 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N CYS q 205 " --> pdb=" O SER q 373 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE q 375 " --> pdb=" O CYS q 205 " (cutoff:3.500A) Processing sheet with id= CZ, first strand: chain 'q' and resid 220 through 223 Processing sheet with id= DA, first strand: chain 'q' and resid 240 through 242 removed outlier: 6.163A pdb=" N MET q 311 " --> pdb=" O VAL q 291 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N THR q 293 " --> pdb=" O MET q 311 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL q 313 " --> pdb=" O THR q 293 " (cutoff:3.500A) Processing sheet with id= DB, first strand: chain 'q' and resid 498 through 500 removed outlier: 3.719A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N VAL q 147 " --> pdb=" O PRO q 410 " (cutoff:3.500A) Processing sheet with id= DC, first strand: chain 'q' and resid 478 through 480 Processing sheet with id= DD, 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= DE, first strand: chain 'z' and resid 45 through 48 Processing sheet with id= DF, first strand: chain 'z' and resid 191 through 196 removed outlier: 6.887A pdb=" N VAL z 372 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N MET z 194 " --> pdb=" O VAL z 372 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N LEU z 374 " --> pdb=" O MET z 194 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N MET z 196 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ILE z 376 " --> pdb=" O MET z 196 " (cutoff:3.500A) Processing sheet with id= DG, first strand: chain 'z' and resid 210 through 212 Processing sheet with id= DH, first strand: chain 'z' and resid 345 through 347 removed outlier: 6.751A pdb=" N GLY z 288 " --> pdb=" O TYR z 229 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N LEU z 231 " --> pdb=" O GLY z 288 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL z 290 " --> pdb=" O LEU z 231 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N CYS z 233 " --> pdb=" O VAL z 290 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ILE z 292 " --> pdb=" O CYS z 233 " (cutoff:3.500A) Processing sheet with id= DI, first strand: chain 'z' and resid 477 through 479 Processing sheet with id= DJ, first strand: chain 'P' and resid 162 through 164 removed outlier: 4.750A pdb=" N LYS P 218 " --> pdb=" O ILE P 164 " (cutoff:3.500A) 3477 hydrogen bonds defined for protein. 9303 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: 24.64 Time building geometry restraints manager: 23.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 22928 1.34 - 1.46: 12788 1.46 - 1.58: 32317 1.58 - 1.70: 48 1.70 - 1.82: 745 Bond restraints: 68826 Sorted by residual: bond pdb=" F2 AF3 g 603 " pdb="AL AF3 g 603 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" F2 AF3 z 603 " pdb="AL AF3 z 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.43e+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 6.36e+01 bond pdb=" F2 AF3 G 603 " pdb="AL AF3 G 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.33e+01 bond pdb=" F2 AF3 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 6.33e+01 ... (remaining 68821 not shown) Histogram of bond angle deviations from ideal: 93.41 - 102.03: 273 102.03 - 110.64: 22725 110.64 - 119.26: 36767 119.26 - 127.87: 32781 127.87 - 136.49: 375 Bond angle restraints: 92921 Sorted by residual: angle pdb=" N ILE P 245 " pdb=" CA ILE P 245 " pdb=" C ILE P 245 " ideal model delta sigma weight residual 113.42 108.57 4.85 1.17e+00 7.31e-01 1.72e+01 angle pdb=" CG MET h 497 " pdb=" SD MET h 497 " pdb=" CE MET h 497 " ideal model delta sigma weight residual 100.90 93.41 7.49 2.20e+00 2.07e-01 1.16e+01 angle pdb=" N ILE h 168 " pdb=" CA ILE h 168 " pdb=" C ILE h 168 " ideal model delta sigma weight residual 111.91 109.08 2.83 8.90e-01 1.26e+00 1.01e+01 angle pdb=" N GLU d 93 " pdb=" CA GLU d 93 " pdb=" CB GLU d 93 " ideal model delta sigma weight residual 110.39 115.58 -5.19 1.66e+00 3.63e-01 9.76e+00 angle pdb=" N GLY Q 209 " pdb=" CA GLY Q 209 " pdb=" C GLY Q 209 " ideal model delta sigma weight residual 113.18 120.45 -7.27 2.37e+00 1.78e-01 9.41e+00 ... (remaining 92916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.25: 41831 35.25 - 70.50: 616 70.50 - 105.75: 55 105.75 - 141.00: 11 141.00 - 176.25: 5 Dihedral angle restraints: 42518 sinusoidal: 17106 harmonic: 25412 Sorted by residual: dihedral pdb=" O2A ADP q 601 " pdb=" O3A ADP q 601 " pdb=" PA ADP q 601 " pdb=" PB ADP q 601 " ideal model delta sinusoidal sigma weight residual 300.00 123.75 176.25 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP z 601 " pdb=" O3A ADP z 601 " pdb=" PA ADP z 601 " pdb=" PB ADP z 601 " ideal model delta sinusoidal sigma weight residual -60.00 109.63 -169.63 1 2.00e+01 2.50e-03 4.76e+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 -60.00 109.53 -169.53 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 42515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 7500 0.035 - 0.069: 2417 0.069 - 0.104: 793 0.104 - 0.139: 331 0.139 - 0.174: 11 Chirality restraints: 11052 Sorted by residual: chirality pdb=" CB ILE G 460 " pdb=" CA ILE G 460 " pdb=" CG1 ILE G 460 " pdb=" CG2 ILE G 460 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.53e-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 2.59 -0.16 2.00e-01 2.50e+01 6.29e-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 -2.47 -0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 11049 not shown) Planarity restraints: 11863 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.034 5.00e-02 4.00e+02 5.19e-02 4.30e+00 pdb=" N PRO e 441 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 52 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO G 53 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU P 274 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.96e+00 pdb=" N PRO P 275 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO P 275 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO P 275 " 0.028 5.00e-02 4.00e+02 ... (remaining 11860 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 545 2.50 - 3.10: 50907 3.10 - 3.70: 105170 3.70 - 4.30: 153011 4.30 - 4.90: 259425 Nonbonded interactions: 569058 Sorted by model distance: nonbonded pdb="MG MG b 602 " pdb=" F1 AF3 b 603 " model vdw 1.905 2.120 nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.915 2.120 nonbonded pdb=" O1A ADP z 601 " pdb="MG MG z 602 " model vdw 1.919 2.170 nonbonded pdb="MG MG H 602 " pdb=" F2 AF3 H 603 " model vdw 1.928 2.120 nonbonded pdb="MG MG z 602 " pdb=" F1 AF3 z 603 " model vdw 1.934 2.120 ... (remaining 569053 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 535 or resid 601 through 603)) selection = chain 'a' } ncs_group { reference = (chain 'B' and (resid 2 through 526 or resid 601 through 603)) selection = chain 'b' } ncs_group { reference = (chain 'D' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 538 or resid 601 through 603)) selection = chain 'd' } ncs_group { reference = (chain 'E' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) selection = (chain 'e' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) } ncs_group { reference = (chain 'G' and (resid 5 through 528 or resid 601 through 603)) selection = (chain 'g' and (resid 5 through 528 or resid 601 through 603)) } ncs_group { reference = (chain 'H' and (resid 1 through 525 or resid 601 through 603)) selection = chain 'h' } ncs_group { reference = (chain 'Q' and (resid 2 through 534 or resid 601 through 603)) selection = chain 'q' } ncs_group { reference = chain 'Z' selection = (chain 'z' and (resid 2 through 526 or resid 601 through 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.080 Extract box with map and model: 8.280 Check model and map are aligned: 0.770 Set scattering table: 0.480 Process input model: 141.680 Find NCS groups from input model: 6.350 Set up NCS constraints: 0.560 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:8.