Starting phenix.real_space_refine on Wed Mar 13 08:04:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shd_40484/03_2024/8shd_40484_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shd_40484/03_2024/8shd_40484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shd_40484/03_2024/8shd_40484.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shd_40484/03_2024/8shd_40484.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shd_40484/03_2024/8shd_40484_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shd_40484/03_2024/8shd_40484_updated.pdb" } resolution = 2.9 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= 0.049 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 407 5.16 5 C 41267 2.51 5 N 11494 2.21 5 O 12789 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 244": "OD1" <-> "OD2" Residue "N ASP 267": "OD1" <-> "OD2" Residue "N PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 529": "OD1" <-> "OD2" Residue "B PHE 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 330": "OE1" <-> "OE2" Residue "D ASP 46": "OD1" <-> "OD2" Residue "E ASP 84": "OD1" <-> "OD2" Residue "E ASP 231": "OD1" <-> "OD2" Residue "E TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 369": "OD1" <-> "OD2" Residue "E TYR 420": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 508": "OE1" <-> "OE2" Residue "G ASP 131": "OD1" <-> "OD2" Residue "G GLU 497": "OE1" <-> "OE2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "Q ASP 357": "OD1" <-> "OD2" Residue "Q GLU 454": "OE1" <-> "OE2" Residue "Q TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 496": "OD1" <-> "OD2" Residue "a ASP 47": "OD1" <-> "OD2" Residue "a GLU 134": "OE1" <-> "OE2" Residue "a ASP 529": "OD1" <-> "OD2" Residue "b GLU 495": "OE1" <-> "OE2" Residue "d GLU 364": "OE1" <-> "OE2" Residue "d GLU 402": "OE1" <-> "OE2" Residue "e ASP 100": "OD1" <-> "OD2" Residue "e GLU 118": "OE1" <-> "OE2" Residue "e GLU 207": "OE1" <-> "OE2" Residue "e GLU 375": "OE1" <-> "OE2" Residue "g ASP 52": "OD1" <-> "OD2" Residue "g GLU 82": "OE1" <-> "OE2" Residue "g ASP 194": "OD1" <-> "OD2" Residue "g GLU 358": "OE1" <-> "OE2" Residue "g PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 46": "OD1" <-> "OD2" Residue "h PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 26": "OE1" <-> "OE2" Residue "q TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 499": "OD1" <-> "OD2" Residue "z ASP 53": "OD1" <-> "OD2" Residue "z GLU 66": "OE1" <-> "OE2" Residue "z TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 480": "OD1" <-> "OD2" 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: 66069 Number of models: 1 Model: "" Number of chains: 49 Chain: "N" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 946 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain breaks: 5 Chain: "A" Number of atoms: 4069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4069 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 14, 'TRANS': 521} Chain: "B" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3952 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 10, 'TRANS': 515} Chain: "D" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3923 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "E" Number of atoms: 4121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} Chain: "G" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4089 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "H" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4054 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 16, 'TRANS': 511} Chain: "Q" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4086 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 18, 'TRANS': 519} Chain: "Z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "a" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4041 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Chain: "b" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3943 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 10, 'TRANS': 514} Chain: "d" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3917 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 4169 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} Conformer: "B" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} bond proxies already assigned to first conformer: 4195 Chain: "g" Number of atoms: 4088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4088 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "h" Number of atoms: 4032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4032 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 16, 'TRANS': 508} Chain: "q" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4053 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 16, 'TRANS': 516} Chain: "z" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4033 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 512} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE e 9 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE e 9 " occ=0.50 Time building chain proxies: 26.58, per 1000 atoms: 0.40 Number of scatterers: 66069 At special positions: 0 Unit cell: (179.86, 177.744, 180.