Starting phenix.real_space_refine on Thu Mar 14 17:24:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shl_40488/03_2024/8shl_40488_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shl_40488/03_2024/8shl_40488.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/8shl_40488/03_2024/8shl_40488.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shl_40488/03_2024/8shl_40488.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shl_40488/03_2024/8shl_40488_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shl_40488/03_2024/8shl_40488_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= 0.047 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 419 5.16 5 C 42201 2.51 5 N 11748 2.21 5 O 13066 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 ASP 223": "OD1" <-> "OD2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A ASP 529": "OD1" <-> "OD2" Residue "B PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 100": "OD1" <-> "OD2" Residue "E PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 511": "OE1" <-> "OE2" Residue "Q ASP 393": "OD1" <-> "OD2" Residue "Q ASP 499": "OD1" <-> "OD2" Residue "Q TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 32": "OD1" <-> "OD2" Residue "Z GLU 357": "OE1" <-> "OE2" Residue "a TYR 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 529": "OD1" <-> "OD2" Residue "b TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 509": "OE1" <-> "OE2" Residue "d GLU 93": "OE1" <-> "OE2" Residue "d TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 532": "OD1" <-> "OD2" Residue "g GLU 202": "OE1" <-> "OE2" Residue "g TYR 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 521": "OD1" <-> "OD2" Residue "h GLU 11": "OE1" <-> "OE2" Residue "h ASP 70": "OD1" <-> "OD2" Residue "z TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 65": "OD1" <-> "OD2" Residue "P PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 67546 Number of models: 1 Model: "" Number of chains: 50 Chain: "N" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 767 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain breaks: 2 Chain: "A" Number of atoms: 4069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4069 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 14, 'TRANS': 521} Chain: "B" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3952 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 10, 'TRANS': 515} Chain: "D" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3923 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "E" Number of atoms: 4094 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 529, 4083 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 18, 'TRANS': 510} Conformer: "C" Number of residues, atoms: 529, 4083 Classifications: {'peptide': 529} Link IDs: {'PTRANS': 18, 'TRANS': 510} bond proxies already assigned to first conformer: 4120 Chain: "G" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4089 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "H" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4054 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 16, 'TRANS': 511} Chain: "Q" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4086 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 18, 'TRANS': 519} Chain: "Z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "a" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4041 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Chain: "b" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3943 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 10, 'TRANS': 514} Chain: "d" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3917 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 4169 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} Conformer: "B" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} bond proxies already assigned to first conformer: 4195 Chain: "g" Number of atoms: 4088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4088 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "h" Number of atoms: 4032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4032 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 16, 'TRANS': 508} Chain: "q" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4053 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 16, 'TRANS': 516} Chain: "z" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4033 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 512} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "P" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1683 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain breaks: 1 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: 27.73, per 1000 atoms: 0.41 Number of scatterers: 67546 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 419 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 13066 8.00 N 11748 7.00 C 42201 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 "HETATM67325 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67133 O3A ADP E 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67197 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67069 O3A ADP B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67101 O3A ADP D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67453 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67389 O3A ADP e 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.45 Conformation dependent library (CDL) restraints added in 9.9 seconds 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16338 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 323 helices and 111 sheets defined 50.8% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.29 Creating SS restraints... Processing helix chain 'A' and resid 15 through 35 removed outlier: 3.682A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 5.779A 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: 3.634A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.608A 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 145 through 156 Processing helix chain 'A' and resid 163 through 179 removed outlier: 4.454A pdb=" N ASP A 166 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N ALA A 169 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 205 through 207 No H-bonds generated for 'chain 'A' and resid 205 through 207' Processing helix chain 'A' and resid 257 through 281 removed outlier: 3.507A pdb=" N LEU A 260 " --> pdb=" O PRO A 257 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP A 261 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N ILE A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 382 through 404 Processing helix chain 'A' and resid 414 through 429 removed outlier: 4.397A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N SER A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 456 removed outlier: 3.782A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 5.207A 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: 3.817A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TRP A 485 " --> pdb=" O ASN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 507 through 525 Processing helix chain 'B' and resid 21 through 39 Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 99 through 119 removed outlier: 3.546A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 143 Processing helix chain 'B' and resid 152 through 168 Processing helix chain 'B' and resid 171 through 190 removed outlier: 3.610A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS B 176 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N ASP B 177 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 198 No H-bonds generated for 'chain 'B' and resid 196 through 198' Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 261 through 285 removed outlier: 4.055A 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: 3.795A 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: 3.711A 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: 4.330A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 5.534A 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: 3.702A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.624A 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 193 Proline residue: D 185 - end of helix Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 269 through 293 removed outlier: 4.183A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 4.045A 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: 4.597A pdb=" N GLU D 334 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE D 340 " --> pdb=" O CYS D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 350 No H-bonds generated for 'chain 'D' and resid 348 through 350' Processing helix chain 'D' and resid 353 through 355 No H-bonds generated for 'chain 'D' and resid 353 through 355' Processing helix chain 'D' and resid 395 through 417 Processing helix chain 'D' and resid 427 through 442 removed outlier: 3.650A pdb=" N THR D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 469 removed outlier: 3.938A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL D 460 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N ILE D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) Proline residue: D 462 - end of helix Processing helix chain 'D' and resid 473 through 486 Processing helix chain 'D' and resid 503 through 506 Processing helix chain 'D' and resid 512 through 531 removed outlier: 3.512A pdb=" N LYS D 531 " --> pdb=" O ARG D 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 51 removed outlier: 4.283A pdb=" N THR E 50 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N SER E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 80 Processing helix chain 'E' and resid 86 through 101 Processing helix chain 'E' and resid 108 through 126 removed outlier: 3.613A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 151 Processing helix chain 'E' and resid 163 through 175 removed outlier: 4.589A pdb=" N SER E 175 " --> pdb=" O THR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 195 removed outlier: 3.951A pdb=" N SER E 180 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N ARG E 183 " --> pdb=" O SER E 180 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR E 195 " --> pdb=" O ALA E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 219 through 221 No H-bonds generated for 'chain 'E' and resid 219 through 221' Processing helix chain 'E' and resid 271 through 295 removed outlier: 3.939A pdb=" N THR E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 316 Processing helix chain 'E' and resid 327 through 337 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 392 through 414 Processing helix chain 'E' and resid 424 through 437 Processing helix chain 'E' and resid 442 through 465 removed outlier: 3.778A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL E 457 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE E 458 " --> pdb=" O ALA E 454 " (cutoff:3.500A) Proline residue: E 459 - end of helix Processing helix chain 'E' and resid 470 through 483 Processing helix chain 'E' and resid 501 through 504 No H-bonds generated for 'chain 'E' and resid 501 through 504' Processing helix chain 'E' and resid 510 through 528 Processing helix chain 'G' and resid 20 through 37 removed outlier: 3.840A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 69 removed outlier: 3.555A pdb=" N GLU G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 90 Processing helix chain 'G' and resid 95 through 115 removed outlier: 3.675A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 139 Processing helix chain 'G' and resid 149 through 160 Processing helix chain 'G' and resid 166 through 183 removed outlier: 5.646A 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: 4.378A pdb=" N LEU G 285 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 307 removed outlier: 3.670A 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: 3.600A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ALA G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 455 removed outlier: 3.594A pdb=" N TRP G 435 " --> pdb=" O VAL G 432 " (cutoff:3.500A) Proline residue: G 436 - end of helix removed outlier: 3.947A 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 470 Processing helix chain 'G' and resid 490 through 493 No H-bonds generated for 'chain 'G' and resid 490 through 493' Processing helix chain 'G' and resid 499 through 517 Processing helix chain 'H' and resid 19 through 35 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: 3.653A pdb=" N GLU H 89 " --> pdb=" O GLN H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 113 removed outlier: 3.873A pdb=" N THR H 98 " --> pdb=" O THR H 94 " (cutoff:3.500A) Proline residue: H 110 - end of helix Processing helix chain 'H' and