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 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 : 0.005 0.161 68826 Z= 0.321 Angle : 0.548 8.143 92921 Z= 0.270 Chirality : 0.042 0.174 11052 Planarity : 0.003 0.052 11863 Dihedral : 14.051 176.251 26060 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.09), residues: 8784 helix: 2.35 (0.08), residues: 4417 sheet: 0.05 (0.16), residues: 1221 loop : -0.42 (0.11), residues: 3146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 304 HIS 0.012 0.001 HIS Z 161 PHE 0.026 0.001 PHE E 386 TYR 0.018 0.001 TYR G 437 ARG 0.005 0.000 ARG G 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 584 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 584 time to evaluate : 5.965 Fit side-chains revert: symmetry clash REVERT: N 333 PHE cc_start: 0.7069 (m-80) cc_final: 0.6724 (m-80) REVERT: N 352 TRP cc_start: 0.7299 (m100) cc_final: 0.6529 (m100) REVERT: A 51 ASP cc_start: 0.8356 (m-30) cc_final: 0.8119 (m-30) REVERT: D 355 MET cc_start: 0.9298 (mmt) cc_final: 0.9078 (mpp) REVERT: E 493 CYS cc_start: 0.8463 (m) cc_final: 0.8004 (m) REVERT: G 15 LYS cc_start: 0.9008 (mptt) cc_final: 0.8779 (mmtt) REVERT: H 14 ASP cc_start: 0.8168 (t70) cc_final: 0.7911 (t0) REVERT: H 308 MET cc_start: 0.8875 (mtt) cc_final: 0.8648 (mtt) REVERT: Q 61 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8592 (mt-10) REVERT: Z 196 MET cc_start: 0.8193 (mtt) cc_final: 0.7980 (mtm) REVERT: Z 430 LYS cc_start: 0.9051 (tmmt) cc_final: 0.8827 (tppt) REVERT: a 430 MET cc_start: 0.8208 (mmt) cc_final: 0.8001 (mpt) REVERT: d 93 GLU cc_start: 0.8423 (mp0) cc_final: 0.8011 (mp0) REVERT: d 279 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8369 (tm-30) REVERT: e 58 ASP cc_start: 0.8071 (m-30) cc_final: 0.7797 (m-30) REVERT: h 324 MET cc_start: 0.9205 (mmm) cc_final: 0.8936 (mmm) REVERT: z 66 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8323 (mm-30) REVERT: z 358 GLU cc_start: 0.7611 (pm20) cc_final: 0.7228 (pm20) REVERT: P 63 ILE cc_start: 0.9167 (tp) cc_final: 0.8861 (tp) REVERT: P 66 TRP cc_start: 0.7169 (t-100) cc_final: 0.6300 (t-100) REVERT: P 67 ARG cc_start: 0.8442 (mmp80) cc_final: 0.8017 (mmp80) REVERT: P 68 ARG cc_start: 0.7296 (tpm170) cc_final: 0.7086 (tpm170) REVERT: P 201 CYS cc_start: 0.8433 (m) cc_final: 0.8210 (m) outliers start: 0 outliers final: 3 residues processed: 584 average time/residue: 1.5975 time to fit residues: 1200.7596 Evaluate side-chains 475 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 472 time to evaluate : 5.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 GLU Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain G residue 519 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 738 optimal weight: 3.9990 chunk 663 optimal weight: 3.9990 chunk 368 optimal weight: 10.0000 chunk 226 optimal weight: 0.9990 chunk 447 optimal weight: 9.9990 chunk 354 optimal weight: 0.9990 chunk 685 optimal weight: 8.9990 chunk 265 optimal weight: 7.9990 chunk 417 optimal weight: 10.0000 chunk 510 optimal weight: 4.9990 chunk 794 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 169 ASN N 275 GLN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 GLN ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS Z 198 HIS ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 122 HIS ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 468 ASN ** g 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 95 ASN z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 80 GLN ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.0523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 68826 Z= 0.268 Angle : 0.559 9.047 92921 Z= 0.279 Chirality : 0.042 0.163 11052 Planarity : 0.004 0.049 11863 Dihedral : 7.704 178.678 9557 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.56 % Allowed : 6.20 % Favored : 93.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.09), residues: 8784 helix: 2.16 (0.08), residues: 4433 sheet: 0.04 (0.16), residues: 1193 loop : -0.44 (0.11), residues: 3158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 222 HIS 0.010 0.001 HIS z 161 PHE 0.019 0.001 PHE E 386 TYR 0.021 0.001 TYR N 290 ARG 0.006 0.000 ARG Z 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 493 time to evaluate : 6.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 350 ASN cc_start: 0.6632 (p0) cc_final: 0.5262 (p0) REVERT: A 47 ASP cc_start: 0.7802 (t0) cc_final: 0.7521 (OUTLIER) REVERT: A 51 ASP cc_start: 0.8365 (m-30) cc_final: 0.7946 (m-30) REVERT: E 48 MET cc_start: 0.9148 (tpp) cc_final: 0.8908 (mmm) REVERT: E 231 ASP cc_start: 0.8452 (t0) cc_final: 0.8163 (t0) REVERT: E 493 CYS cc_start: 0.8474 (m) cc_final: 0.8005 (m) REVERT: G 15 LYS cc_start: 0.9009 (mptt) cc_final: 0.8774 (mmtt) REVERT: G 152 MET cc_start: 0.9249 (mmm) cc_final: 0.9028 (mmm) REVERT: H 14 ASP cc_start: 0.8180 (t70) cc_final: 0.7932 (t0) REVERT: Q 61 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8738 (mt-10) REVERT: Z 196 MET cc_start: 0.8295 (mtt) cc_final: 0.8061 (mtm) REVERT: Z 286 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.7864 (t0) REVERT: Z 357 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.8016 (mm-30) REVERT: a 354 GLU cc_start: 0.7799 (tp30) cc_final: 0.7519 (tm-30) REVERT: a 430 MET cc_start: 0.8229 (mmt) cc_final: 0.8019 (mpt) REVERT: b 415 MET cc_start: 0.9300 (mmm) cc_final: 0.8980 (mmp) REVERT: d 93 GLU cc_start: 0.8413 (mp0) cc_final: 0.8008 (mp0) REVERT: d 279 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8289 (tm-30) REVERT: e 58 ASP cc_start: 0.8073 (m-30) cc_final: 0.7813 (m-30) REVERT: g 110 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8189 (tt0) REVERT: h 7 ILE cc_start: 0.8754 (OUTLIER) cc_final: 0.8362 (pp) REVERT: h 14 ASP cc_start: 0.8693 (t0) cc_final: 0.8487 (t0) REVERT: h 324 MET cc_start: 0.9170 (mmm) cc_final: 0.8876 (mmm) REVERT: z 66 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8333 (mm-30) REVERT: z 244 VAL cc_start: 0.8976 (OUTLIER) cc_final: 0.8735 (t) REVERT: z 358 GLU cc_start: 0.7491 (pm20) cc_final: 0.7175 (pm20) REVERT: P 63 ILE cc_start: 0.9171 (tp) cc_final: 0.8944 (tp) REVERT: P 66 TRP cc_start: 0.7255 (t-100) cc_final: 0.6572 (t-100) REVERT: P 67 ARG cc_start: 0.8534 (mmp80) cc_final: 0.8285 (mmp80) REVERT: P 149 ARG cc_start: 0.8639 (ptt-90) cc_final: 0.8353 (ptt-90) outliers start: 41 outliers final: 16 residues processed: 510 average time/residue: 1.5581 time to fit residues: 1032.5236 Evaluate side-chains 480 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 460 time to evaluate : 6.