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 407 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 12789 8.00 N 11494 7.00 C 41267 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 "HETATM65976 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65720 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65848 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65592 O3A ADP B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65912 O3A ADP e 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65624 O3A ADP D 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65656 O3A ADP E 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 21.41 Conformation dependent library (CDL) restraints added in 9.3 seconds 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15998 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 310 helices and 111 sheets defined 50.5% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.45 Creating SS restraints... Processing helix chain 'A' and resid 15 through 35 removed outlier: 3.631A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N SER A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N SER A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 70 through 85 removed outlier: 3.669A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 110 removed outlier: 3.658A 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 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 144 through 156 removed outlier: 3.554A pdb=" N THR A 154 " --> pdb=" O ALA A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 178 removed outlier: 4.540A pdb=" N ASP A 166 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALA A 169 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN A 170 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL A 173 " --> pdb=" O ASN A 170 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASP A 174 " --> pdb=" O MET A 171 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 177 " --> pdb=" O ASP A 174 " (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: 4.332A pdb=" N ASP A 261 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN A 262 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR A 271 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 303 removed outlier: 4.221A pdb=" N TYR A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A 300 " --> pdb=" O CYS A 296 " (cutoff:3.500A) 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: 4.319A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N SER A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 455 removed outlier: 3.810A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 5.074A 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: 3.706A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 484 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TRP A 485 " --> pdb=" O ASN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 507 through 525 Processing helix chain 'B' and resid 21 through 39 Processing helix chain 'B' and resid 67 through 72 Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 99 through 118 removed outlier: 3.578A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 144 Processing helix chain 'B' and resid 152 through 168 Processing helix chain 'B' and resid 171 through 190 removed outlier: 3.543A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS B 176 " --> pdb=" O THR B 173 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ASP B 177 " --> pdb=" O HIS B 174 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE B 179 " --> pdb=" O LYS B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 261 through 285 removed outlier: 3.945A 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: 3.772A 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: 3.613A 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: 4.452A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N SER D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 80 Processing helix chain 'D' and resid 86 through 101 Processing helix chain 'D' and resid 106 through 125 removed outlier: 3.725A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.822A 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 192 Proline residue: D 185 - end of helix Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 269 through 293 removed outlier: 3.985A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.980A 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: 4.590A pdb=" N GLU D 334 " --> pdb=" O GLU D 331 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE D 340 " --> pdb=" O CYS D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 350 No H-bonds generated for 'chain 'D' and resid 348 through 350' Processing helix chain 'D' and resid 353 through 355 No H-bonds generated for 'chain 'D' and resid 353 through 355' Processing helix chain 'D' and resid 395 through 417 Processing helix chain 'D' and resid 427 through 442 removed outlier: 3.768A pdb=" N