resid 118 through 139 Processing helix chain 'H' and resid 148 through 163 Processing helix chain 'H' and resid 169 through 185 removed outlier: 5.249A pdb=" N ALA H 173 " --> pdb=" O GLN H 170 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET H 184 " --> pdb=" O ASP H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'H' and resid 205 through 207 No H-bonds generated for 'chain 'H' and resid 205 through 207' Processing helix chain 'H' and resid 225 through 227 No H-bonds generated for 'chain 'H' and resid 225 through 227' Processing helix chain 'H' and resid 260 through 284 Processing helix chain 'H' and resid 297 through 305 Processing helix chain 'H' and resid 316 through 326 Processing helix chain 'H' and resid 339 through 341 No H-bonds generated for 'chain 'H' and resid 339 through 341' Processing helix chain 'H' and resid 379 through 401 Processing helix chain 'H' and resid 411 through 426 removed outlier: 4.055A pdb=" N THR H 426 " --> pdb=" O ASP H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 453 removed outlier: 4.038A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE H 444 " --> pdb=" O LYS H 440 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ILE H 445 " --> pdb=" O ALA H 441 " (cutoff:3.500A) Proline residue: H 446 - end of helix Processing helix chain 'H' and resid 457 through 469 Processing helix chain 'H' and resid 496 through 515 Processing helix chain 'Q' and resid 11 through 14 No H-bonds generated for 'chain 'Q' and resid 11 through 14' Processing helix chain 'Q' and resid 25 through 46 removed outlier: 4.277A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N ALA Q 46 " --> pdb=" O THR Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 75 Processing helix chain 'Q' and resid 81 through 96 Processing helix chain 'Q' and resid 101 through 121 Processing helix chain 'Q' and resid 125 through 146 Proline residue: Q 144 - end of helix Processing helix chain 'Q' and resid 157 through 167 removed outlier: 4.303A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 177 through 189 Processing helix chain 'Q' and resid 212 through 214 No H-bonds generated for 'chain 'Q' and resid 212 through 214' Processing helix chain 'Q' and resid 262 through 286 removed outlier: 4.842A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) removed outlier: 3.733A 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: 3.631A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 456 removed outlier: 3.545A 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 Processing helix chain 'Z' and resid 17 through 37 removed outlier: 4.885A pdb=" N THR Z 36 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 5.100A 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: 3.676A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) removed outlier: 4.227A 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: 4.149A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 162 through 179 removed outlier: 3.610A pdb=" N GLU Z 170 " --> pdb=" O ASP Z 166 " (cutoff:3.500A) Processing helix chain 'Z' and resid 188 through 190 No H-bonds generated for 'chain 'Z' and resid 188 through 190' Processing helix chain 'Z' and resid 201 through 203 No H-bonds generated for 'chain 'Z' and resid 201 through 203' Processing helix chain 'Z' and resid 253 through 281 removed outlier: 4.044A pdb=" N ARG Z 264 " --> pdb=" O VAL Z 260 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LYS Z 265 " --> pdb=" O LYS Z 261 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N PHE Z 266 " --> pdb=" O ALA Z 262 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N ILE Z 267 " --> pdb=" O GLU Z 263 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 299 through 308 removed outlier: 3.624A pdb=" N GLU Z 308 " --> pdb=" O ALA Z 304 " (cutoff:3.500A) Processing helix chain 'Z' and resid 318 through 328 removed outlier: 4.220A pdb=" N GLU Z 322 " --> pdb=" O ARG Z 318 " (cutoff:3.500A) Processing helix chain 'Z' and resid 341 through 343 No H-bonds generated for 'chain 'Z' and resid 341 through 343' Processing helix chain 'Z' and resid 381 through 403 Processing helix chain 'Z' and resid 413 through 428 Proline residue: Z 427 - end of helix Processing helix chain 'Z' and resid 431 through 455 removed outlier: 4.130A pdb=" N GLN Z 434 " --> pdb=" O GLY Z 431 " (cutoff:3.500A) removed outlier: 3.810A 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: 3.754A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N SER a 34 " --> pdb=" O ASN a 30 " (cutoff:3.500A) removed outlier: 5.882A 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: 3.932A 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: 4.388A pdb=" N ASP a 166 " --> pdb=" O ILE a 163 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ALA a 169 " --> pdb=" O ASP a 166 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 186 No H-bonds generated for 'chain 'a' and resid 184 through 186' Processing helix chain 'a' and resid 205 through 207 No H-bonds generated for 'chain 'a' and resid 205 through 207' Processing helix chain 'a' and resid 257 through 281 removed outlier: 4.752A pdb=" N ASP a 261 " --> pdb=" O GLU a 258 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ILE a 270 " --> pdb=" O GLU a 267 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA a 280 " --> pdb=" O LYS a 277 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N THR a 281 " --> pdb=" O ILE a 278 " (cutoff:3.500A) Processing helix chain 'a' and resid 294 through 302 Processing helix chain 'a' and resid 313 through 323 Processing helix chain 'a' and resid 342 through 344 No H-bonds generated for 'chain 'a' and resid 342 through 344' Processing helix chain 'a' and resid 382 through 404 Processing helix chain 'a' and resid 414 through 429 removed outlier: 4.453A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) Processing helix chain 'a' and resid 434 through 455 removed outlier: 3.674A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ILE a 448 " --> pdb=" O SER a 444 " (cutoff:3.500A) Proline residue: a 449 - end of helix Processing helix chain 'a' and resid 460 through 476 Processing helix chain 'a' and resid 481 through 485 removed outlier: 3.802A 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 144 Processing helix chain 'b' and resid 152 through 169 removed outlier: 4.544A pdb=" N SER b 169 " --> pdb=" O THR b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 171 through 190 removed outlier: 3.720A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS b 176 " --> pdb=" O THR b 173 " (cutoff:3.500A) removed outlier: 5.939A 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: 3.939A pdb=" N HIS b 285 " --> pdb=" O ARG b 281 " (cutoff:3.500A) Processing helix chain 'b' and resid 298 through 306 Processing helix chain 'b' and resid 317 through 327 Processing helix chain 'b' and resid 338 through 340 No H-bonds generated for 'chain 'b' and resid 338 through 340' Processing helix chain 'b' and resid 380 through 402 Processing helix chain 'b' and resid 412 through 427 removed outlier: 3.659A 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: 3.779A pdb=" N ALA b 454 " --> pdb=" O ILE b 450 " (cutoff:3.500A) Processing helix chain 'b' and resid 458 through 471 Processing helix chain 'b' and resid 488 through 491 No H-bonds generated for 'chain 'b' and resid 488 through 491' Processing helix chain 'b' and resid 497 through 515 Processing helix chain 'd' and resid 29 through 49 Processing helix chain 'd' and resid 74 through 80 Processing helix chain 'd' and resid 86 through 101 Processing helix chain 'd' and resid 106 through 125 removed outlier: 3.725A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.734A 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: 4.471A pdb=" N SER d 173 " --> pdb=" O THR d 169 " (cutoff:3.500A) Processing helix chain 'd' and resid 175 through 192 removed outlier: 4.331A pdb=" N GLN d 178 " --> pdb=" O VAL d 175 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N SER d 181 " --> pdb=" O GLN d 178 " (cutoff:3.500A) removed outlier: 5.131A 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: 3.654A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.920A 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: 4.533A pdb=" N GLU d 334 " --> pdb=" O GLU d 331 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE d 340 " --> pdb=" O CYS d 337 " (cutoff:3.500A) Processing helix chain 'd' and resid 348 through 350 No H-bonds generated for 'chain 'd' and resid 348 through 350' Processing helix chain 'd' and resid 353 through 355 No H-bonds generated for 'chain 'd' and resid 353 through 355' Processing helix chain 'd' and resid 395 through 416 Processing helix chain 'd' and resid 427 through 442 Processing helix chain 'd' and resid 446 through 466 removed outlier: 3.867A pdb=" N VAL d 460 " --> pdb=" O ASP d 456 " (cutoff:3.500A) removed outlier: 4.866A 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 504 through 506 No H-bonds generated for 'chain 'd' and resid 504 through 506' Processing helix chain 'd' and resid 512 through 530 removed outlier: 4.885A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 22 through 24 No H-bonds generated for 'chain 'e' and resid 22 through 24' Processing helix chain 'e' and resid 30 through 51 removed outlier: 3.625A pdb=" N ARG e 49 " --> pdb=" O ASN e 46 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N THR e 50 " --> pdb=" O THR e 47 " (cutoff:3.500A) Processing helix chain 'e' and resid 74 through 80 Processing helix chain 'e' and resid 86 through 101 Processing helix chain 'e' and resid 108 through 126 Processing helix chain 'e' and resid 130 through 151 Processing helix chain 'e' and resid 163 through 175 removed outlier: 4.669A pdb=" N SER e 175 " --> pdb=" O THR e 171 " (cutoff:3.500A) Processing helix chain 'e' and resid 177 through 195 removed outlier: 3.956A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG e 183 " --> pdb=" O SER e 180 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR e 195 " --> pdb=" O ALA e 192 " (cutoff:3.500A) Processing helix chain 'e' and resid 206 through 208 No H-bonds generated for 'chain 'e' and resid 206 through 208' Processing helix chain 'e' and resid 219 through 221 No H-bonds generated for 'chain 'e' and resid 219 through 221' Processing helix chain 'e' and resid 271 through 295 removed outlier: 3.902A 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 437 Processing helix chain 'e' and resid 442 through 465 removed outlier: 3.984A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL e 457 " --> pdb=" O ASP e 453 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE e 458 " --> pdb=" O ALA e 454 " (cutoff:3.500A) Proline residue: e 459 - end of helix Processing helix chain 'e' and resid 470 through 483 Processing helix chain 'e' and resid 501 through 504 No H-bonds generated for 'chain 'e' and resid 501 through 504' Processing helix chain 'e' and resid 510 through 529 Processing helix chain 'g' and resid 20 through 40 removed outlier: 3.888A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N THR g 39 " --> pdb=" O ASP g 35 " (cutoff:3.500A) removed outlier: 5.962A 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: 3.655A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE g 112 " --> pdb=" O VAL g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 119 through 139 Processing helix chain 'g' and resid 149 through 160 Processing helix chain 'g' and resid 164 through 183 removed outlier: 3.640A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER g 169 " --> pdb=" O SER g 166 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N SER g 170 " --> pdb=" O ARG g 167 " (cutoff:3.500A) Processing helix chain 'g' and resid 209 through 211 No H-bonds generated for 'chain 'g' and resid 209 through 211' Processing helix chain 'g' and resid 261 through 285 removed outlier: 4.127A pdb=" N PHE g 264 " --> pdb=" O GLU g 261 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN g 284 " --> pdb=" O ASP g 281 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU g 285 " --> pdb=" O ILE g 282 " (cutoff:3.500A) Processing helix chain 'g' and resid 298 through 307 removed outlier: 3.545A pdb=" N ALA g 307 " --> pdb=" O TYR g 303 " (cutoff:3.500A) Processing helix chain 'g' and resid 317 through 327 Processing helix chain 'g' and resid 335 through 337 No H-bonds generated for 'chain 'g' and resid 335 through 337' Processing helix chain 'g' and resid 340 through 342 No H-bonds generated for 'chain 'g' and resid 340 through 342' Processing helix chain 'g' and resid 381 through 403 Processing helix chain 'g' and resid 413 through 428 removed outlier: 3.751A pdb=" N LYS g 427 " --> pdb=" O THR g 423 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ALA