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 169 ASN Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 349 ILE Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain E residue 468 MET Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 318 LYS Chi-restraints excluded: chain Z residue 286 ASP Chi-restraints excluded: chain Z residue 357 GLU Chi-restraints excluded: chain a residue 392 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 118 ASP Chi-restraints excluded: chain d residue 458 MET Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 233 HIS Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 441 optimal weight: 0.0060 chunk 246 optimal weight: 0.0670 chunk 661 optimal weight: 5.9990 chunk 541 optimal weight: 1.9990 chunk 219 optimal weight: 0.9980 chunk 796 optimal weight: 0.5980 chunk 859 optimal weight: 20.0000 chunk 708 optimal weight: 8.9990 chunk 789 optimal weight: 5.9990 chunk 271 optimal weight: 2.9990 chunk 638 optimal weight: 1.9990 overall best weight: 0.7336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 275 GLN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 GLN ** D 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 227 ASN ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 468 ASN z 161 HIS P 80 GLN ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 68826 Z= 0.133 Angle : 0.511 10.311 92921 Z= 0.252 Chirality : 0.040 0.166 11052 Planarity : 0.003 0.048 11863 Dihedral : 7.215 179.930 9552 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.76 % Allowed : 7.73 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.09), residues: 8784 helix: 2.20 (0.08), residues: 4428 sheet: 0.04 (0.16), residues: 1166 loop : -0.42 (0.11), residues: 3190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 222 HIS 0.014 0.001 HIS z 161 PHE 0.038 0.001 PHE P 136 TYR 0.015 0.001 TYR N 174 ARG 0.009 0.000 ARG P 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 521 time to evaluate : 6.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7803 (t0) cc_final: 0.7513 (OUTLIER) REVERT: A 51 ASP cc_start: 0.8332 (m-30) cc_final: 0.7874 (m-30) REVERT: A 230 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.7785 (t) REVERT: A 294 ASP cc_start: 0.8277 (m-30) cc_final: 0.8072 (m-30) REVERT: B 20 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8025 (mmt-90) REVERT: E 48 MET cc_start: 0.9127 (tpp) cc_final: 0.8876 (mmm) REVERT: E 231 ASP cc_start: 0.8462 (t0) cc_final: 0.8222 (t0) REVERT: E 493 CYS cc_start: 0.8446 (m) cc_final: 0.7960 (m) REVERT: G 152 MET cc_start: 0.9224 (mmm) cc_final: 0.8955 (mmm) REVERT: H 14 ASP cc_start: 0.8165 (t70) cc_final: 0.7901 (t0) REVERT: H 524 ARG cc_start: 0.7250 (ttp80) cc_final: 0.6633 (ttp80) REVERT: Q 61 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8746 (mt-10) REVERT: Z 196 MET cc_start: 0.8006 (mtt) cc_final: 0.7790 (mtm) REVERT: Z 286 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.7804 (t0) REVERT: Z 357 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7972 (tp30) REVERT: Z 498 TYR cc_start: 0.8525 (t80) cc_final: 0.8035 (t80) REVERT: a 354 GLU cc_start: 0.7858 (tp30) cc_final: 0.7529 (tm-30) REVERT: a 430 MET cc_start: 0.8230 (mmt) cc_final: 0.7957 (mpt) REVERT: b 415 MET cc_start: 0.9385 (mmm) cc_final: 0.9088 (mmp) REVERT: d 93 GLU cc_start: 0.8401 (mp0) cc_final: 0.7959 (mp0) REVERT: d 279 GLU cc_start: 0.8681 (tm-30) cc_final: 0.8198 (tm-30) REVERT: d 446 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.7686 (mmm) REVERT: d 513 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8667 (tm) REVERT: e 58 ASP cc_start: 0.8106 (m-30) cc_final: 0.7815 (m-30) REVERT: e 118 GLU cc_start: 0.8519 (tt0) cc_final: 0.8180 (tm-30) REVERT: g 110 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8088 (tm-30) REVERT: h 7 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8288 (pp) REVERT: h 14 ASP cc_start: 0.8724 (t0) cc_final: 0.8471 (t0) REVERT: h 324 MET cc_start: 0.9179 (mmm) cc_final: 0.8878 (mmm) REVERT: q 169 MET cc_start: 0.8858 (ttp) cc_final: 0.8645 (ttp) REVERT: z 66 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8129 (mm-30) REVERT: z 358 GLU cc_start: 0.7401 (pm20) cc_final: 0.7134 (pm20) REVERT: P 63 ILE cc_start: 0.9170 (tp) cc_final: 0.8933 (tp) REVERT: P 66 TRP cc_start: 0.7251 (t-100) cc_final: 0.6658 (t-100) REVERT: P 77 ARG cc_start: 0.6973 (tmm160) cc_final: 0.5676 (ppt170) outliers start: 56 outliers final: 18 residues processed: 547 average time/residue: 1.5283 time to fit residues: 1093.8291 Evaluate side-chains 492 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 467 time to evaluate : 5.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 349 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 318 LYS Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 286 ASP Chi-restraints excluded: chain Z residue 357 GLU Chi-restraints excluded: chain a residue 392 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 118 ASP Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 233 HIS Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain h residue 482 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 786 optimal weight: 9.9990 chunk 598 optimal weight: 7.9990 chunk 413 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 379 optimal weight: 6.9990 chunk 534 optimal weight: 0.9990 chunk 798 optimal weight: 5.9990 chunk 845 optimal weight: 8.9990 chunk 417 optimal weight: 10.0000 chunk 757 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 391 HIS ** D 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 426 ASN e 122 GLN ** g 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 68826 Z= 0.426 Angle : 0.611 10.438 92921 Z= 0.302 Chirality : 0.044 0.166 11052 Planarity : 0.004 0.047 11863 Dihedral : 7.336 178.829 9550 Min Nonbonded Distance : 1.740 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.30 % Favored : 95.69 % Rotamer: Outliers : 1.07 % Allowed : 9.34 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.09), residues: 8784 helix: 2.04 (0.08), residues: 4442 sheet: -0.07 (0.15), residues: 1206 loop : -0.48 (0.11), residues: 3136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP P 66 HIS 0.013 0.001 HIS z 161 PHE 0.021 0.002 PHE E 386 TYR 0.027 0.002 TYR N 290 ARG 0.007 0.000 ARG P 230 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 475 time to evaluate : 5.921 Fit side-chains revert: symmetry clash REVERT: N 182 GLU cc_start: 0.8469 (tm-30) cc_final: 0.8047 (tm-30) REVERT: N 262 LYS cc_start: 0.7480 (mmtm) cc_final: 0.6888 (mmmt) REVERT: N 264 MET cc_start: 0.8082 (mtp) cc_final: 0.7806 (mtp) REVERT: A 47 ASP cc_start: 0.7999 (t0) cc_final: 0.7587 (OUTLIER) REVERT: A 51 ASP cc_start: 0.8397 (m-30) cc_final: 0.7902 (m-30) REVERT: A 230 VAL cc_start: 0.7881 (OUTLIER) cc_final: 0.7576 (t) REVERT: E 48 MET cc_start: 0.9145 (tpp) cc_final: 0.8896 (mmm) REVERT: E 474 MET cc_start: 0.8565 (tmt) cc_final: 0.8076 (tmm) REVERT: E 493 CYS cc_start: 0.8521 (m) cc_final: 0.8021 (m) REVERT: G 152 MET cc_start: 0.9277 (mmm) cc_final: 0.8950 (mmm) REVERT: H 14 ASP cc_start: 0.8186 (t70) cc_final: 0.7937 (t0) REVERT: Q 61 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8682 (mt-10) REVERT: Z 196 MET cc_start: 0.8335 (mtt) cc_final: 0.8128 (mtm) REVERT: Z 286 ASP cc_start: 0.8388 (OUTLIER) cc_final: 0.7967 (t0) REVERT: Z 357 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8018 (tp30) REVERT: a 354 GLU cc_start: 