THR D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 469 removed outlier: 3.608A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL D 460 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ILE D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) Proline residue: D 462 - end of helix Processing helix chain 'D' and resid 473 through 486 Processing helix chain 'D' and resid 503 through 506 Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'E' and resid 22 through 24 No H-bonds generated for 'chain 'E' and resid 22 through 24' Processing helix chain 'E' and resid 30 through 51 removed outlier: 3.570A pdb=" N ARG E 49 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N THR E 50 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 80 Processing helix chain 'E' and resid 86 through 101 Processing helix chain 'E' and resid 108 through 126 removed outlier: 3.606A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 150 Processing helix chain 'E' and resid 163 through 175 removed outlier: 4.651A pdb=" N SER E 175 " --> pdb=" O THR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 180 removed outlier: 4.007A pdb=" N SER E 180 " --> pdb=" O VAL E 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 177 through 180' Processing helix chain 'E' and resid 182 through 195 Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 219 through 221 No H-bonds generated for 'chain 'E' and resid 219 through 221' Processing helix chain 'E' and resid 271 through 294 Processing helix chain 'E' and resid 308 through 316 Processing helix chain 'E' and resid 327 through 337 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 392 through 414 Processing helix chain 'E' and resid 424 through 439 removed outlier: 3.637A pdb=" N LYS E 439 " --> pdb=" O GLN E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 442 through 465 removed outlier: 3.929A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL E 457 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 4.837A 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 19 through 37 Processing helix chain 'G' and resid 63 through 68 Processing helix chain 'G' and resid 75 through 90 Processing helix chain 'G' and resid 95 through 113 removed outlier: 3.710A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.086A 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: 4.262A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) removed outlier: 5.526A 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 261 through 285 removed outlier: 4.206A pdb=" N PHE G 264 " --> pdb=" O GLU G 261 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR G 265 " --> pdb=" O GLU G 262 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN G 284 " --> pdb=" O ASP G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 307 removed outlier: 3.778A 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: 3.559A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA G 428 " --> pdb=" O GLU G 424 " (cutoff:3.500A) Processing helix chain 'G' and resid 432 through 455 removed outlier: 3.651A pdb=" N TRP G 435 " --> pdb=" O VAL G 432 " (cutoff:3.500A) Proline residue: G 436 - end of helix removed outlier: 3.933A 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 39 removed outlier: 3.552A pdb=" N ALA H 35 " --> pdb=" O VAL H 31 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL H 36 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N THR H 38 " --> pdb=" O GLU H 34 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N THR H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 68 Processing helix chain 'H' and resid 76 through 89 removed outlier: 3.635A pdb=" N GLU H 89 " --> pdb=" O GLN H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 113 removed outlier: 4.238A 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: 5.307A pdb=" N ALA H 173 " --> pdb=" O GLN H 170 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 194 No H-bonds generated for 'chain 'H' and resid 192 through 194' Processing helix chain 'H' and resid 205 through 207 No H-bonds generated for 'chain 'H' and resid 205 through 207' Processing helix chain 'H' and resid 225 through 227 No H-bonds generated for 'chain 'H' and resid 225 through 227' Processing helix chain 'H' and resid 260 through 284 removed outlier: 3.569A pdb=" N SER H 284 " --> pdb=" O LYS H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 305 Processing helix chain 'H' and resid 316 through 326 Processing helix chain 'H' and resid 339 through 341 No H-bonds generated for 'chain 'H' and resid 339 through 341' Processing helix chain 'H' and resid 379 through 401 Processing helix chain 'H' and resid 411 through 426 removed outlier: 4.098A pdb=" N THR H 426 " --> pdb=" O ASP H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 452 removed outlier: 4.082A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLU H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ILE H 444 " --> pdb=" O LYS H 440 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ILE H 445 " --> pdb=" O ALA H 441 " (cutoff:3.500A) Proline residue: H 446 - end of helix Processing helix chain 'H' and resid 457 through 470 Processing helix chain 'H' and resid 496 through 515 Processing helix chain 'Q' and resid 11 through 14 No H-bonds generated for 'chain 'Q' and resid 11 through 14' Processing helix chain 'Q' and resid 25 through 46 removed outlier: 4.405A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N ALA Q 46 " --> pdb=" O THR Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 75 Processing helix chain 'Q' and resid 81 through 96 Processing helix chain 'Q' and resid 101 through 121 Processing helix chain 'Q' and resid 125 through 146 Proline residue: Q 144 - end of helix Processing helix chain 'Q' and resid 158 through 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: 4.909A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) removed outlier: 3.742A 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 427 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 501 through 520 Processing helix chain 'Z' and resid 3 through 7 removed outlier: 3.726A pdb=" N LEU Z 7 " --> pdb=" O ALA Z 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 3 through 7' Processing helix chain 'Z' and resid 17 through 37 removed outlier: 4.864A pdb=" N THR Z 36 " --> pdb=" O ASP Z 32 " (cutoff:3.500A) removed outlier: 5.114A 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: 3.607A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) removed outlier: 4.654A 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: 4.193A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 162 through 179 Processing helix chain 'Z' and resid 188 through 190 No H-bonds generated for 'chain 'Z' and resid 188 through 190' Processing helix chain 'Z' and resid 201 through 203 No H-bonds generated for 'chain 'Z' and resid 201 through 203' Processing helix chain 'Z' and resid 253 through 281 removed outlier: 4.213A pdb=" N ARG Z 264 " --> pdb=" O VAL Z 260 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N LYS Z 265 " --> pdb=" O LYS Z 261 " (cutoff:3.500A) removed outlier: 5.266A pdb=" N PHE Z 266 " --> pdb=" O ALA Z 262 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ILE Z 267 " --> pdb=" O GLU Z 263 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 299 through 308 removed outlier: 3.825A pdb=" N GLU Z 308 " --> pdb=" O ALA Z 304 " (cutoff:3.500A) Processing helix chain 'Z' and resid 318 through 327 removed outlier: 4.320A 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: 4.038A pdb=" N GLN Z 434 " --> pdb=" O GLY Z 431 " (cutoff:3.500A) removed outlier: 3.764A 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 14 through 35 removed outlier: 3.508A pdb=" N ILE a 17 " --> pdb=" O GLY a 14 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS a 33 " --> pdb=" O ASN a 30 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N SER a 34 " --> pdb=" O ILE a 31 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 64 Processing helix chain 'a' and resid 70 through 85 Processing helix chain 'a' and resid 90 through 109 removed outlier: 3.704A 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 165 through 179 removed outlier: 4.298A pdb=" N ASN a 170 " --> pdb=" O ASP a 166 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE a 179 " --> pdb=" O ALA a 175 " (cutoff:3.500A) 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: 3.513A pdb=" N LEU a 260 " --> pdb=" O PRO a 257 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASP a 261 " --> pdb=" O GLU a 258 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ILE a 270 " --> pdb=" O GLU a 267 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA a 280 " --> pdb=" O LYS a 277 " (cutoff:3.500A) removed outlier: 3.574A 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: 4.380A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) Processing helix chain 'a' and resid 434 through 455 removed outlier: 3.847A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 5.181A 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: 3.908A pdb=" N LYS a 481 " --> pdb=" O PRO a 478 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ASN a 482 " --> pdb=" O GLU a 479 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TRP a 485 " --> pdb=" O ASN a 482 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 501 No H-bonds generated for 'chain 'a' and resid 498 through 501' Processing helix chain 'a' and resid 507 through 526 Processing helix chain 'b' and resid 21 through 39 Processing helix chain 'b' and resid 67 through 72 Processing helix chain 'b' and resid 79 through 94 Processing helix chain 'b' and resid 99 through 118 Processing helix chain 'b' and resid 123 through 144 Processing helix chain 'b' and resid 152 through 168 Processing helix chain 'b' and resid 171 through 190 removed outlier: 3.625A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS b 176 " --> pdb=" O THR b 173 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ASP b 177 " --> pdb=" O HIS b 174 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE b 179 " --> pdb=" O