g 428 " --> pdb=" O GLU g 424 " (cutoff:3.500A) Processing helix chain 'g' and resid 434 through 455 removed outlier: 3.931A pdb=" N LEU g 444 " --> pdb=" O VAL g 440 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU g 445 " --> pdb=" O ALA g 441 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N VAL g 446 " --> pdb=" O GLN g 442 " (cutoff:3.500A) removed outlier: 5.219A 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: 3.555A pdb=" N GLU h 89 " --> pdb=" O GLN h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 113 removed outlier: 4.095A pdb=" N THR h 98 " --> pdb=" O THR h 94 " (cutoff:3.500A) Proline residue: h 110 - end of helix Processing helix chain 'h' and resid 118 through 139 Processing helix chain 'h' and resid 148 through 163 Processing helix chain 'h' and resid 169 through 185 removed outlier: 5.692A pdb=" N ALA h 173 " --> pdb=" O GLN h 170 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE h 175 " --> pdb=" O LYS h 172 " (cutoff:3.500A) Processing helix chain 'h' and resid 192 through 194 No H-bonds generated for 'chain 'h' and resid 192 through 194' Processing helix chain 'h' and resid 205 through 207 No H-bonds generated for 'chain 'h' and resid 205 through 207' Processing helix chain 'h' and resid 225 through 227 No H-bonds generated for 'chain 'h' and resid 225 through 227' Processing helix chain 'h' and resid 260 through 283 Processing helix chain 'h' and resid 297 through 305 Processing helix chain 'h' and resid 316 through 326 Processing helix chain 'h' and resid 339 through 341 No H-bonds generated for 'chain 'h' and resid 339 through 341' Processing helix chain 'h' and resid 379 through 401 Processing helix chain 'h' and resid 411 through 426 removed outlier: 4.171A pdb=" N THR h 426 " --> pdb=" O ASP h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 430 through 453 removed outlier: 4.129A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU h 443 " --> pdb=" O ALA h 439 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE h 444 " --> pdb=" O LYS h 440 " (cutoff:3.500A) removed outlier: 5.287A 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: 4.200A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ALA q 46 " --> pdb=" O THR q 42 " (cutoff:3.500A) Processing helix chain 'q' and resid 69 through 74 Processing helix chain 'q' and resid 81 through 96 Processing helix chain 'q' and resid 101 through 120 Processing helix chain 'q' and resid 125 through 146 Proline residue: q 144 - end of helix Processing helix chain 'q' and resid 157 through 165 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: 4.762A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) removed outlier: 3.919A 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: 3.690A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 456 Proline residue: q 449 - end of helix Processing helix chain 'q' and resid 460 through 473 Processing helix chain 'q' and resid 492 through 495 No H-bonds generated for 'chain 'q' and resid 492 through 495' Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'z' and resid 3 through 7 Processing helix chain 'z' and resid 16 through 37 removed outlier: 3.720A pdb=" N ARG z 35 " --> pdb=" O ASP z 32 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N THR z 36 " --> pdb=" O VAL z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 60 through 65 Processing helix chain 'z' and resid 72 through 87 Processing helix chain 'z' and resid 93 through 112 removed outlier: 3.531A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU z 112 " --> pdb=" O LEU z 108 " (cutoff:3.500A) Processing helix chain 'z' and resid 116 through 137 Processing helix chain 'z' and resid 145 through 159 removed outlier: 4.295A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 162 through 179 removed outlier: 3.583A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) Processing helix chain 'z' and resid 188 through 190 No H-bonds generated for 'chain 'z' and resid 188 through 190' Processing helix chain 'z' and resid 201 through 203 No H-bonds generated for 'chain 'z' and resid 201 through 203' Processing helix chain 'z' and resid 253 through 281 removed outlier: 4.246A pdb=" N ARG z 264 " --> pdb=" O VAL z 260 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LYS z 265 " --> pdb=" O LYS z 261 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N PHE z 266 " --> pdb=" O ALA z 262 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ILE z 267 " --> pdb=" O GLU z 263 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 299 through 308 removed outlier: 3.868A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 318 through 327 removed outlier: 4.305A 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: 3.723A pdb=" N ILE z 447 " --> pdb=" O LEU z 444 " (cutoff:3.500A) Proline residue: z 448 - end of helix Processing helix chain 'z' and resid 459 through 473 Processing helix chain 'z' and resid 489 through 492 No H-bonds generated for 'chain 'z' and resid 489 through 492' Processing helix chain 'z' and resid 498 through 516 Processing helix chain 'P' and resid 57 through 61 Processing helix chain 'P' and resid 63 through 84 removed outlier: 3.737A pdb=" N LEU P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU P 83 " --> pdb=" O GLU P 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 92 No H-bonds generated for 'chain 'P' and resid 89 through 92' Processing helix chain 'P' and resid 137 through 139 No H-bonds generated for 'chain 'P' and resid 137 through 139' Processing helix chain 'P' and resid 141 through 151 removed outlier: 4.431A pdb=" N MET P 145 " --> pdb=" O ARG P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 174 Processing helix chain 'P' and resid 195 through 208 Processing helix chain 'P' and resid 219 through 222 No H-bonds generated for 'chain 'P' and resid 219 through 222' Processing helix chain 'P' and resid 226 through 231 Processing helix chain 'P' and resid 251 through 255 Processing helix chain 'P' and resid 261 through 271 removed outlier: 3.829A pdb=" N PHE P 271 " --> pdb=" O PHE P 267 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'N' and resid 200 through 203 removed outlier: 4.612A pdb=" N ALA N 200 " --> pdb=" O ALA N 213 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA N 213 " --> pdb=" O ALA N 200 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN N 231 " --> pdb=" O LEU N 221 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASP N 223 " --> pdb=" O LEU N 229 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU N 229 " --> pdb=" O ASP N 223 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'N' and resid 240 through 245 removed outlier: 6.729A pdb=" N GLY N 257 " --> pdb=" O LEU N 241 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N LEU N 243 " --> pdb=" O VAL N 255 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL N 255 " --> pdb=" O LEU N 243 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N LEU N 245 " --> pdb=" O THR N 253 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N THR N 253 " --> pdb=" O LEU N 245 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ASP N 267 " --> pdb=" O CYS N 273 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N CYS N 273 " --> pdb=" O ASP N 267 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 9 through 13 Processing sheet with id= D, first strand: chain 'A' and resid 180 through 182 Processing sheet with id= E, first strand: chain 'A' and resid 196 through 199 Processing sheet with id= F, first strand: chain 'A' and resid 213 through 216 Processing sheet with id= G, first strand: chain 'A' and resid 346 through 348 removed outlier: 6.513A pdb=" N VAL A 285 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU A 237 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N LEU A 287 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N MET A 306 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N THR A 288 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL A 308 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 408 through 410 Processing sheet with id= I, first strand: chain 'A' and resid 486 through 489 Processing sheet with id= J, first strand: chain 'B' and resid 17 through 19 Processing sheet with id= K, first strand: chain 'B' and resid 50 through 53 Processing sheet with id= L, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.355A pdb=" N CYS B 371 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N ILE B 202 " --> pdb=" O CYS B 371 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N ILE B 373 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LYS B 204 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LEU B 375 " --> pdb=" O LYS B 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'B' and resid 218 through 220 Processing sheet with id= N, first strand: chain 'B' and resid 344 through 346 removed outlier: 6.919A pdb=" N CYS B 289 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ALA B 240 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ILE B 291 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N MET B 310 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N ASN B 292 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE B 312 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 406 through 408 Processing sheet with id= P, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= Q, first strand: chain 'D' and resid 59 through 62 Processing sheet with id= R, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.795A pdb=" N VAL D 386 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N VAL D 211 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE D 388 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LYS D 213 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL D 390 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 227 through 229 Processing sheet with id= T, first strand: chain 'D' and resid 246 through 249 removed outlier: 6.936A pdb=" N VAL D 297 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE D 249 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU D 299 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N MET D 323 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE D 300 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE D 325 " --> pdb=" O ILE D 300 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'D' and resid 421 through 423 Processing sheet with id= V, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.654A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 59 through 62 Processing sheet with id= X, first strand: chain 'E' and resid 209 through 215 removed outlier: 7.138A pdb=" N VAL E 383 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N GLU E 212 " --> pdb=" O VAL E 383 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ILE E 385 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LYS E 214 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ILE E 387 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 228 through 230 Processing sheet with id= Z, first strand: chain 'E' and resid 354 through 356 removed outlier: 6.978A pdb=" N LEU E 299 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 418 through 420 Processing sheet with id= AB, first strand: chain 'G' and resid 15 through 17 Processing sheet with id= AC, first strand: chain 'G' and resid 48 through 51 Processing sheet with id= AD, first strand: chain 'G' and resid 185 through 187 removed outlier: 3.565A pdb=" N GLU G 187 " --> pdb=" O ARG G 190 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.507A pdb=" N CYS G 372 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N GLU G 202 " --> pdb=" O CYS G 372 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE G 374 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE G 204 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU G 376 " --> pdb=" O ILE G 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'G' and resid 238 through 241 removed outlier: 6.538A pdb=" N VAL G 289 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N LEU G 241 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N ILE G 291 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N THR G 310 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N THR G 292 " --> pdb=" O THR G 310 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE G 312 " --> pdb=" O THR G 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'G' and resid 351 through 355 Processing sheet with id= AH, first strand: chain 'G' and resid 407 through 409 Processing sheet with id= AI, first strand: chain 'G' and resid 478 through 480 Processing sheet with id= AJ, first strand: chain 'H' and resid 14 through 17 Processing sheet with id= AK, first strand: chain 'H' and resid 47 