0.7874 (tp30) cc_final: 0.7544 (tm-30) REVERT: a 430 MET cc_start: 0.8334 (mmt) cc_final: 0.8033 (mpt) REVERT: b 415 MET cc_start: 0.9480 (mmm) cc_final: 0.9063 (mmp) REVERT: d 93 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8128 (mp0) REVERT: d 279 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8329 (tm-30) REVERT: d 513 LEU cc_start: 0.9033 (tt) cc_final: 0.8764 (tm) REVERT: e 58 ASP cc_start: 0.8128 (m-30) cc_final: 0.7831 (m-30) REVERT: g 110 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8265 (tt0) REVERT: h 7 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8305 (pp) REVERT: h 14 ASP cc_start: 0.8730 (t0) cc_final: 0.8505 (t0) REVERT: h 324 MET cc_start: 0.9197 (mmm) cc_final: 0.8914 (mmm) REVERT: h 350 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8313 (tt0) REVERT: z 66 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8410 (mm-30) REVERT: z 244 VAL cc_start: 0.8958 (OUTLIER) cc_final: 0.8698 (t) REVERT: z 358 GLU cc_start: 0.7398 (pm20) cc_final: 0.7134 (pm20) REVERT: P 77 ARG cc_start: 0.7014 (tmm160) cc_final: 0.6795 (tmm160) outliers start: 79 outliers final: 30 residues processed: 517 average time/residue: 1.4918 time to fit residues: 1014.2174 Evaluate side-chains 484 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 447 time to evaluate : 5.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 349 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain E residue 468 MET Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 221 MET Chi-restraints excluded: chain Q residue 318 LYS Chi-restraints excluded: chain Z residue 286 ASP Chi-restraints excluded: chain Z residue 357 GLU Chi-restraints excluded: chain a residue 7 VAL Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 392 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 93 GLU Chi-restraints excluded: chain d residue 118 ASP Chi-restraints excluded: chain d residue 320 MET Chi-restraints excluded: chain d residue 458 MET Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 149 VAL Chi-restraints excluded: chain h residue 233 HIS Chi-restraints excluded: chain h residue 350 GLU Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain h residue 482 GLU Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 704 optimal weight: 0.9990 chunk 480 optimal weight: 0.9990 chunk 12 optimal weight: 20.0000 chunk 629 optimal weight: 4.9990 chunk 348 optimal weight: 4.9990 chunk 721 optimal weight: 0.6980 chunk 584 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 431 optimal weight: 0.9990 chunk 759 optimal weight: 8.9990 chunk 213 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 275 GLN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 122 GLN z 161 HIS P 160 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.0930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 68826 Z= 0.151 Angle : 0.519 10.235 92921 Z= 0.256 Chirality : 0.040 0.168 11052 Planarity : 0.003 0.046 11863 Dihedral : 7.061 177.451 9550 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.43 % Favored : 96.56 % Rotamer: Outliers : 1.15 % Allowed : 10.11 % Favored : 88.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.09), residues: 8784 helix: 2.18 (0.08), residues: 4418 sheet: -0.03 (0.16), residues: 1176 loop : -0.42 (0.11), residues: 3190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 222 HIS 0.014 0.001 HIS z 161 PHE 0.043 0.001 PHE P 136 TYR 0.012 0.001 TYR E 420 ARG 0.007 0.000 ARG P 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 482 time to evaluate : 5.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 182 GLU cc_start: 0.8375 (tm-30) cc_final: 0.7911 (tm-30) REVERT: A 47 ASP cc_start: 0.7896 (t0) cc_final: 0.7558 (OUTLIER) REVERT: A 51 ASP cc_start: 0.8356 (m-30) cc_final: 0.7899 (m-30) REVERT: A 230 VAL cc_start: 0.8044 (OUTLIER) cc_final: 0.7755 (t) REVERT: B 20 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7968 (mmt-90) REVERT: E 48 MET cc_start: 0.9122 (tpp) cc_final: 0.8794 (mmm) REVERT: E 493 CYS cc_start: 0.8374 (m) cc_final: 0.7908 (m) REVERT: E 533 ILE cc_start: 0.9050 (mm) cc_final: 0.8839 (mm) REVERT: G 17 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7491 (mt-10) REVERT: G 152 MET cc_start: 0.9206 (mmm) cc_final: 0.8872 (mmm) REVERT: H 14 ASP cc_start: 0.8186 (t70) cc_final: 0.7931 (t0) REVERT: H 524 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6541 (ttp80) REVERT: Z 196 MET cc_start: 0.7992 (mtt) cc_final: 0.7785 (mtm) REVERT: Z 357 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7956 (tp30) REVERT: Z 498 TYR cc_start: 0.8617 (t80) cc_final: 0.8166 (t80) REVERT: a 15 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7886 (mt-10) REVERT: a 354 GLU cc_start: 0.7838 (tp30) cc_final: 0.7247 (tm-30) REVERT: a 430 MET cc_start: 0.8226 (mmt) cc_final: 0.7940 (mpt) REVERT: b 415 MET cc_start: 0.9499 (mmm) cc_final: 0.9096 (mmp) REVERT: d 279 GLU cc_start: 0.8748 (tm-30) cc_final: 0.8207 (tm-30) REVERT: d 446 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7746 (mmm) REVERT: d 513 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8679 (tm) REVERT: e 58 ASP cc_start: 0.8165 (m-30) cc_final: 0.7856 (m-30) REVERT: g 110 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8119 (tm-30) REVERT: h 7 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8280 (pp) REVERT: h 14 ASP cc_start: 0.8725 (t0) cc_final: 0.8507 (t0) REVERT: h 324 MET cc_start: 0.9165 (mmm) cc_final: 0.8855 (mmm) REVERT: z 66 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8193 (mm-30) REVERT: z 244 VAL cc_start: 0.8852 (OUTLIER) cc_final: 0.8586 (t) REVERT: z 358 GLU cc_start: 0.7365 (pm20) cc_final: 0.7101 (pm20) REVERT: P 63 ILE cc_start: 0.9254 (tp) cc_final: 0.9048 (tp) REVERT: P 84 MET cc_start: 0.5984 (tmm) cc_final: 0.5621 (tmm) REVERT: P 149 ARG cc_start: 0.8675 (ptt-90) cc_final: 0.8375 (ptp90) outliers start: 85 outliers final: 33 residues processed: 530 average time/residue: 1.5299 time to fit residues: 1058.7562 Evaluate side-chains 498 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 456 time to evaluate : 5.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain N residue 349 ILE Chi-restraints excluded: chain A residue 166 ASP Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 246 LEU Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain H residue 524 ARG Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 357 GLU Chi-restraints excluded: chain a residue 15 GLU Chi-restraints excluded: chain a residue 146 ASP Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 392 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 488 MET Chi-restraints excluded: chain d residue 118 ASP Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain d residue 320 MET Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain d residue 458 MET Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 214 VAL Chi-restraints excluded: chain g residue 483 GLU Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 149 VAL Chi-restraints excluded: chain h residue 233 HIS Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 285 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 284 optimal weight: 9.9990 chunk 761 optimal weight: 10.0000 chunk 167 optimal weight: 0.9990 chunk 496 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 846 optimal weight: 10.0000 chunk 702 optimal weight: 2.9990 chunk 391 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 280 optimal weight: 4.9990 chunk 444 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 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS Z 514 ASN ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 122 GLN ** g 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 68826 Z= 0.295 Angle : 0.556 10.034 92921 Z= 0.274 Chirality : 0.042 0.161 11052 Planarity : 0.003 0.046 11863 Dihedral : 7.053 178.946 9550 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.95 % Favored : 96.03 % Rotamer: Outliers : 1.28 % Allowed : 10.88 % Favored : 87.