LYS b 176 " (cutoff:3.500A) Processing helix chain 'b' and resid 196 through 198 No H-bonds generated for 'chain 'b' and resid 196 through 198' Processing helix chain 'b' and resid 209 through 211 No H-bonds generated for 'chain 'b' and resid 209 through 211' Processing helix chain 'b' and resid 261 through 285 removed outlier: 3.920A 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: 3.801A pdb=" N ARG b 427 " --> pdb=" O GLN b 423 " (cutoff:3.500A) Processing helix chain 'b' and resid 431 through 454 Proline residue: b 447 - end of helix removed outlier: 3.832A pdb=" N ALA b 454 " --> pdb=" O ILE b 450 " (cutoff:3.500A) Processing helix chain 'b' and resid 458 through 471 Processing helix chain 'b' and resid 488 through 491 No H-bonds generated for 'chain 'b' and resid 488 through 491' Processing helix chain 'b' and resid 497 through 515 Processing helix chain 'd' and resid 29 through 49 Processing helix chain 'd' and resid 74 through 80 Processing helix chain 'd' and resid 86 through 101 Processing helix chain 'd' and resid 108 through 125 removed outlier: 3.892A 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 172 Processing helix chain 'd' and resid 175 through 177 No H-bonds generated for 'chain 'd' and resid 175 through 177' Processing helix chain 'd' and resid 180 through 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: 3.618A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR d 293 " --> pdb=" O GLN d 289 " (cutoff:3.500A) Processing helix chain 'd' and resid 311 through 320 Processing helix chain 'd' and resid 330 through 340 removed outlier: 4.263A pdb=" N GLU d 334 " --> pdb=" O GLU d 331 " (cutoff:3.500A) removed outlier: 4.150A 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: 4.115A pdb=" N VAL d 460 " --> pdb=" O ASP d 456 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ILE d 461 " --> pdb=" O ALA d 457 " (cutoff:3.500A) Proline residue: d 462 - end of helix Processing helix chain 'd' and resid 473 through 486 Processing helix chain 'd' and resid 512 through 530 removed outlier: 5.017A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 51 removed outlier: 3.519A pdb=" N LEU e 34 " --> pdb=" O GLY e 30 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N THR e 50 " --> pdb=" O ASN e 46 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N SER e 51 " --> pdb=" O THR e 47 " (cutoff:3.500A) Processing helix chain 'e' and resid 74 through 80 Processing helix chain 'e' and resid 86 through 101 Processing helix chain 'e' and resid 106 through 125 removed outlier: 4.303A pdb=" N VAL e 110 " --> pdb=" O THR e 106 " (cutoff:3.500A) Processing helix chain 'e' and resid 130 through 150 Processing helix chain 'e' and resid 163 through 175 removed outlier: 4.692A pdb=" N SER e 175 " --> pdb=" O THR e 171 " (cutoff:3.500A) Processing helix chain 'e' and resid 177 through 195 removed outlier: 3.848A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ARG e 183 " --> pdb=" O SER e 180 " (cutoff:3.500A) Processing helix chain 'e' and resid 206 through 208 No H-bonds generated for 'chain 'e' and resid 206 through 208' Processing helix chain 'e' and resid 219 through 221 No H-bonds generated for 'chain 'e' and resid 219 through 221' Processing helix chain 'e' and resid 271 through 294 Processing helix chain 'e' and resid 308 through 316 Processing helix chain 'e' and resid 327 through 337 Processing helix chain 'e' and resid 345 through 347 No H-bonds generated for 'chain 'e' and resid 345 through 347' Processing helix chain 'e' and resid 392 through 414 Processing helix chain 'e' and resid 424 through 439 removed outlier: 3.793A pdb=" N LYS e 439 " --> pdb=" O GLN e 435 " (cutoff:3.500A) Processing helix chain 'e' and resid 442 through 465 removed outlier: 3.807A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL e 457 " --> pdb=" O ASP e 453 " (cutoff:3.500A) removed outlier: 4.891A 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: 3.796A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N THR g 39 " --> pdb=" O ASP g 35 " (cutoff:3.500A) removed outlier: 5.976A 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: 3.756A pdb=" N PHE g 112 " --> pdb=" O VAL g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 119 through 139 Processing helix chain 'g' and resid 149 through 160 Processing helix chain 'g' and resid 164 through 167 removed outlier: 4.030A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 164 through 167' Processing helix chain 'g' and resid 169 through 183 Processing helix chain 'g' and resid 209 through 211 No H-bonds generated for 'chain 'g' and resid 209 through 211' Processing helix chain 'g' and resid 263 through 285 removed outlier: 4.278A pdb=" N LEU g 285 " --> pdb=" O ASP g 281 " (cutoff:3.500A) Processing helix chain 'g' and resid 298 through 307 removed outlier: 3.656A 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: 3.611A pdb=" N LYS g 427 " --> pdb=" O THR g 423 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ALA g 428 " --> pdb=" O GLU g 424 " (cutoff:3.500A) Processing