through 50 Processing sheet with id= AL, first strand: chain 'H' and resid 195 through 201 removed outlier: 6.234A pdb=" N CYS H 370 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N LYS H 198 " --> pdb=" O CYS H 370 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N PHE H 372 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL H 200 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LEU H 374 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR H 371 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'H' and resid 214 through 217 Processing sheet with id= AN, first strand: chain 'H' and resid 342 through 344 removed outlier: 6.848A pdb=" N VAL H 288 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU H 240 " --> pdb=" O VAL H 288 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N LEU H 290 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N PHE H 309 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N SER H 291 " --> pdb=" O PHE H 309 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ALA H 311 " --> pdb=" O SER H 291 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'H' and resid 405 through 407 Processing sheet with id= AP, first strand: chain 'H' and resid 475 through 478 removed outlier: 3.706A pdb=" N ALA H 485 " --> pdb=" O GLY H 476 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'Q' and resid 20 through 23 Processing sheet with id= AR, first strand: chain 'Q' and resid 54 through 57 Processing sheet with id= AS, first strand: chain 'Q' and resid 202 through 206 removed outlier: 6.614A pdb=" N SER Q 373 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N CYS Q 205 " --> pdb=" O SER Q 373 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE Q 375 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'Q' and resid 220 through 223 Processing sheet with id= AU, first strand: chain 'Q' and resid 240 through 242 removed outlier: 6.071A pdb=" N MET Q 311 " --> pdb=" O VAL Q 291 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N THR Q 293 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL Q 313 " --> pdb=" O THR Q 293 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'Q' and resid 498 through 500 removed outlier: 4.091A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N VAL Q 147 " --> pdb=" O PRO Q 410 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id= AX, first strand: chain 'Z' and resid 12 through 15 removed outlier: 3.527A pdb=" N GLU Z 12 " --> pdb=" O ARG Z 523 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'Z' and resid 45 through 48 Processing sheet with id= AZ, first strand: chain 'Z' and resid 191 through 196 removed outlier: 7.038A pdb=" N VAL Z 372 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N MET Z 194 " --> pdb=" O VAL Z 372 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LEU Z 374 " --> pdb=" O MET Z 194 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N MET Z 196 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ILE Z 376 " --> pdb=" O MET Z 196 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER Z 205 " --> pdb=" O LEU Z 375 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id= BB, first strand: chain 'Z' and resid 345 through 347 Processing sheet with id= BC, first strand: chain 'Z' and resid 407 through 409 Processing sheet with id= BD, first strand: chain 'Z' and resid 477 through 479 removed outlier: 3.670A pdb=" N MET Z 487 " --> pdb=" O GLY Z 478 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'a' and resid 9 through 13 Processing sheet with id= BF, first strand: chain 'a' and resid 43 through 46 Processing sheet with id= BG, first strand: chain 'a' and resid 180 through 182 Processing sheet with id= BH, first strand: chain 'a' and resid 196 through 201 removed outlier: 3.532A pdb=" N GLY a 379 " --> pdb=" O ALA a 200 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'a' and resid 213 through 216 Processing sheet with id= BJ, first strand: chain 'a' and resid 346 through 348 removed outlier: 6.621A pdb=" N VAL a 285 " --> pdb=" O ALA a 235 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N LEU a 237 " --> pdb=" O VAL a 285 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU a 287 " --> pdb=" O LEU a 237 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N MET a 306 " --> pdb=" O ILE a 286 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N THR a 288 " --> pdb=" O MET a 306 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL a 308 " --> pdb=" O THR a 288 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'a' and resid 408 through 410 Processing sheet with id= BL, first strand: chain 'a' and resid 486 through 489 Processing sheet with id= BM, first strand: chain 'b' and resid 17 through 19 Processing sheet with id= BN, first strand: chain 'b' and resid 50 through 53 Processing sheet with id= BO, first strand: chain 'b' and resid 199 through 205 removed outlier: 6.376A pdb=" N CYS b 371 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE b 202 " --> pdb=" O CYS b 371 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ILE b 373 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LYS b 204 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N LEU b 375 " --> pdb=" O LYS b 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= BO Processing sheet with id= BP, first strand: chain 'b' and resid 218 through 220 Processing sheet with id= BQ, first strand: chain 'b' and resid 344 through 346 removed outlier: 6.882A pdb=" N CYS b 289 " --> pdb=" O LEU b 238 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N ALA b 240 " --> pdb=" O CYS b 289 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE b 291 " --> pdb=" O ALA b 240 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N MET b 310 " --> pdb=" O PHE b 290 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ASN b 292 " --> pdb=" O MET b 310 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE b 312 " --> pdb=" O ASN b 292 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'b' and resid 406 through 408 Processing sheet with id= BS, first strand: chain 'b' and resid 476 through 479 Processing sheet with id= BT, first strand: chain 'd' and resid 59 through 62 Processing sheet with id= BU, first strand: chain 'd' and resid 208 through 214 removed outlier: 6.638A pdb=" N VAL d 386 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N VAL d 211 " --> pdb=" O VAL d 386 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE d 388 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LYS d 213 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N VAL d 390 " --> pdb=" O LYS d 213 " (cutoff:3.500A) No H-bonds generated for sheet with id= BU Processing sheet with id= BV, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.602A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) Processing sheet with id= BW, first strand: chain 'd' and resid 357 through 359 removed outlier: 6.649A pdb=" N VAL d 297 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ILE d 249 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU d 299 " --> pdb=" O ILE d 249 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N MET d 323 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ILE d 300 " --> pdb=" O MET d 323 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE d 325 " --> pdb=" O ILE d 300 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'd' and resid 421 through 423 Processing sheet with id= BY, first strand: chain 'd' and resid 491 through 494 Processing sheet with id= BZ, first strand: chain 'e' and resid 59 through 62 Processing sheet with id= CA, first strand: chain 'e' and resid 209 through 215 removed outlier: 7.273A pdb=" N VAL e 383 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N GLU e 212 " --> pdb=" O VAL e 383 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ILE e 385 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LYS e 214 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ILE e 387 " --> pdb=" O LYS e 214 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'e' and resid 228 through 230 Processing sheet with id= CC, first strand: chain 'e' and resid 354 through 356 removed outlier: 7.057A pdb=" N LEU e 299 " --> pdb=" O ALA e 249 " (cutoff:3.500A) Processing sheet with id= CD, first strand: chain 'e' and resid 418 through 420 Processing sheet with id= CE, first strand: chain 'g' and resid 15 through 18 Processing sheet with id= CF, first strand: chain 'g' and resid 48 through 51 Processing sheet with id= CG, first strand: chain 'g' and resid 185 through 187 Processing sheet with id= CH, first strand: chain 'g' and resid 200 through 205 removed outlier: 3.840A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR g 373 " --> pdb=" O LEU g 215 " (cutoff:3.500A) Processing sheet with id= CI, first strand: chain 'g' and resid 218 through 220 Processing sheet with id= CJ, first strand: chain 'g' and resid 238 through 241 removed outlier: 6.473A pdb=" N VAL g 289 " --> pdb=" O VAL g 239 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LEU g 241 " --> pdb=" O VAL g 289 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE g 291 " --> pdb=" O LEU g 241 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR g 310 " --> pdb=" O VAL g 290 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N THR g 292 " --> pdb=" O THR g 310 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ILE g 312 " --> pdb=" O THR g 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= CJ Processing sheet with id= CK, first strand: chain 'g' and resid 407 through 409 Processing sheet with id= CL, first strand: chain 'g' and resid 478 through 480 Processing sheet with id= CM, first strand: chain 'h' and resid 14 through 17 Processing sheet with id= CN, first strand: chain 'h' and resid 47 through 50 Processing sheet with id= CO, first strand: chain 'h' and resid 195 through 201 removed outlier: 6.646A pdb=" N CYS h 370 " --> pdb=" O GLY h 196 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N LYS h 198 " --> pdb=" O CYS h 370 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N PHE h 372 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N VAL h 200 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU h 374 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR h 371 " --> pdb=" O VAL h 211 " (cutoff:3.500A) Processing sheet with id= CP, first strand: chain 'h' and resid 214 through 217 Processing sheet with id= CQ, first strand: chain 'h' and resid 237 through 240 removed outlier: 6.999A pdb=" N VAL h 288 " --> pdb=" O ALA h 238 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N LEU h 240 " --> pdb=" O VAL h 288 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU h 290 " --> pdb=" O LEU h 240 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N PHE h 309 " --> pdb=" O VAL h 289 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N SER h 291 " --> pdb=" O PHE h 309 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ALA h 311 " --> pdb=" O SER h 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= CQ Processing sheet with id= CR, first strand: chain 'h' and resid 405 through 407 Processing sheet with id= CS, first strand: chain 'h' and resid 475 through 478 Processing sheet with id= CT, first strand: chain 'q' and resid 20 through 23 Processing sheet with id= CU, first strand: chain 'q' and resid 54 through 57 Processing sheet with id= CV, first strand: chain 'q' and resid 202 through 206 removed outlier: 6.592A pdb=" N SER q 373 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N CYS q 205 " --> pdb=" O SER q 373 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N ILE q 375 " --> pdb=" O CYS q 205 " (cutoff:3.500A) Processing sheet with id= CW, first strand: chain 'q' and resid 220 through 223 Processing sheet with id= CX, first strand: chain 'q' and resid 240 through 242 removed outlier: 6.095A pdb=" N MET q 311 " --> pdb=" O VAL q 291 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N THR q 293 " --> pdb=" O MET q 311 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL q 313 " --> pdb=" O THR q 293 " (cutoff:3.500A) Processing sheet with id= CY, first strand: chain 'q' and resid 498 through 500 removed outlier: 3.702A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N VAL q 147 " --> pdb=" O PRO q 410 " (cutoff:3.500A) Processing sheet with id= CZ, first strand: chain 'q' and resid 478 through 480 Processing sheet with id= DA, first strand: chain 'z' and resid 12 through 15 removed outlier: 3.542A pdb=" N GLU z 12 " --> pdb=" O ARG z 523 " (cutoff:3.500A) Processing sheet with id= DB, first strand: chain 'z' and resid 45 through 48 Processing sheet with id= DC, first strand: chain 'z' and resid 192 through 196 Processing sheet with id= DD, first strand: chain 'z' and resid 210 through 212 Processing sheet with id= DE, first strand: chain 'z' and resid 345 through 347 removed outlier: 6.674A pdb=" N VAL z 311 " --> pdb=" O VAL z 291 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N ASN z 293 " --> pdb=" O VAL z 311 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N LEU z 313 " --> pdb=" O ASN z 293 " (cutoff:3.500A) Processing sheet with id= DF, first strand: chain 'z' and resid 477 through 479 Processing sheet with id= DG, first strand: chain 'P' and resid 162 through 164 removed outlier: 4.871A pdb=" N LYS P 218 " --> pdb=" O ILE P 164 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE P 187 " --> pdb=" O ALA P 235 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA P 235 " --> pdb=" O ILE P 187 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE P 238 " --> pdb=" O GLY P 246 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LYS P 240 " --> pdb=" O LEU P 244 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N LEU P 244 " --> pdb=" O LYS P 240 " (cutoff:3.500A) 3487 hydrogen bonds defined for protein. 