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.09), residues: 8784 helix: 2.13 (0.08), residues: 4430 sheet: -0.05 (0.15), residues: 1212 loop : -0.47 (0.11), residues: 3142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 66 HIS 0.013 0.001 HIS z 161 PHE 0.018 0.001 PHE N 296 TYR 0.026 0.001 TYR N 290 ARG 0.009 0.000 ARG P 230 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 474 time to evaluate : 6.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 182 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8078 (tm-30) REVERT: N 262 LYS cc_start: 0.7235 (mmtm) cc_final: 0.6865 (mmmt) REVERT: N 264 MET cc_start: 0.7977 (mtp) cc_final: 0.7332 (mtp) REVERT: A 47 ASP cc_start: 0.7929 (t0) cc_final: 0.7565 (OUTLIER) REVERT: A 51 ASP cc_start: 0.8392 (m-30) cc_final: 0.7919 (m-30) REVERT: A 230 VAL cc_start: 0.8064 (OUTLIER) cc_final: 0.7775 (t) REVERT: B 20 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7832 (mmt-90) REVERT: B 62 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7733 (ttp) REVERT: D 50 THR cc_start: 0.9473 (OUTLIER) cc_final: 0.9161 (p) REVERT: E 48 MET cc_start: 0.9140 (tpp) cc_final: 0.8886 (mmm) REVERT: E 493 CYS cc_start: 0.8439 (m) cc_final: 0.7937 (m) REVERT: E 533 ILE cc_start: 0.9054 (mm) cc_final: 0.8835 (mm) REVERT: G 152 MET cc_start: 0.9255 (mmm) cc_final: 0.8904 (mmm) REVERT: H 14 ASP cc_start: 0.8183 (t70) cc_final: 0.7935 (t0) REVERT: Z 196 MET cc_start: 0.8192 (mtt) cc_final: 0.7970 (mtm) REVERT: Z 286 ASP cc_start: 0.8325 (OUTLIER) cc_final: 0.7904 (t0) REVERT: Z 357 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.8000 (tp30) REVERT: a 354 GLU cc_start: 0.7843 (tp30) cc_final: 0.7247 (tm-30) REVERT: a 430 MET cc_start: 0.8260 (mmt) cc_final: 0.7972 (mpt) REVERT: b 310 MET cc_start: 0.8804 (ttm) cc_final: 0.8512 (ttp) REVERT: b 415 MET cc_start: 0.9479 (mmm) cc_final: 0.9060 (mmp) REVERT: d 90 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8758 (mmt) REVERT: d 279 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8270 (tm-30) REVERT: d 513 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8773 (tm) REVERT: e 58 ASP cc_start: 0.8133 (m-30) cc_final: 0.7831 (m-30) REVERT: e 118 GLU cc_start: 0.8537 (tt0) cc_final: 0.8169 (tm-30) REVERT: g 110 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8185 (tt0) REVERT: h 7 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8295 (pp) REVERT: h 14 ASP cc_start: 0.8712 (t0) cc_final: 0.8492 (t0) REVERT: h 324 MET cc_start: 0.9176 (mmm) cc_final: 0.8879 (mmm) REVERT: h 350 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8003 (tt0) REVERT: q 368 GLU cc_start: 0.8237 (tm-30) cc_final: 0.7713 (tm-30) REVERT: z 66 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8327 (mm-30) REVERT: z 244 VAL cc_start: 0.8899 (OUTLIER) cc_final: 0.8634 (t) REVERT: z 358 GLU cc_start: 0.7381 (pm20) cc_final: 0.7114 (pm20) outliers start: 94 outliers final: 44 residues processed: 531 average time/residue: 1.5188 time to fit residues: 1062.5539 Evaluate side-chains 507 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 452 time to evaluate : 5.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain N residue 349 ILE 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 532 LYS Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 221 MET Chi-restraints excluded: chain Q residue 324 LEU Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 286 ASP Chi-restraints excluded: chain Z residue 357 GLU Chi-restraints excluded: chain a residue 146 ASP Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 392 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 488 MET Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 118 ASP Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 260 MET Chi-restraints excluded: chain d residue 320 MET Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 458 MET Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 214 VAL Chi-restraints excluded: chain g residue 229 MET Chi-restraints excluded: chain g residue 483 GLU Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 149 VAL Chi-restraints excluded: chain h residue 233 HIS Chi-restraints excluded: chain h residue 350 GLU Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 285 VAL Chi-restraints excluded: chain P residue 298 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 816 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 482 optimal weight: 9.9990 chunk 618 optimal weight: 10.0000 chunk 479 optimal weight: 10.0000 chunk 712 optimal weight: 6.9990 chunk 472 optimal weight: 1.9990 chunk 843 optimal weight: 6.9990 chunk 527 optimal weight: 0.5980 chunk 514 optimal weight: 5.9990 chunk 389 optimal weight: 8.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 68826 Z= 0.203 Angle : 0.534 10.651 92921 Z= 0.263 Chirality : 0.041 0.206 11052 Planarity : 0.003 0.046 11863 Dihedral : 6.979 176.609 9550 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.57 % Favored : 96.41 % Rotamer: Outliers : 1.15 % Allowed : 11.48 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.09), residues: 8784 helix: 2.16 (0.08), residues: 4419 sheet: 0.01 (0.16), residues: 1190 loop : -0.44 (0.11), residues: 3175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 66 HIS 0.016 0.001 HIS z 161 PHE 0.037 0.001 PHE P 136 TYR 0.013 0.001 TYR G 274 ARG 0.007 0.000 ARG P 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 468 time to evaluate : 6.054 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 182 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8052 (tm-30) REVERT: A 47 ASP cc_start: 0.7936 (t0) cc_final: 0.7581 (t0) REVERT: A 51 ASP cc_start: 0.8379 (m-30) cc_final: 0.7896 (m-30) REVERT: A 156 MET cc_start: 0.8799 (mtp) cc_final: 0.8516 (mtp) REVERT: A 230 VAL cc_start: 0.7942 (OUTLIER) cc_final: 0.7647 (t) REVERT: A 299 TYR cc_start: 0.7973 (m-80) cc_final: 0.7525 (m-80) REVERT: A 358 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8206 (m-30) REVERT: B 20 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7905 (mmt-90) REVERT: E 48 MET cc_start: 0.9132 (tpp) cc_final: 0.8881 (mmm) REVERT: E 493 CYS cc_start: 0.8424 (m) cc_final: 0.7937 (m) REVERT: E 533 ILE cc_start: 0.9063 (mm) cc_final: 0.8844 (mm) REVERT: G 59 MET cc_start: 0.9171 (ttt) cc_final: 0.8821 (tpp) REVERT: G 152 MET cc_start: 0.9228 (mmm) cc_final: 0.8898 (mmm) REVERT: G 182 MET cc_start: 0.8623 (ptp) cc_final: 0.8403 (ptp) REVERT: G 337 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.8643 (mt-10) REVERT: H 14 ASP cc_start: 0.8122 (t70) cc_final: 0.7871 (t0) REVERT: Z 196 MET cc_start: 0.8077 (mtt) cc_final: 0.7857 (mtm) REVERT: Z 286 