helix chain 'g' and resid 434 through 455 removed outlier: 3.944A pdb=" N LEU g 444 " --> pdb=" O VAL g 440 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLU g 445 " --> pdb=" O ALA g 441 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N VAL g 446 " --> pdb=" O GLN g 442 " (cutoff:3.500A) removed outlier: 5.242A 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 36 removed outlier: 3.638A pdb=" N ALA h 35 " --> pdb=" O VAL h 31 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL h 36 " --> pdb=" O ILE h 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 68 Processing helix chain 'h' and resid 76 through 89 removed outlier: 3.642A pdb=" N GLU h 89 " --> pdb=" O GLN h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 96 through 113 Proline residue: h 110 - end of helix Processing helix chain 'h' and resid 118 through 139 Processing helix chain 'h' and resid 148 through 163 Processing helix chain 'h' and resid 169 through 185 removed outlier: 5.335A pdb=" N ALA h 173 " --> pdb=" O GLN h 170 " (cutoff:3.500A) Processing helix chain 'h' and resid 192 through 194 No H-bonds generated for 'chain 'h' and resid 192 through 194' Processing helix chain 'h' and resid 205 through 207 No H-bonds generated for 'chain 'h' and resid 205 through 207' Processing helix chain 'h' and resid 260 through 283 Processing helix chain 'h' and resid 297 through 305 Processing helix chain 'h' and resid 316 through 326 Processing helix chain 'h' and resid 339 through 341 No H-bonds generated for 'chain 'h' and resid 339 through 341' Processing helix chain 'h' and resid 379 through 401 Processing helix chain 'h' and resid 411 through 426 removed outlier: 4.058A pdb=" N THR h 426 " --> pdb=" O ASP h 422 " (cutoff:3.500A) Processing helix chain 'h' and resid 430 through 453 removed outlier: 4.174A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU h 443 " --> pdb=" O ALA h 439 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE h 444 " --> pdb=" O LYS h 440 " (cutoff:3.500A) removed outlier: 5.372A 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: 4.335A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ALA q 46 " --> pdb=" O THR q 42 " (cutoff:3.500A) Processing helix chain 'q' and resid 69 through 75 Processing helix chain 'q' and resid 81 through 96 Processing helix chain 'q' and resid 101 through 121 Processing helix chain 'q' and resid 125 through 146 Proline residue: q 144 - end of helix Processing helix chain 'q' and resid 158 through 167 removed outlier: 4.303A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER q 167 " --> pdb=" O LEU q 163 " (cutoff:3.500A) Processing helix chain 'q' and resid 177 through 189 Processing helix chain 'q' and resid 199 through 201 No H-bonds generated for 'chain 'q' and resid 199 through 201' Processing helix chain 'q' and resid 212 through 214 No H-bonds generated for 'chain 'q' and resid 212 through 214' Processing helix chain 'q' and resid 262 through 286 removed outlier: 4.858A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) removed outlier: 3.754A 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: 3.699A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 434 through 456 removed outlier: 3.827A pdb=" N PHE q 445 " --> pdb=" O PHE q 441 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLU q 446 " --> pdb=" O ALA q 442 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA q 447 " --> pdb=" O GLU q 443 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ILE q 448 " --> pdb=" O ALA q 444 " (cutoff:3.500A) Proline residue: q 449 - end of helix Processing helix chain 'q' and resid 460 through 473 Processing helix chain 'q' and resid 492 through 495 No H-bonds generated for 'chain 'q' and resid 492 through 495' Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'z' and resid 3 through 7 Processing helix chain 'z' and resid 17 through 37 removed outlier: 4.887A pdb=" N THR z 36 " --> pdb=" O ASP z 32 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N ASN z 37 " --> pdb=" O VAL z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 60 through 65 Processing helix chain 'z' and resid 72 through 87 Processing helix chain 'z' and resid 92 through 112 removed outlier: 3.603A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) removed outlier: 4.564A 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: 4.169A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 162 through 179 removed outlier: 3.611A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) Processing helix chain 'z' and resid 188 through 190 No H-bonds generated for 'chain 'z' and resid 188 through 190' Processing helix chain 'z' and resid 201 through 203 No H-bonds generated for 'chain 'z' and resid 201 through 203' Processing helix chain 'z' and resid 253 through 262 Processing helix chain 'z' and resid 265 through 281 removed outlier: 3.675A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 299 through 308 removed outlier: 3.669A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 318 through 327 removed outlier: 4.203A 