9060 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: 25.85 Time building geometry restraints manager: 21.44 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: 22735 1.34 - 1.46: 11880 1.46 - 1.58: 32916 1.58 - 1.70: 48 1.70 - 1.81: 740 Bond restraints: 68319 Sorted by residual: bond pdb=" F2 AF3 z 603 " pdb="AL AF3 z 603 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.50e+01 bond pdb=" F2 AF3 G 603 " pdb="AL AF3 G 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.37e+01 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 6.35e+01 bond pdb=" F2 AF3 B 603 " pdb="AL AF3 B 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.34e+01 bond pdb=" F2 AF3 Q 603 " pdb="AL AF3 Q 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.33e+01 ... (remaining 68314 not shown) Histogram of bond angle deviations from ideal: 97.35 - 105.19: 1048 105.19 - 113.03: 39349 113.03 - 120.88: 32191 120.88 - 128.72: 19359 128.72 - 136.56: 295 Bond angle restraints: 92242 Sorted by residual: angle pdb=" CA ARG P 77 " pdb=" CB ARG P 77 " pdb=" CG ARG P 77 " ideal model delta sigma weight residual 114.10 122.67 -8.57 2.00e+00 2.50e-01 1.84e+01 angle pdb=" CB ARG P 149 " pdb=" CG ARG P 149 " pdb=" CD ARG P 149 " ideal model delta sigma weight residual 111.30 119.94 -8.64 2.30e+00 1.89e-01 1.41e+01 angle pdb=" C MET P 148 " pdb=" N ARG P 149 " pdb=" CA ARG P 149 " ideal model delta sigma weight residual 122.38 115.68 6.70 1.81e+00 3.05e-01 1.37e+01 angle pdb=" CA ARG P 149 " pdb=" CB ARG P 149 " pdb=" CG ARG P 149 " ideal model delta sigma weight residual 114.10 121.22 -7.12 2.00e+00 2.50e-01 1.27e+01 angle pdb=" C GLN P 76 " pdb=" N ARG P 77 " pdb=" CA ARG P 77 " ideal model delta sigma weight residual 121.14 115.06 6.08 1.75e+00 3.27e-01 1.21e+01 ... (remaining 92237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 41568 35.54 - 71.09: 590 71.09 - 106.63: 59 106.63 - 142.17: 9 142.17 - 177.71: 6 Dihedral angle restraints: 42232 sinusoidal: 17002 harmonic: 25230 Sorted by residual: dihedral pdb=" O2A ADP g 601 " pdb=" O3A ADP g 601 " pdb=" PA ADP g 601 " pdb=" PB ADP g 601 " ideal model delta sinusoidal sigma weight residual -60.00 117.72 -177.71 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP q 601 " pdb=" O3A ADP q 601 " pdb=" PA ADP q 601 " pdb=" PB ADP q 601 " ideal model delta sinusoidal sigma weight residual 300.00 122.97 177.03 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP z 601 " pdb=" O3A ADP z 601 " pdb=" PA ADP z 601 " pdb=" PB ADP z 601 " ideal model delta sinusoidal sigma weight residual -60.00 116.80 -176.80 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 42229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 7978 0.039 - 0.078: 2107 0.078 - 0.117: 784 0.117 - 0.155: 102 0.155 - 0.194: 4 Chirality restraints: 10975 Sorted by residual: chirality pdb=" CA ARG P 77 " pdb=" N ARG P 77 " pdb=" C ARG P 77 " pdb=" CB ARG P 77 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CB VAL Z 160 " pdb=" CA VAL Z 160 " pdb=" CG1 VAL Z 160 " pdb=" CG2 VAL Z 160 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CB VAL B 320 " pdb=" CA VAL B 320 " pdb=" CG1 VAL B 320 " pdb=" CG2 VAL B 320 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.30e-01 ... (remaining 10972 not shown) Planarity restraints: 11780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 14 " -0.049 5.00e-02 4.00e+02 7.38e-02 8.71e+00 pdb=" N PRO E 15 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO E 15 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 15 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.033 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO e 441 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE b 11 " -0.010 2.00e-02 2.50e+03 2.03e-02 4.14e+00 pdb=" C ILE b 11 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE b 11 " -0.013 2.00e-02 2.50e+03 pdb=" N PHE b 12 " -0.012 2.00e-02 2.50e+03 ... (remaining 11777 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 570 2.53 - 3.12: 51927 3.12 - 3.71: 106746 3.71 - 4.31: 149429 4.31 - 4.90: 255563 Nonbonded interactions: 564235 Sorted by model distance: nonbonded pdb="MG MG H 602 " pdb=" F2 AF3 H 603 " model vdw 1.935 2.120 nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.943 2.120 nonbonded pdb=" OD1 ASP b 97 " pdb="MG MG b 602 " model vdw 1.952 2.170 nonbonded pdb="MG MG e 602 " pdb=" F1 AF3 e 603 " model vdw 1.961 2.120 nonbonded pdb="MG MG z 602 " pdb=" F1 AF3 z 603 " model vdw 1.975 2.120 ... (remaining 564230 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 535 or resid 601 through 603)) selection = chain 'a' } ncs_group { reference = (chain 'B' and (resid 2 through 526 or resid 601 through 603)) selection = chain 'b' } ncs_group { reference = (chain 'D' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 538 or resid 601 through 603)) selection = chain 'd' } ncs_group { reference = (chain 'E' and (resid 8 or resid 10 through 536 or resid 601 through 603)) selection = (chain 'e' and (resid 8 or resid 10 through 536 or resid 601 through 603)) } ncs_group { reference = (chain 'G' and (resid 5 through 528 or resid 601 through 603)) selection = (chain 'g' and (resid 5 through 528 or resid 601 through 603)) } ncs_group { reference = (chain 'H' and (resid 1 through 525 or resid 601 through 603)) selection = chain 'h' } ncs_group { reference = (chain 'Q' and (resid 2 through 534 or resid 601 through 603)) selection = chain 'q' } ncs_group { reference = chain 'Z' selection = (chain 'z' and (resid 2 through 526 or resid 601 through 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 0.040 Extract box with map and model: 8.140 Check model and map are aligned: 0.730 Set scattering table: 0.440 Process input model: 140.990 Find NCS groups from input model: 6.140 Set up NCS constraints: 0.550 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 167.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.161 68319 Z= 0.270 Angle : 0.534 10.330 92242 Z= 0.263 Chirality : 0.041 0.194 10975 Planarity : 0.003 0.074 11780 Dihedral : 14.108 177.714 25894 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.49 % Favored : 96.48 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.09), residues: 8734 helix: 2.46 (0.08), residues: 4471 sheet: 0.18 (0.16), residues: 1173 loop : -0.48 (0.11), residues: 3090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP g 168 HIS 0.013 0.001 HIS Z 161 PHE 0.024 0.001 PHE b 12 TYR 0.016 0.001 TYR h 475 ARG 0.015 0.000 ARG P 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 626 time to evaluate : 5.896 Fit side-chains revert: symmetry clash REVERT: N 228 GLN cc_start: 0.8102 (mp10) cc_final: 0.7606 (mp10) REVERT: N 250 THR cc_start: 0.6852 (t) cc_final: 0.6632 (p) REVERT: A 416 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7752 (mp0) REVERT: A 430 MET cc_start: 0.8180 (mmm) cc_final: 0.7947 (mmm) REVERT: B 30 ILE cc_start: 0.9241 (mm) cc_final: 0.8964 (tt) REVERT: D 63 ASP cc_start: 0.8599 (t70) cc_final: 0.8396 (t70) REVERT: E 21 ASP cc_start: 0.8300 (t70) cc_final: 0.8020 (t0) REVERT: E 532 ASP cc_start: 0.7716 (m-30) cc_final: 0.7410 (m-30) REVERT: H 14 ASP cc_start: 0.8169 (t0) cc_final: 0.7812 (t0) REVERT: H 524 ARG cc_start: 0.7255 (ttp80) cc_final: 0.6896 (tmm160) REVERT: Q 41 GLN cc_start: 0.8710 (tm-30) cc_final: 0.8489 (tm-30) REVERT: Q 318 LYS cc_start: 0.8911 (pptt) cc_final: 0.8585 (pptt) REVERT: e 82 ASP cc_start: 0.8286 (t0) cc_final: 0.7688 (t0) REVERT: g 59 MET cc_start: 0.9062 (ttp) cc_final: 0.8809 (ttp) REVERT: h 70 ASP cc_start: 0.7551 (t0) cc_final: 0.7249 (t0) REVERT: h 130 GLN cc_start: 0.8379 (tp40) cc_final: 0.8036 (tp-100) REVERT: h 324 MET cc_start: 0.9107 (mmm) cc_final: 0.8798 (mmm) REVERT: q 130 GLU cc_start: 0.8307 (tp30) cc_final: 0.7949 (tp30) REVERT: q 249 MET cc_start: 0.8059 (pmm) cc_final: 0.7838 (pmt) REVERT: z 53 ASP cc_start: 0.8578 (m-30) cc_final: 0.8304 (p0) REVERT: z 381 LYS cc_start: 0.8544 (tptm) cc_final: 0.8328 (tppt) REVERT: P 68 ARG cc_start: 0.7855 (tpm170) cc_final: 0.7213 (tpm170) REVERT: P 80 GLN cc_start: 0.8267 (tp-100) cc_final: 0.7761 (tp40) REVERT: P 163 GLU cc_start: 0.8701 (tt0) cc_final: 0.8426 (pp20) outliers start: 0 outliers final: 3 residues processed: 626 average time/residue: 1.5980 time to fit residues: 1289.1793 Evaluate side-chains 473 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 470 time to evaluate : 5.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain a residue 479 GLU Chi-restraints excluded: chain e residue 292 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 733 optimal weight: 6.9990 chunk 658 optimal weight: 9.9990 chunk 365 optimal weight: 6.9990 chunk 224 optimal weight: 4.9990 chunk 444 optimal weight: 9.9990 chunk 351 optimal weight: 5.9990 chunk 681 optimal weight: 10.0000 chunk 263 optimal weight: 6.9990 chunk 414 optimal weight: 8.9990 chunk 506 optimal weight: 10.0000 chunk 789 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 431 GLN Z 161 HIS ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 250 GLN g 390 ASN ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 346 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.052 68319 Z= 0.518 Angle : 0.676 9.751 92242 Z= 0.338 Chirality : 0.045 0.165 10975 Planarity : 0.005 0.065 11780 Dihedral : 7.713 178.084 9492 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.30 % Favored : 95.68 % Rotamer: Outliers : 1.04 % Allowed : 7.27 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.09), residues: 8734 helix: 1.91 (0.08), residues: 4479 sheet: -0.11 (0.16), residues: 1167 loop : -0.56 (0.11), residues: 3088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 266 HIS 0.013 0.001 HIS Z 161 PHE 0.021 0.002 PHE A 167 TYR 0.024 0.002 TYR A 181 ARG 0.008 0.001 ARG e 201 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 463 time to evaluate : 5.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 228 GLN cc_start: 0.8280 (mp10) cc_final: 0.7527 (mp10) REVERT: A 47 ASP cc_start: 0.8055 (t70) cc_final: 0.7642 (t0) REVERT: A 306 MET cc_start: 0.8785 (mtp) cc_final: 0.8389 (mtm) REVERT: A 416 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7918 (mp0) REVERT: A 430 MET cc_start: 0.8186 (mmm) cc_final: 0.7971 (mmm) REVERT: A 473 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8451 (tt0) REVERT: D 63 ASP cc_start: 0.8609 (t70) cc_final: 0.8317 (t70) REVERT: D 320 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8604 (mtt) REVERT: D 332 ASP cc_start: 0.9001 (OUTLIER) cc_final: 0.8787 (m-30) REVERT: E 21 ASP cc_start: 0.8359 (t70) cc_final: 0.8127 (t0) REVERT: E 259 LYS cc_start: 0.9231 (mtpp) cc_final: 0.8990 (mtmm) REVERT: E 474 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.7836 (tmm) REVERT: G 59 MET cc_start: 0.8813 (ttm) cc_final: 0.8590 (ttp) REVERT: G 113 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9022 (mp) REVERT: H 524 ARG cc_start: 0.7255 (ttp80) cc_final: 0.6850 (ttt-90) REVERT: Q 41 GLN cc_start: 0.8761 (tm-30) cc_final: 0.8556 (tm-30) REVERT: Q 318 LYS cc_start: 0.8899 (pptt) cc_final: 0.8599 (pptt) REVERT: g 59 MET cc_start: 0.9152 (ttp) cc_final: 0.8859 (ttp) REVERT: h 7 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8370 (pp) REVERT: h 11 GLU cc_start: 0.8074 (mp0) cc_final: 0.7836 (mp0) REVERT: h 70 ASP cc_start: 0.7710 (t0) cc_final: 0.7339 (t0) REVERT: h 130 GLN cc_start: 0.8490 (tp40) cc_final: 0.8129 (tp-100) REVERT: h 324 MET cc_start: 0.9206 (mmm) cc_final: 0.8847 (mmm) REVERT: h 473 THR cc_start: 0.9276 (OUTLIER) cc_final: 0.9064 (m) REVERT: q 37 LYS cc_start: 0.8950 (tttt) cc_final: 0.8680 (ttmm) REVERT: q 75 GLU cc_start: 0.8262 (mm-30) cc_final: 0.8046 (mp0) REVERT: q 130 GLU cc_start: 0.8419 (tp30) cc_final: 0.8067 (tp30) REVERT: z 53 ASP cc_start: 0.8513 (m-30) cc_final: 0.8176 (p0) outliers start: 76 outliers final: 26 residues processed: 497 average time/residue: 1.4985 time to fit residues: 973.9196 Evaluate side-chains 478 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 445 time to evaluate : 5.