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7867 (t0) REVERT: Z 357 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7931 (tp30) REVERT: a 15 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7909 (mt-10) REVERT: a 354 GLU cc_start: 0.7846 (tp30) cc_final: 0.7390 (tm-30) REVERT: a 430 MET cc_start: 0.8239 (mmt) cc_final: 0.7940 (mpt) REVERT: b 310 MET cc_start: 0.8805 (ttm) cc_final: 0.8541 (ttp) REVERT: b 415 MET cc_start: 0.9491 (mmm) cc_final: 0.9064 (mmp) REVERT: d 90 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8713 (mmt) REVERT: d 279 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8237 (tm-30) REVERT: d 446 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.7732 (mmm) REVERT: d 513 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8692 (tm) REVERT: e 29 MET cc_start: 0.7921 (OUTLIER) cc_final: 0.7577 (mtm) REVERT: g 110 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8139 (tm-30) REVERT: h 7 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8231 (pp) REVERT: h 14 ASP cc_start: 0.8703 (t0) cc_final: 0.8464 (t0) REVERT: h 324 MET cc_start: 0.9157 (mmm) cc_final: 0.8841 (mmm) REVERT: z 66 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8220 (mm-30) REVERT: z 244 VAL cc_start: 0.8890 (OUTLIER) cc_final: 0.8625 (t) REVERT: z 358 GLU cc_start: 0.7394 (pm20) cc_final: 0.7104 (pm20) REVERT: P 66 TRP cc_start: 0.7163 (t-100) cc_final: 0.6755 (t-100) REVERT: P 84 MET cc_start: 0.6163 (tmm) cc_final: 0.5729 (tmm) outliers start: 85 outliers final: 42 residues processed: 517 average time/residue: 1.4993 time to fit residues: 1027.2800 Evaluate side-chains 515 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 459 time to evaluate : 5.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain N residue 349 ILE 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 532 LYS Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Q residue 324 LEU Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain Z residue 286 ASP Chi-restraints excluded: chain Z residue 357 GLU Chi-restraints excluded: chain a residue 15 GLU Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 392 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 488 MET Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 118 ASP Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 186 MET Chi-restraints excluded: chain d residue 320 MET Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain d residue 458 MET Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 214 VAL Chi-restraints excluded: chain g residue 483 GLU Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 149 VAL Chi-restraints excluded: chain h residue 233 HIS Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 285 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 521 optimal weight: 5.9990 chunk 336 optimal weight: 4.9990 chunk 503 optimal weight: 1.9990 chunk 254 optimal weight: 7.9990 chunk 165 optimal weight: 0.9990 chunk 163 optimal weight: 9.9990 chunk 536 optimal weight: 6.9990 chunk 574 optimal weight: 1.9990 chunk 416 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 662 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 160 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 68826 Z= 0.265 Angle : 0.556 11.823 92921 Z= 0.272 Chirality : 0.041 0.168 11052 Planarity : 0.003 0.046 11863 Dihedral : 6.962 178.486 9550 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.93 % Favored : 96.05 % Rotamer: Outliers : 1.18 % Allowed : 11.82 % Favored : 87.00 % 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: 8784 helix: 2.13 (0.08), residues: 4423 sheet: -0.02 (0.15), residues: 1205 loop : -0.47 (0.11), residues: 3156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 66 HIS 0.015 0.001 HIS z 161 PHE 0.014 0.001 PHE N 341 TYR 0.019 0.001 TYR N 290 ARG 0.007 0.000 ARG P 230 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 472 time to evaluate : 6.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 182 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8066 (tm-30) REVERT: A 47 ASP cc_start: 0.7970 (t0) cc_final: 0.7621 (t0) REVERT: A 51 ASP cc_start: 0.8419 (m-30) cc_final: 0.7925 (m-30) REVERT: A 156 MET cc_start: 0.8752 (mtp) cc_final: 0.8457 (mtp) REVERT: A 230 VAL cc_start: 0.8077 (OUTLIER) cc_final: 0.7778 (t) REVERT: A 358 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8228 (m-30) REVERT: B 20 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.7843 (mmt-90) REVERT: B 62 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7709 (ttp) REVERT: D 50 THR cc_start: 0.9469 (OUTLIER) cc_final: 0.9165 (p) REVERT: E 48 MET cc_start: 0.9140 (tpp) cc_final: 0.8881 (mmm) REVERT: E 493 CYS cc_start: 0.8432 (m) cc_final: 0.7929 (m) REVERT: E 533 ILE cc_start: 0.9058 (mm) cc_final: 0.8840 (mm) REVERT: G 54 MET cc_start: 0.8922 (mmm) cc_final: 0.8688 (mmm) REVERT: G 59 MET cc_start: 0.9212 (ttt) cc_final: 0.8865 (tpp) REVERT: G 152 MET cc_start: 0.9239 (mmm) cc_final: 0.8905 (mmm) REVERT: G 337 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8519 (mt-10) REVERT: H 14 ASP cc_start: 0.8123 (t70) cc_final: 0.7877 (t0) REVERT: Z 196 MET cc_start: 0.8142 (mtt) cc_final: 0.7917 (mtm) REVERT: Z 286 ASP cc_start: 0.8324 (OUTLIER) cc_final: 0.7898 (t0) REVERT: Z 357 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7948 (tp30) REVERT: a 15 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7889 (mt-10) REVERT: a 354 GLU cc_start: 0.7866 (tp30) cc_final: 0.7230 (tm-30) REVERT: a 430 MET cc_start: 0.8241 (mmt) cc_final: 0.7940 (mpt) REVERT: b 310 MET cc_start: 0.8804 (ttm) cc_final: 0.8556 (ttp) REVERT: b 415 MET cc_start: 0.9471 (mmm) cc_final: 0.9046 (mmp) REVERT: d 90 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8726 (mmt) REVERT: d 279 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8262 (tm-30) REVERT: d 446 MET cc_start: 0.8487 (OUTLIER) cc_final: 0.7720 (mmm) REVERT: d 513 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8743 (tm) REVERT: e 29 MET cc_start: 0.7899 (OUTLIER) cc_final: 0.7553 (mtm) REVERT: e 58 ASP cc_start: 0.8098 (m-30) cc_final: 0.7802 (m-30) REVERT: e 118 GLU cc_start: 0.8535 (tt0) cc_final: 0.8165 (tm-30) REVERT: g 47 MET cc_start: 0.9343 (tpp) cc_final: 0.8978 (mmp) REVERT: g 110 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8173 (tt0) REVERT: h 7 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8216 (pp) REVERT: h 14 ASP cc_start: 0.8714 (t0) cc_final: 0.8476 (t0) REVERT: h 324 MET cc_start: 0.9143 (mmm) cc_final: 0.8831 (mmm) REVERT: h 350 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.7965 (tt0) REVERT: z 66 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8320 (mm-30) REVERT: z 244 VAL cc_start: 0.8891 (OUTLIER) cc_final: 0.8624 (t) REVERT: z 358 GLU cc_start: 0.7389 (pm20) cc_final: 0.7094 (pm20) REVERT: P 66 TRP cc_start: 0.7140 (t-100) cc_final: 0.6285 (t-100) REVERT: P 67 ARG cc_start: 0.8658 (mmp80) cc_final: 0.7849 (mmp80) outliers start: 87 outliers final: 46 residues processed: 522 average time/residue: 1.5220 time to fit residues: 1049.0037 Evaluate side-chains 522 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 459 time to evaluate : 5.