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 189 LYS Chi-restraints excluded: chain N residue 253 THR Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 332 ASP Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 233 HIS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain a residue 244 THR Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 503 ILE Chi-restraints excluded: chain e residue 288 MET Chi-restraints excluded: chain g residue 111 HIS Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 185 MET Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain h residue 473 THR Chi-restraints excluded: chain z residue 59 ASP Chi-restraints excluded: chain P residue 69 PHE Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain P residue 252 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 438 optimal weight: 0.7980 chunk 244 optimal weight: 6.9990 chunk 656 optimal weight: 0.9990 chunk 537 optimal weight: 6.9990 chunk 217 optimal weight: 0.9990 chunk 790 optimal weight: 8.9990 chunk 854 optimal weight: 30.0000 chunk 704 optimal weight: 1.9990 chunk 783 optimal weight: 1.9990 chunk 269 optimal weight: 0.8980 chunk 634 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 236 HIS G 390 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS Z 514 ASN ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 390 ASN h 431 GLN ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 80 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 68319 Z= 0.140 Angle : 0.533 9.504 92242 Z= 0.264 Chirality : 0.040 0.154 10975 Planarity : 0.004 0.060 11780 Dihedral : 7.152 178.303 9485 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.01 % Favored : 96.97 % Rotamer: Outliers : 0.93 % Allowed : 9.23 % Favored : 89.84 % 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: 1.24 (0.09), residues: 8734 helix: 1.98 (0.08), residues: 4464 sheet: -0.03 (0.16), residues: 1167 loop : -0.51 (0.11), residues: 3103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 266 HIS 0.012 0.001 HIS Z 161 PHE 0.049 0.001 PHE P 69 TYR 0.022 0.001 TYR A 181 ARG 0.009 0.000 ARG e 201 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 497 time to evaluate : 5.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 225 GLU cc_start: 0.8564 (tp30) cc_final: 0.8192 (tp30) REVERT: N 228 GLN cc_start: 0.8337 (mp10) cc_final: 0.7637 (mp10) REVERT: A 47 ASP cc_start: 0.7918 (t70) cc_final: 0.7497 (t0) REVERT: A 430 MET cc_start: 0.8143 (mmm) cc_final: 0.7897 (mmm) REVERT: A 473 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8174 (tt0) REVERT: B 30 ILE cc_start: 0.9267 (OUTLIER) cc_final: 0.8970 (tt) REVERT: D 63 ASP cc_start: 0.8560 (t70) cc_final: 0.8225 (t70) REVERT: D 320 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8616 (mtt) REVERT: D 524 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7761 (mp0) REVERT: E 21 ASP cc_start: 0.8283 (t70) cc_final: 0.7999 (t0) REVERT: G 52 ASP cc_start: 0.8323 (t0) cc_final: 0.8086 (t0) REVERT: G 59 MET cc_start: 0.8790 (ttm) cc_final: 0.8576 (ttp) REVERT: H 7 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8236 (pp) REVERT: Q 41 GLN cc_start: 0.8704 (tm-30) cc_final: 0.8492 (tm-30) REVERT: Q 116 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8260 (tt0) REVERT: Q 318 LYS cc_start: 0.8889 (pptt) cc_final: 0.8591 (pptt) REVERT: a 44 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8825 (ptp) REVERT: g 20 ARG cc_start: 0.7845 (tpp80) cc_final: 0.7560 (mmm-85) REVERT: g 59 MET cc_start: 0.9101 (ttp) cc_final: 0.8886 (ttp) REVERT: h 7 ILE cc_start: 0.8790 (OUTLIER) cc_final: 0.8342 (pp) REVERT: h 70 ASP cc_start: 0.7633 (t0) cc_final: 0.7284 (t0) REVERT: h 130 GLN cc_start: 0.8344 (tp40) cc_final: 0.8018 (tp-100) REVERT: h 324 MET cc_start: 0.9158 (mmm) cc_final: 0.8762 (mmm) REVERT: q 130 GLU cc_start: 0.8341 (tp30) cc_final: 0.7954 (tp30) REVERT: z 53 ASP cc_start: 0.8501 (m-30) cc_final: 0.8228 (p0) REVERT: P 80 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7813 (tp40) REVERT: P 86 ARG cc_start: 0.8225 (tpt170) cc_final: 0.8018 (tpt170) outliers start: 68 outliers final: 23 residues processed: 536 average time/residue: 1.4616 time to fit residues: 1028.9046 Evaluate side-chains 495 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 463 time to evaluate : 5.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 233 HIS Chi-restraints excluded: chain Q residue 116 GLU Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 44 MET Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain e residue 292 ILE Chi-restraints excluded: chain g residue 246 GLU Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 59 ASP Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 80 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 781 optimal weight: 8.9990 chunk 594 optimal weight: 10.0000 chunk 410 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 377 optimal weight: 9.9990 chunk 530 optimal weight: 3.9990 chunk 793 optimal weight: 6.9990 chunk 839 optimal weight: 3.9990 chunk 414 optimal weight: 10.0000 chunk 751 optimal weight: 10.0000 chunk 226 optimal weight: 0.7980 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 236 HIS ** D 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 390 ASN z 218 HIS ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 80 GLN ** P 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 68319 Z= 0.409 Angle : 0.612 9.789 92242 Z= 0.301 Chirality : 0.043 0.159 10975 Planarity : 0.004 0.060 11780 Dihedral : 7.200 178.152 9485 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.21 % Favored : 95.78 % Rotamer: Outliers : 1.33 % Allowed : 10.54 % Favored : 88.13 % 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: 1.13 (0.09), residues: 8734 helix: 1.87 (0.08), residues: 4479 sheet: -0.08 (0.16), residues: 1155 loop : -0.54 (0.11), residues: 3100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP g 168 HIS 0.015 0.001 HIS P 186 PHE 0.017 0.002 PHE P 69 TYR 0.019 0.001 TYR A 181 ARG 0.006 0.000 ARG P 250 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 456 time to evaluate : 5.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 225 GLU cc_start: 0.8527 (tp30) cc_final: 0.8290 (tp30) REVERT: A 47 ASP cc_start: 0.8025 (t70) cc_final: 0.7569 (t0) REVERT: A 306 MET cc_start: 0.8690 (mtp) cc_final: 0.8302 (mtm) REVERT: A 344 MET cc_start: 0.8528 (mmm) cc_final: 0.8308 (mmm) REVERT: A 430 MET cc_start: 0.8191 (mmm) cc_final: 0.7971 (mmm) REVERT: A 473 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8317 (tt0) REVERT: D 63 ASP cc_start: 0.8640 (t70) cc_final: 0.8307 (t70) REVERT: D 320 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8554 (mtt) REVERT: D 524 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7844 (mp0) REVERT: E 21 ASP cc_start: 0.8325 (t70) cc_final: 0.8047 (t0) REVERT: E 259 LYS cc_start: 0.9172 (mtmm) cc_final: 0.8939 (mtpp) REVERT: G 59 MET cc_start: 0.8841 (ttm) cc_final: 0.8636 (ttp) REVERT: Q 41 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8549 (tm-30) REVERT: Q 116 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8392 (tt0) REVERT: Q 318 LYS cc_start: 0.8893 (pptt) cc_final: 0.8600 (pptt) REVERT: b 415 MET cc_start: 0.9282 (mmm) cc_final: 0.8882 (mmp) REVERT: b 452 ASP cc_start: 0.8378 (m-30) cc_final: 0.8023 (m-30) REVERT: g 59 MET cc_start: 0.9110 (ttp) cc_final: 0.8843 (ttp) REVERT: h 70 ASP cc_start: 0.7705 (t0) cc_final: 0.7343 (t0) REVERT: h 130 GLN cc_start: 0.8499 (tp40) cc_final: 0.8161 (tp-100) REVERT: h 324 MET cc_start: 0.9181 (mmm) cc_final: 0.8831 (mmm) REVERT: h 473 THR cc_start: 0.9250 (OUTLIER) cc_final: 0.9034 (m) REVERT: q 37 LYS cc_start: 0.8939 (tttt) cc_final: 0.8712 (ttmm) REVERT: q 130 GLU cc_start: 0.8415 (tp30) cc_final: 0.8019 (tp30) REVERT: z 53 ASP cc_start: 0.8514 (m-30) cc_final: 0.8153 (p0) REVERT: P 80 GLN cc_start: 0.8246 (tp-100) cc_final: 0.7881 (mm110) REVERT: P 82 ARG cc_start: 0.7803 (tpp80) cc_final: 0.7505 (tpp80) REVERT: P 198 MET cc_start: 0.8715 (pp-130) cc_final: 0.8458 (pp-130) outliers start: 97 outliers final: 47 residues processed: 513 average time/residue: 1.4864 time to fit residues: 1003.1944 Evaluate side-chains 501 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 449 time to evaluate : 5.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 189 LYS Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 219 CYS Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain N residue 232 SER Chi-restraints excluded: chain N residue 253 THR Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 233 HIS Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 116 GLU Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 415 LEU Chi-restraints excluded: chain d residue 503 ILE Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain g residue 246 GLU Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 39 THR Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain h residue 473 THR Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain z residue 59 ASP Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 699 optimal weight: 6.9990 chunk 476 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 625 optimal weight: 4.9990 chunk 346 optimal weight: 2.9990 chunk 716 optimal weight: 9.9990 chunk 580 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 428 optimal weight: 9.9990 chunk 753 optimal weight: 1.9990 chunk 211 optimal weight: 6.9990 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 236 HIS ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 390 ASN ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 68319 Z= 0.261 Angle : 0.562 10.350 92242 Z= 0.275 Chirality : 0.041 0.151 10975 Planarity : 0.004 0.058 11780 Dihedral : 7.094 178.030 9485 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.74 % Favored : 96.25 % Rotamer: Outliers : 1.34 % Allowed : 11.44 % Favored : 87.22 % 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: 1.14 (0.09), residues: 8734 helix: 1.90 (0.08), residues: 4467 sheet: -0.13 (0.16), residues: 1151 loop : -0.54 (0.11), residues: 3116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 168 HIS 0.015 0.001 HIS Z 161 PHE 0.021 0.001 PHE P 69 TYR 0.019 0.001 TYR A 181 ARG 0.006 0.000 ARG h 524 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 471 time to evaluate : 5.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 225 GLU cc_start: 0.8523 (tp30) cc_final: 0.8251 (tp30) REVERT: A 47 ASP cc_start: 0.7988 (t70) cc_final: 0.7536 (t0) REVERT: A 430 MET cc_start: 0.8168 (mmm) cc_final: 0.7938 (mmm) REVERT: A 473 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8185 (tt0) REVERT: D 63 ASP cc_start: 0.8601 (t70) cc_final: 0.8255 (t70) REVERT: D 320 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8551 (mtt) REVERT: D 524 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7814 (mp0) REVERT: E 21 ASP cc_start: 0.8311 (t70) cc_final: 0.8026 (t0) REVERT: E 474 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7790 (tmm) REVERT: G 59 MET cc_start: 0.8842 (ttm) cc_final: 0.8632 (ttp) REVERT: H 7 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8273 (pp) REVERT: Q 41 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8529 (tm-30) REVERT: Q 116 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8340 (tt0) REVERT: Q 318 LYS cc_start: 0.8904 (pptt) cc_final: 0.8618 (pptt) REVERT: b 415 MET cc_start: 0.9300 (mmm) cc_final: 0.8841 (mmp) REVERT: b 452 ASP cc_start: 0.8345 (m-30) cc_final: 0.7963 (m-30) REVERT: g 59 MET cc_start: 0.9093 (ttp) cc_final: 0.8892 (ttp) REVERT: h 70 ASP cc_start: 0.7692 (t0) cc_final: 0.7317 (t0) REVERT: h 130 GLN cc_start: 0.8438 (tp40) cc_final: 0.8106 (tp-100) REVERT: h 324 MET cc_start: 0.9158 (mmm) cc_final: 0.8834 (mmm) REVERT: q 37 LYS cc_start: 0.8896 (tttt) cc_final: 0.8661 (ttmm) REVERT: q 130 GLU cc_start: 0.8401 (tp30) cc_final: 0.8011 (tp30) REVERT: z 53 ASP cc_start: 0.8515 (m-30) cc_final: 0.8164 (p0) REVERT: P 80 GLN cc_start: 0.8242 (tp-100) cc_final: 0.7771 (mm110) REVERT: P 82 ARG cc_start: 0.7857 (tpp80) cc_final: 0.7345 (tpp80) REVERT: P 84 MET cc_start: 0.8491 (mmp) cc_final: 0.8137 (mmp) outliers start: 98 outliers final: 48 residues processed: 533 average time/residue: 1.4864 time to fit residues: 1044.8252 Evaluate side-chains 508 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 454 time to evaluate : 5.