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 201 CYS Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain N residue 349 ILE 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 532 LYS Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 118 GLU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 468 MET Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Q residue 324 LEU Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain Z residue 286 ASP Chi-restraints excluded: chain Z residue 357 GLU Chi-restraints excluded: chain a residue 15 GLU Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 392 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 118 ASP Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 186 MET Chi-restraints excluded: chain d residue 260 MET Chi-restraints excluded: chain d residue 320 MET Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain d residue 458 MET Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 501 MET Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 214 VAL Chi-restraints excluded: chain g residue 483 GLU Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 149 VAL Chi-restraints excluded: chain h residue 233 HIS Chi-restraints excluded: chain h residue 350 GLU Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 285 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 767 optimal weight: 0.9980 chunk 807 optimal weight: 3.9990 chunk 737 optimal weight: 5.9990 chunk 785 optimal weight: 5.9990 chunk 473 optimal weight: 0.6980 chunk 342 optimal weight: 6.9990 chunk 617 optimal weight: 6.9990 chunk 241 optimal weight: 0.7980 chunk 710 optimal weight: 4.9990 chunk 743 optimal weight: 0.8980 chunk 783 optimal weight: 4.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 275 GLN ** D 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS P 160 GLN P 199 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 68826 Z= 0.171 Angle : 0.533 13.887 92921 Z= 0.260 Chirality : 0.040 0.164 11052 Planarity : 0.003 0.046 11863 Dihedral : 6.855 178.047 9550 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.60 % Favored : 96.38 % Rotamer: Outliers : 1.00 % Allowed : 12.17 % Favored : 86.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.09), residues: 8784 helix: 2.17 (0.08), residues: 4423 sheet: 0.03 (0.16), residues: 1181 loop : -0.46 (0.11), residues: 3180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 222 HIS 0.016 0.001 HIS z 161 PHE 0.039 0.001 PHE P 136 TYR 0.026 0.001 TYR N 174 ARG 0.007 0.000 ARG P 230 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 475 time to evaluate : 6.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 182 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8057 (tm-30) REVERT: A 47 ASP cc_start: 0.7915 (t0) cc_final: 0.7579 (t0) REVERT: A 51 ASP cc_start: 0.8373 (m-30) cc_final: 0.7881 (m-30) REVERT: A 230 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.7777 (t) REVERT: A 358 ASP cc_start: 0.8451 (OUTLIER) cc_final: 0.8182 (m-30) REVERT: B 20 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7902 (mmt-90) REVERT: B 488 MET cc_start: 0.9346 (mmp) cc_final: 0.9083 (mmp) REVERT: D 50 THR cc_start: 0.9449 (OUTLIER) cc_final: 0.9132 (p) REVERT: E 48 MET cc_start: 0.9159 (tpp) cc_final: 0.8809 (mmm) REVERT: E 493 CYS cc_start: 0.8361 (m) cc_final: 0.7885 (m) REVERT: G 54 MET cc_start: 0.8921 (mmm) cc_final: 0.8688 (mmm) REVERT: G 59 MET cc_start: 0.9213 (ttt) cc_final: 0.8899 (tpp) REVERT: G 152 MET cc_start: 0.9215 (mmm) cc_final: 0.8861 (mmm) REVERT: G 337 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8662 (mt-10) REVERT: H 14 ASP cc_start: 0.8120 (t70) cc_final: 0.7866 (t0) REVERT: Q 200 ASP cc_start: 0.8697 (m-30) cc_final: 0.8346 (t0) REVERT: Q 526 MET cc_start: 0.8864 (mtm) cc_final: 0.8589 (ttm) REVERT: Z 196 MET cc_start: 0.8011 (mtt) cc_final: 0.7785 (mtm) REVERT: Z 357 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7940 (tp30) REVERT: a 15 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7913 (mt-10) REVERT: a 344 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8266 (mtp) REVERT: a 354 GLU cc_start: 0.7830 (tp30) cc_final: 0.7215 (tm-30) REVERT: a 430 MET cc_start: 0.8212 (mmt) cc_final: 0.7967 (mpt) REVERT: b 310 MET cc_start: 0.8797 (ttm) cc_final: 0.8529 (ttp) REVERT: b 415 MET cc_start: 0.9486 (mmm) cc_final: 0.9053 (mmp) REVERT: d 90 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8655 (mmt) REVERT: d 279 GLU cc_start: 0.8783 (tm-30) cc_final: 0.8214 (tm-30) REVERT: d 446 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.7680 (mmm) REVERT: d 513 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8672 (tm) REVERT: e 29 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.7492 (mtm) REVERT: e 58 ASP cc_start: 0.8132 (m-30) cc_final: 0.7825 (m-30) REVERT: e 118 GLU cc_start: 0.8536 (tt0) cc_final: 0.8168 (tm-30) REVERT: g 47 MET cc_start: 0.9326 (tpp) cc_final: 0.8901 (mmp) REVERT: g 110 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.8135 (tm-30) REVERT: h 7 ILE cc_start: 0.8566 (OUTLIER) cc_final: 0.8146 (pp) REVERT: h 14 ASP cc_start: 0.8710 (t0) cc_final: 0.8456 (t0) REVERT: h 324 MET cc_start: 0.9144 (mmm) cc_final: 0.8825 (mmm) REVERT: h 350 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.7876 (tt0) REVERT: z 66 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8206 (mm-30) REVERT: z 244 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8607 (t) REVERT: z 358 GLU cc_start: 0.7368 (pm20) cc_final: 0.7102 (pm20) REVERT: P 66 TRP cc_start: 0.7179 (t-100) cc_final: 0.6329 (t-100) REVERT: P 67 ARG cc_start: 0.8723 (mmp80) cc_final: 0.8030 (mmp80) outliers start: 74 outliers final: 45 residues processed: 519 average time/residue: 1.5151 time to fit residues: 1039.0401 Evaluate side-chains 525 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 464 time to evaluate : 5.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 201 CYS Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 349 ILE 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 416 GLU Chi-restraints excluded: chain A residue 532 LYS Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Q residue 324 LEU Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain Z residue 357 GLU Chi-restraints excluded: chain a residue 15 GLU Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain a residue 392 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 118 ASP Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 186 MET Chi-restraints excluded: chain d residue 320 MET Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain d residue 458 MET Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 501 MET Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 214 VAL Chi-restraints excluded: chain g residue 483 GLU Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 149 VAL Chi-restraints excluded: chain h residue 233 HIS Chi-restraints excluded: chain h residue 350 GLU Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain h residue 482 GLU Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 285 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 516 optimal weight: 0.9980 chunk 831 optimal weight: 10.0000 chunk 507 optimal weight: 0.9990 chunk 394 optimal weight: 0.8980 chunk 577 optimal weight: 10.0000 chunk 871 optimal weight: 10.0000 chunk 802 optimal weight: 7.9990 chunk 694 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 536 optimal weight: 6.9990 chunk 425 optimal weight: 4.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 160 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.1079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 68826 Z= 0.262 Angle : 0.558 12.298 92921 Z= 0.272 Chirality : 0.041 0.181 11052 Planarity : 0.003 0.046 11863 Dihedral : 6.847 174.814 9550 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.82 % Favored : 96.16 % Rotamer: Outliers : 0.99 % Allowed : 12.28 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.09), residues: 8784 helix: 2.15 (0.08), residues: 4422 sheet: -0.01 (0.15), residues: 1201 loop : -0.48 (0.11), residues: 3161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP P 66 HIS 0.015 0.001 HIS z 161 PHE 0.011 0.001 PHE E 386 TYR 0.014 0.001 TYR G 274 ARG 0.007 0.000 ARG P 230 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17568 Ramachandran restraints generated. 8784 Oldfield, 0 Emsley, 8784 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 471 time to evaluate : 6.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 182 GLU cc_start: 0.8387 (tm-30) cc_final: 0.8054 (tm-30) REVERT: A 47 ASP cc_start: 0.7963 (t0) cc_final: 0.7619 (t0) REVERT: A 51 ASP cc_start: 0.8408 (m-30) cc_final: 0.7919 (m-30) REVERT: A 230 VAL cc_start: 0.8104 (OUTLIER) cc_final: 0.7801 (t) REVERT: A 358 ASP cc_start: 0.8378 (OUTLIER) cc_final: 0.8110 (m-30) REVERT: B 20 ARG cc_start: 0.8553 (OUTLIER) cc_final: 0.7819 (mmt-90) REVERT: D 50 THR cc_start: 0.9463 (OUTLIER) cc_final: 0.9151 (p) REVERT: E 48 MET cc_start: 0.9144 (tpp) cc_final: 0.8885 (mmm) REVERT: E 493 CYS cc_start: 0.8378 (m) cc_final: 0.7886 (m) REVERT: G 59 MET cc_start: 0.9241 (ttt) cc_final: 0.8914 (tpp) REVERT: G 152 MET cc_start: 0.9241 (mmm) cc_final: 0.8901 (mmm) REVERT: G 337 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8677 (mt-10) REVERT: H 14 ASP cc_start: 0.8121 (t70) cc_final: 0.7873 (t0) REVERT: Q 526 MET cc_start: 0.8869 (mtm) cc_final: 0.8581 (ttm) REVERT: Z 196 MET cc_start: 0.8102 (mtt) cc_final: 0.7877 (mtm) REVERT: Z 286 ASP cc_start: 0.8322 (OUTLIER) cc_final: 0.7896 (t0) REVERT: Z 357 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7927 (tp30) REVERT: a 15 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7937 (mt-10) REVERT: a 354 GLU cc_start: 0.7857 (tp30) cc_final: 0.7209 (tm-30) REVERT: a 430 MET cc_start: 0.8227 (mmt) cc_final: 0.7924 (mpt) REVERT: b 310 MET cc_start: 0.8818 (ttm) cc_final: 0.8560 (ttp) REVERT: b 415 MET cc_start: 0.9461 (mmm) cc_final: 0.9038 (mmp) REVERT: d 90 MET cc_start: 0.9252 (OUTLIER) cc_final: 0.8709 (mmt) REVERT: d 279 GLU cc_start: 0.8812 (tm-30) cc_final: 0.8252 (tm-30) REVERT: d 446 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.7707 (mmm) REVERT: d 513 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8713 (tm) REVERT: e 29 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7538 (mtm) REVERT: e 58 ASP cc_start: 0.8100 (m-30) cc_final: 0.7796 (m-30) REVERT: e 118 GLU cc_start: 0.8536 (tt0) cc_final: 0.8163 (tm-30) REVERT: g 47 MET cc_start: 0.9303 (tpp) cc_final: 0.8953 (mmp) REVERT: g 110 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8199 (tm-30) REVERT: h 7 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8160 (pp) REVERT: h 14 ASP cc_start: 0.8717 (t0) cc_final: 0.8471 (t0) REVERT: h 324 MET cc_start: 0.9141 (mmm) cc_final: 0.8828 (mmm) REVERT: h 350 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.7956 (tt0) REVERT: z 66 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8230 (mm-30) REVERT: z 244 VAL cc_start: 0.8883 (OUTLIER) cc_final: 0.8625 (t) REVERT: z 358 GLU cc_start: 0.7376 (pm20) cc_final: 0.7086 (pm20) REVERT: P 66 TRP cc_start: 0.7154 (t-100) cc_final: 0.6427 (t-100) REVERT: P 67 ARG cc_start: 0.8727 (mmp80) cc_final: 0.8146 (mmp80) REVERT: P 168 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7313 (tm-30) outliers start: 73 outliers final: 44 residues processed: 513 average time/residue: 1.5376 time to fit residues: 1036.9985 Evaluate side-chains 524 residues out of total 7368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 464 time to evaluate : 5.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 201 CYS Chi-restraints excluded: chain N residue 316 VAL Chi-restraints excluded: chain N residue 349 ILE 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 532 LYS Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 468 MET Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 337 GLU Chi-restraints excluded: chain H residue 21 GLN Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Q residue 324 LEU Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain Z residue 286 ASP Chi-restraints excluded: chain Z residue 357 GLU Chi-restraints excluded: chain a residue 15 GLU Chi-restraints excluded: chain a residue 147 CYS Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 392 LEU Chi-restraints excluded: chain a residue 464 VAL Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 118 ASP Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 186 MET Chi-restraints excluded: chain d residue 320 MET Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 446 MET Chi-restraints excluded: chain d residue 458 MET Chi-restraints excluded: chain d residue 513 LEU Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 501 MET Chi-restraints excluded: chain g residue 110 GLU Chi-restraints excluded: chain g residue 161 THR Chi-restraints excluded: chain g residue 214 VAL Chi-restraints excluded: chain g residue 483 GLU Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 149 VAL Chi-restraints excluded: chain h residue 233 HIS Chi-restraints excluded: chain h residue 350 GLU Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain h residue 482 GLU Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 285 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 875 random chunks: chunk 551 optimal weight: 3.9990 chunk 739 optimal weight: 6.9990 chunk 212 optimal weight: 9.9990 chunk 640 optimal weight: 0.3980 chunk 102 optimal weight: 0.0050 chunk 192 optimal weight: 10.0000 chunk 695 optimal weight: 8.9990 chunk 290 optimal weight: 0.8980 chunk 713 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** Q 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS P 160 GLN P 199 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.069462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.056519 restraints weight = 194813.689| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 3.01 r_work: 0.2571 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 68826 Z= 0.168 Angle : 0.533 12.350 92921 Z= 0.260 Chirality : 0.040 0.173 11052 Planarity : 0.003 0.045 11863 Dihedral : 6.747 173.946 9550 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.59 % Favored : 96.39 % Rotamer: Outliers : 0.91 % Allowed : 12.42 % Favored : 86.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.09), residues: 8784 helix: 2.20 (0.08), residues: 4422 sheet: 0.04 (0.16), residues: 1183 loop : -0.43 (0.11), residues: 3179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 222 HIS 0.017 0.001 HIS z 161 PHE 0.042 0.001 PHE P 136 TYR 0.020 0.001 TYR N 174 ARG 0.007 0.000 ARG P 230 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16761.06 seconds wall clock time: 295 minutes 31.07 seconds (17731.07 seconds total)