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 189 LYS Chi-restraints excluded: chain N residue 219 CYS Chi-restraints excluded: chain N residue 232 SER Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 184 MET Chi-restraints excluded: chain H residue 233 HIS Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 116 GLU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 7 LEU Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 415 LEU Chi-restraints excluded: chain d residue 503 ILE Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain g residue 246 GLU Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 39 THR Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain h residue 473 THR Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 59 ASP Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 77 ARG Chi-restraints excluded: chain P residue 165 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 282 optimal weight: 6.9990 chunk 756 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 493 optimal weight: 0.6980 chunk 207 optimal weight: 6.9990 chunk 840 optimal weight: 6.9990 chunk 697 optimal weight: 6.9990 chunk 389 optimal weight: 7.9990 chunk 69 optimal weight: 8.9990 chunk 278 optimal weight: 5.9990 chunk 441 optimal weight: 10.0000 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 236 HIS B 469 HIS ** D 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 467 GLN P 199 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 68319 Z= 0.431 Angle : 0.627 13.483 92242 Z= 0.309 Chirality : 0.044 0.166 10975 Planarity : 0.004 0.061 11780 Dihedral : 7.155 176.897 9485 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.43 % Favored : 95.54 % Rotamer: Outliers : 1.57 % Allowed : 11.85 % Favored : 86.57 % 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: 1.01 (0.09), residues: 8734 helix: 1.78 (0.08), residues: 4479 sheet: -0.21 (0.16), residues: 1169 loop : -0.58 (0.11), residues: 3086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 168 HIS 0.014 0.001 HIS Z 161 PHE 0.021 0.002 PHE P 69 TYR 0.017 0.001 TYR A 181 ARG 0.005 0.000 ARG P 250 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 457 time to evaluate : 5.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8033 (t70) cc_final: 0.7558 (t0) REVERT: A 344 MET cc_start: 0.8642 (mmm) cc_final: 0.8416 (mmm) REVERT: A 430 MET cc_start: 0.8175 (mmm) cc_final: 0.7944 (mmm) REVERT: A 473 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8304 (tt0) REVERT: D 63 ASP cc_start: 0.8621 (t70) cc_final: 0.8262 (t70) REVERT: D 320 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8534 (mtt) REVERT: D 524 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: E 21 ASP cc_start: 0.8336 (t70) cc_final: 0.8062 (t0) REVERT: E 259 LYS cc_start: 0.9180 (mtmm) cc_final: 0.8949 (mtpp) REVERT: E 474 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.7803 (tmm) REVERT: Q 41 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8563 (tm-30) REVERT: Q 116 GLU cc_start: 0.8854 (OUTLIER) cc_final: 0.8453 (tt0) REVERT: b 452 ASP cc_start: 0.8409 (m-30) cc_final: 0.8055 (m-30) REVERT: d 48 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8424 (pp) REVERT: g 20 ARG cc_start: 0.7996 (tpp80) cc_final: 0.7758 (mmm-85) REVERT: g 59 MET cc_start: 0.9108 (ttp) cc_final: 0.8896 (ttp) REVERT: h 70 ASP cc_start: 0.7729 (t0) cc_final: 0.7341 (t0) REVERT: h 130 GLN cc_start: 0.8516 (tp40) cc_final: 0.8164 (tp-100) REVERT: h 185 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.7883 (mpp) REVERT: h 324 MET cc_start: 0.9159 (mmm) cc_final: 0.8837 (mmm) REVERT: q 37 LYS cc_start: 0.8954 (tttt) cc_final: 0.8708 (ttmm) REVERT: q 130 GLU cc_start: 0.8420 (tp30) cc_final: 0.8033 (tp30) REVERT: z 53 ASP cc_start: 0.8541 (m-30) cc_final: 0.8156 (p0) REVERT: P 68 ARG cc_start: 0.7929 (tpm170) cc_final: 0.7125 (tpm170) REVERT: P 80 GLN cc_start: 0.8226 (tp-100) cc_final: 0.7699 (mm110) REVERT: P 84 MET cc_start: 0.8501 (mmp) cc_final: 0.7984 (mmm) REVERT: P 198 MET cc_start: 0.8665 (pp-130) cc_final: 0.8424 (pp-130) outliers start: 115 outliers final: 64 residues processed: 531 average time/residue: 1.4871 time to fit residues: 1032.0435 Evaluate side-chains 519 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 448 time to evaluate : 5.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 189 LYS Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 219 CYS Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain N residue 232 SER Chi-restraints excluded: chain N residue 253 THR Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 316 ASP Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 184 MET Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 233 HIS Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 116 GLU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 67 VAL Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 415 LEU Chi-restraints excluded: chain d residue 503 ILE Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain g residue 111 HIS Chi-restraints excluded: chain g residue 194 ASP Chi-restraints excluded: chain g residue 246 GLU Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 39 THR Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 185 MET Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 276 MET Chi-restraints excluded: chain q residue 344 MET Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 59 ASP Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 77 ARG Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain P residue 252 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 810 optimal weight: 9.9990 chunk 94 optimal weight: 7.9990 chunk 479 optimal weight: 1.9990 chunk 614 optimal weight: 7.9990 chunk 475 optimal weight: 6.9990 chunk 707 optimal weight: 3.9990 chunk 469 optimal weight: 5.9990 chunk 837 optimal weight: 7.9990 chunk 524 optimal weight: 7.9990 chunk 510 optimal weight: 1.9990 chunk 386 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 236 HIS B 469 HIS ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 68319 Z= 0.277 Angle : 0.578 12.357 92242 Z= 0.282 Chirality : 0.042 0.159 10975 Planarity : 0.004 0.059 11780 Dihedral : 7.000 173.020 9485 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.74 % Favored : 96.24 % Rotamer: Outliers : 1.37 % Allowed : 12.73 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.09), residues: 8734 helix: 1.86 (0.08), residues: 4466 sheet: -0.18 (0.16), residues: 1155 loop : -0.55 (0.11), residues: 3113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 168 HIS 0.015 0.001 HIS Z 161 PHE 0.019 0.001 PHE P 69 TYR 0.018 0.001 TYR A 181 ARG 0.005 0.000 ARG e 201 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 466 time to evaluate : 6.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 209 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8664 (pt0) REVERT: N 228 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.7470 (mp10) REVERT: A 47 ASP cc_start: 0.7965 (t70) cc_final: 0.7491 (t0) REVERT: A 430 MET cc_start: 0.8227 (mmm) cc_final: 0.7987 (mmm) REVERT: A 473 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8229 (tt0) REVERT: B 18 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8474 (pt0) REVERT: D 63 ASP cc_start: 0.8580 (t70) cc_final: 0.8213 (t70) REVERT: D 524 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7837 (mp0) REVERT: E 21 ASP cc_start: 0.8318 (t70) cc_final: 0.8042 (t0) REVERT: E 474 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.7811 (tmm) REVERT: H 524 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.6744 (ptm-80) REVERT: Q 41 GLN cc_start: 0.8777 (tm-30) cc_final: 0.8526 (tm-30) REVERT: Q 116 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8351 (tt0) REVERT: b 452 ASP cc_start: 0.8371 (m-30) cc_final: 0.8003 (m-30) REVERT: g 20 ARG cc_start: 0.7911 (tpp80) cc_final: 0.7669 (mmm-85) REVERT: h 1 MET cc_start: 0.4152 (tpt) cc_final: 0.3866 (tpt) REVERT: h 70 ASP cc_start: 0.7702 (t0) cc_final: 0.7312 (t0) REVERT: h 130 GLN cc_start: 0.8463 (tp40) cc_final: 0.8133 (tp-100) REVERT: h 324 MET cc_start: 0.9143 (mmm) cc_final: 0.8813 (mmm) REVERT: q 37 LYS cc_start: 0.8943 (tttt) cc_final: 0.8686 (ttmm) REVERT: q 130 GLU cc_start: 0.8392 (tp30) cc_final: 0.7997 (tp30) REVERT: z 53 ASP cc_start: 0.8573 (m-30) cc_final: 0.8213 (p0) REVERT: P 80 GLN cc_start: 0.8195 (tp-100) cc_final: 0.7633 (mm110) REVERT: P 84 MET cc_start: 0.8522 (mmp) cc_final: 0.8018 (mmm) outliers start: 100 outliers final: 57 residues processed: 532 average time/residue: 1.4890 time to fit residues: 1045.4048 Evaluate side-chains 515 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 450 time to evaluate : 5.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 189 LYS Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 209 GLN Chi-restraints excluded: chain N residue 219 CYS Chi-restraints excluded: chain N residue 228 GLN Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain N residue 253 THR Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain D residue 276 LEU Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 184 MET Chi-restraints excluded: chain H residue 233 HIS Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain H residue 524 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 116 GLU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 67 VAL 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 b residue 39 VAL Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 415 LEU Chi-restraints excluded: chain d residue 503 ILE Chi-restraints excluded: chain g residue 246 GLU Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 39 THR Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 276 MET Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 59 ASP Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 77 ARG Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain P residue 212 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 518 optimal weight: 7.9990 chunk 334 optimal weight: 8.9990 chunk 500 optimal weight: 0.9990 chunk 252 optimal weight: 3.9990 chunk 164 optimal weight: 0.8980 chunk 162 optimal weight: 9.9990 chunk 532 optimal weight: 0.9990 chunk 570 optimal weight: 5.9990 chunk 414 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 658 optimal weight: 0.5980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 469 HIS ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 68319 Z= 0.172 Angle : 0.545 15.182 92242 Z= 0.265 Chirality : 0.041 0.232 10975 Planarity : 0.003 0.053 11780 Dihedral : 6.715 164.889 9485 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.63 % Favored : 96.36 % Rotamer: Outliers : 1.04 % Allowed : 13.36 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.09), residues: 8734 helix: 1.96 (0.08), residues: 4461 sheet: -0.10 (0.16), residues: 1154 loop : -0.50 (0.11), residues: 3119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP q 319 HIS 0.016 0.001 HIS Z 161 PHE 0.017 0.001 PHE P 69 TYR 0.018 0.001 TYR A 181 ARG 0.007 0.000 ARG e 201 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 493 time to evaluate : 6.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 209 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.8669 (pt0) REVERT: N 225 GLU cc_start: 0.8398 (tp30) cc_final: 0.8190 (tp30) REVERT: A 47 ASP cc_start: 0.7835 (t70) cc_final: 0.7400 (OUTLIER) REVERT: A 430 MET cc_start: 0.8200 (mmm) cc_final: 0.7975 (mmm) REVERT: A 473 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8202 (tt0) REVERT: B 86 ASP cc_start: 0.8955 (t0) cc_final: 0.8728 (t0) REVERT: D 63 ASP cc_start: 0.8536 (t70) cc_final: 0.8175 (t70) REVERT: D 118 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8270 (m-30) REVERT: D 320 MET cc_start: 0.8920 (OUTLIER) cc_final: 0.8507 (mtt) REVERT: D 524 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: E 21 ASP cc_start: 0.8297 (t70) cc_final: 0.8009 (t0) REVERT: E 468 MET cc_start: 0.8790 (mtm) cc_final: 0.8552 (ptm) REVERT: Q 41 GLN cc_start: 0.8739 (tm-30) cc_final: 0.8486 (tm-30) REVERT: Q 116 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8215 (tt0) REVERT: Q 318 LYS cc_start: 0.8896 (pptt) cc_final: 0.8666 (pptt) REVERT: a 473 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7746 (tm-30) REVERT: b 415 MET cc_start: 0.9171 (mmm) cc_final: 0.8870 (mmp) REVERT: b 452 ASP cc_start: 0.8375 (m-30) cc_final: 0.7950 (m-30) REVERT: e 456 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8126 (mt-10) REVERT: g 20 ARG cc_start: 0.7846 (tpp80) cc_final: 0.7580 (mmm-85) REVERT: h 70 ASP cc_start: 0.7672 (t0) cc_final: 0.7307 (t0) REVERT: h 130 GLN cc_start: 0.8383 (tp40) cc_final: 0.8053 (tp-100) REVERT: h 324 MET cc_start: 0.9124 (mmm) cc_final: 0.8801 (mmm) REVERT: q 37 LYS cc_start: 0.8887 (tttt) cc_final: 0.8627 (ttmm) REVERT: q 130 GLU cc_start: 0.8362 (tp30) cc_final: 0.7958 (tp30) REVERT: q 249 MET cc_start: 0.8160 (pmm) cc_final: 0.7904 (pmt) REVERT: q 498 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9036 (mt) REVERT: z 53 ASP cc_start: 0.8556 (m-30) cc_final: 0.8231 (p0) REVERT: z 520 GLU cc_start: 0.8241 (tt0) cc_final: 0.7965 (tt0) REVERT: P 82 ARG cc_start: 0.7845 (tpp80) cc_final: 0.7638 (tpp80) REVERT: P 173 MET cc_start: 0.8725 (ppp) cc_final: 0.8508 (ppp) REVERT: P 231 ASN cc_start: 0.8501 (m110) cc_final: 0.8230 (p0) outliers start: 76 outliers final: 48 residues processed: 546 average time/residue: 1.4552 time to fit residues: 1054.2600 Evaluate side-chains 514 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 460 time to evaluate : 5.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 189 LYS Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 209 GLN Chi-restraints excluded: chain N residue 219 CYS Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain N residue 236 HIS Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 184 MET Chi-restraints excluded: chain H residue 233 HIS Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain Q residue 116 GLU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 108 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 503 ILE Chi-restraints excluded: chain e residue 292 ILE Chi-restraints excluded: chain g residue 246 GLU Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 39 THR Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 498 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 59 ASP Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 77 ARG Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain P residue 212 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 761 optimal weight: 8.9990 chunk 802 optimal weight: 10.0000 chunk 732 optimal weight: 6.9990 chunk 780 optimal weight: 6.9990 chunk 469 optimal weight: 9.9990 chunk 340 optimal weight: 0.8980 chunk 612 optimal weight: 6.9990 chunk 239 optimal weight: 10.0000 chunk 705 optimal weight: 0.0040 chunk 738 optimal weight: 8.9990 chunk 777 optimal weight: 8.9990 overall best weight: 4.3798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 HIS ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 501 ASN Z 161 HIS ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 68319 Z= 0.365 Angle : 0.613 12.595 92242 Z= 0.299 Chirality : 0.043 0.198 10975 Planarity : 0.004 0.058 11780 Dihedral : 6.869 165.274 9485 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.30 % Favored : 95.68 % Rotamer: Outliers : 1.09 % Allowed : 13.49 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.09), residues: 8734 helix: 1.88 (0.08), residues: 4470 sheet: -0.18 (0.16), residues: 1164 loop : -0.54 (0.11), residues: 3100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP q 319 HIS 0.014 0.001 HIS Z 161 PHE 0.017 0.001 PHE P 69 TYR 0.017 0.001 TYR z 353 ARG 0.004 0.000 ARG G 228 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 455 time to evaluate : 5.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 209 GLN cc_start: 0.9074 (OUTLIER) cc_final: 0.8801 (pt0) REVERT: N 228 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.7443 (mp10) REVERT: A 47 ASP cc_start: 0.7963 (t70) cc_final: 0.7482 (t0) REVERT: A 306 MET cc_start: 0.8728 (mtp) cc_final: 0.8253 (mtm) REVERT: A 344 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8153 (mmm) REVERT: A 416 GLU cc_start: 0.8465 (mp0) cc_final: 0.7906 (mp0) REVERT: A 430 MET cc_start: 0.8187 (mmm) cc_final: 0.7973 (mmm) REVERT: A 473 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8311 (tt0) REVERT: D 63 ASP cc_start: 0.8578 (t70) cc_final: 0.8210 (t70) REVERT: D 118 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8283 (m-30) REVERT: D 524 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7843 (mp0) REVERT: E 21 ASP cc_start: 0.8324 (t70) cc_final: 0.8035 (t0) REVERT: E 468 MET cc_start: 0.8841 (mtm) cc_final: 0.8457 (ptm) REVERT: E 474 MET cc_start: 0.8464 (OUTLIER) cc_final: 0.7829 (tmm) REVERT: Q 41 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8517 (tm-30) REVERT: Z 46 MET cc_start: 0.8859 (tpp) cc_final: 0.8469 (ttt) REVERT: b 452 ASP cc_start: 0.8417 (m-30) cc_final: 0.8008 (m-30) REVERT: e 29 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.7737 (ttm) REVERT: h 130 GLN cc_start: 0.8486 (tp40) cc_final: 0.8137 (tp-100) REVERT: h 324 MET cc_start: 0.9132 (mmm) cc_final: 0.8813 (mmm) REVERT: q 37 LYS cc_start: 0.8950 (tttt) cc_final: 0.8683 (ttmm) REVERT: q 130 GLU cc_start: 0.8397 (tp30) cc_final: 0.8004 (tp30) REVERT: z 53 ASP cc_start: 0.8559 (m-30) cc_final: 0.8187 (p0) REVERT: P 84 MET cc_start: 0.8574 (mmp) cc_final: 0.8306 (mmm) REVERT: P 198 MET cc_start: 0.8786 (pp-130) cc_final: 0.8514 (pp-130) outliers start: 80 outliers final: 52 residues processed: 503 average time/residue: 1.5140 time to fit residues: 1002.5517 Evaluate side-chains 508 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 448 time to evaluate : 5.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 209 GLN Chi-restraints excluded: chain N residue 219 CYS Chi-restraints excluded: chain N residue 228 GLN Chi-restraints excluded: chain N residue 230 LEU Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 184 MET Chi-restraints excluded: chain H residue 233 HIS Chi-restraints excluded: chain H residue 251 ASP Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 56 LEU Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 415 LEU Chi-restraints excluded: chain d residue 503 ILE Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain g residue 246 GLU Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 39 THR Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 276 MET Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 59 ASP Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 77 ARG Chi-restraints excluded: chain P residue 165 SER Chi-restraints excluded: chain P residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 512 optimal weight: 7.9990 chunk 825 optimal weight: 4.9990 chunk 503 optimal weight: 4.9990 chunk 391 optimal weight: 2.9990 chunk 573 optimal weight: 10.0000 chunk 865 optimal weight: 9.9990 chunk 796 optimal weight: 9.9990 chunk 689 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 532 optimal weight: 0.9990 chunk 422 optimal weight: 6.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 HIS ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 501 ASN Z 161 HIS ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 68319 Z= 0.209 Angle : 0.568 13.750 92242 Z= 0.275 Chirality : 0.041 0.149 10975 Planarity : 0.004 0.052 11780 Dihedral : 6.751 161.490 9485 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.74 % Favored : 96.25 % Rotamer: Outliers : 0.98 % Allowed : 13.74 % Favored : 85.27 % 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: 1.16 (0.09), residues: 8734 helix: 1.92 (0.08), residues: 4468 sheet: -0.13 (0.16), residues: 1151 loop : -0.52 (0.11), residues: 3115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP q 319 HIS 0.016 0.001 HIS Z 161 PHE 0.016 0.001 PHE P 69 TYR 0.017 0.001 TYR A 181 ARG 0.021 0.000 ARG P 149 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 471 time to evaluate : 6.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 209 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8745 (pt0) REVERT: N 228 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.7428 (mp10) REVERT: A 47 ASP cc_start: 0.7917 (t70) cc_final: 0.7441 (OUTLIER) REVERT: A 293 ASP cc_start: 0.8159 (OUTLIER) cc_final: 0.7952 (p0) REVERT: A 344 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8061 (mmm) REVERT: A 416 GLU cc_start: 0.8404 (mp0) cc_final: 0.7837 (mp0) REVERT: A 430 MET cc_start: 0.8222 (mmm) cc_final: 0.7994 (mmm) REVERT: A 473 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.8155 (tt0) REVERT: B 18 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8428 (pt0) REVERT: D 63 ASP cc_start: 0.8570 (t70) cc_final: 0.8219 (t70) REVERT: D 118 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.8272 (m-30) REVERT: D 524 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: E 21 ASP cc_start: 0.8303 (t70) cc_final: 0.8008 (t0) REVERT: E 48 MET cc_start: 0.9082 (tpp) cc_final: 0.8827 (mmm) REVERT: E 468 MET cc_start: 0.8786 (mtm) cc_final: 0.8401 (ptm) REVERT: E 474 MET cc_start: 0.8444 (OUTLIER) cc_final: 0.7810 (tmm) REVERT: Q 41 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8489 (tm-30) REVERT: Z 46 MET cc_start: 0.8811 (tpp) cc_final: 0.8430 (ttt) REVERT: b 415 MET cc_start: 0.9154 (mmm) cc_final: 0.8746 (mmp) REVERT: b 452 ASP cc_start: 0.8382 (m-30) cc_final: 0.7968 (m-30) REVERT: e 456 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8061 (mm-30) REVERT: e 460 MET cc_start: 0.8444 (mtt) cc_final: 0.8192 (mtt) REVERT: g 20 ARG cc_start: 0.7899 (tpp80) cc_final: 0.7655 (mmm-85) REVERT: h 130 GLN cc_start: 0.8411 (tp40) cc_final: 0.8060 (tp-100) REVERT: h 324 MET cc_start: 0.9114 (mmm) cc_final: 0.8790 (mmm) REVERT: q 37 LYS cc_start: 0.8899 (tttt) cc_final: 0.8633 (ttmm) REVERT: q 130 GLU cc_start: 0.8369 (tp30) cc_final: 0.7976 (tp30) REVERT: z 53 ASP cc_start: 0.8564 (m-30) cc_final: 0.8218 (p0) REVERT: z 520 GLU cc_start: 0.8253 (tt0) cc_final: 0.7967 (tt0) REVERT: P 82 ARG cc_start: 0.7763 (tpp80) cc_final: 0.7435 (tpp80) REVERT: P 84 MET cc_start: 0.8542 (mmp) cc_final: 0.8269 (mmm) REVERT: P 231 ASN cc_start: 0.8675 (m-40) cc_final: 0.7519 (t0) outliers start: 72 outliers final: 51 residues processed: 518 average time/residue: 1.5071 time to fit residues: 1023.6643 Evaluate side-chains 521 residues out of total 7312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 462 time to evaluate : 6.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 190 SER Chi-restraints excluded: chain N residue 209 GLN Chi-restraints excluded: chain N residue 219 CYS Chi-restraints excluded: chain N residue 228 GLN Chi-restraints excluded: chain N residue 236 HIS Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain B residue 18 GLU Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 524 GLU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain G residue 341 ASP Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 70 ASP Chi-restraints excluded: chain H residue 184 MET Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 233 HIS Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain H residue 400 ILE Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 44 MET Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain a residue 344 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 503 ILE Chi-restraints excluded: chain e residue 292 ILE Chi-restraints excluded: chain g residue 246 GLU Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain h residue 39 THR Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 251 ASP Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 59 ASP Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 65 ASP Chi-restraints excluded: chain P residue 77 ARG Chi-restraints excluded: chain P residue 165 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 547 optimal weight: 9.9990 chunk 734 optimal weight: 9.9990 chunk 211 optimal weight: 6.9990 chunk 635 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 191 optimal weight: 1.9990 chunk 690 optimal weight: 0.9990 chunk 288 optimal weight: 0.9980 chunk 709 optimal weight: 0.3980 chunk 87 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 469 HIS ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS a 217 ASN ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.068973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.056336 restraints weight = 197024.514| |-----------------------------------------------------------------------------| r_work (start): 0.2693 rms_B_bonded: 3.13 r_work: 0.2545 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2551 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2551 r_free = 0.2551 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2551 r_free = 0.2551 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2551 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 68319 Z= 0.208 Angle : 0.565 14.396 92242 Z= 0.273 Chirality : 0.041 0.154 10975 Planarity : 0.003 0.058 11780 Dihedral : 6.684 159.791 9485 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.78 % Favored : 96.21 % Rotamer: Outliers : 1.00 % Allowed : 13.86 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.09), residues: 8734 helix: 1.94 (0.08), residues: 4471 sheet: -0.10 (0.16), residues: 1145 loop : -0.52 (0.11), residues: 3118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP q 319 HIS 0.016 0.001 HIS Z 161 PHE 0.015 0.001 PHE P 69 TYR 0.019 0.001 TYR z 353 ARG 0.014 0.000 ARG P 149 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16507.00 seconds wall clock time: 291 minutes 11.58 seconds (17471.58 seconds total)