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: 3.983A pdb=" N GLN z 434 " --> pdb=" O GLY z 431 " (cutoff:3.500A) removed outlier: 3.691A 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 sheet with id= A, first strand: chain 'N' and resid 209 through 213 removed outlier: 4.019A pdb=" N CYS N 219 " --> pdb=" O PHE N 233 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN N 231 " --> pdb=" O LEU N 221 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ASP N 223 " --> pdb=" O LEU N 229 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU N 229 " --> pdb=" O ASP N 223 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'N' and resid 287 through 289 Processing sheet with id= C, first strand: chain 'N' and resid 263 through 267 removed outlier: 7.091A pdb=" N ASP N 267 " --> pdb=" O CYS N 273 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N CYS N 273 " --> pdb=" O ASP N 267 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 9 through 13 Processing sheet with id= E, first strand: chain 'A' and resid 43 through 46 Processing sheet with id= F, first strand: chain 'A' and resid 137 through 139 Processing sheet with id= G, first strand: chain 'A' and resid 196 through 199 Processing sheet with id= H, first strand: chain 'A' and resid 213 through 216 Processing sheet with id= I, first strand: chain 'A' and resid 345 through 348 removed outlier: 6.581A pdb=" N VAL A 285 " --> pdb=" O ALA A 235 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N LEU A 237 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU A 287 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N MET A 306 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N THR A 288 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL A 308 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 486 through 489 Processing sheet with id= K, first strand: chain 'B' and resid 17 through 19 Processing sheet with id= L, first strand: chain 'B' and resid 50 through 53 Processing sheet with id= M, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.198A pdb=" N CYS B 371 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 7.461A pdb=" N ILE B 202 " --> pdb=" O CYS B 371 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE B 373 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N LYS B 204 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LEU B 375 " --> pdb=" O LYS B 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'B' and resid 218 through 220 Processing sheet with id= O, first strand: chain 'B' and resid 344 through 346 removed outlier: 3.599A pdb=" N CYS B 346 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N CYS B 289 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N ALA B 240 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE B 291 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N MET B 310 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ASN B 292 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE B 312 " --> pdb=" O ASN B 292 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 406 through 408 Processing sheet with id= Q, first strand: chain 'B' and resid 476 through 479 Processing sheet with id= R, first strand: chain 'D' and resid 59 through 62 Processing sheet with id= S, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.744A pdb=" N VAL D 386 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N VAL D 211 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE D 388 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N LYS D 213 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL D 390 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 227 through 229 removed outlier: 3.554A pdb=" N LEU D 361 " --> pdb=" O THR D 377 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 246 through 249 removed outlier: 6.682A pdb=" N VAL D 297 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N ILE D 249 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU D 299 " --> pdb=" O ILE D 249 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N MET D 323 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N ILE D 300 " --> pdb=" O MET D 323 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE D 325 " --> pdb=" O ILE D 300 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'D' and resid 421 through 423 Processing sheet with id= W, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.670A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 59 through 62 Processing sheet with id= Y, first strand: chain 'E' and resid 209 through 215 removed outlier: 6.716A pdb=" N VAL E 383 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 7.943A pdb=" N GLU E 212 " --> pdb=" O VAL E 383 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ILE E 385 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N LYS E 214 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ILE E 387 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 228 through 230 Processing sheet with id= AA, first strand: chain 'E' and resid 354 through 356 removed outlier: 6.850A pdb=" N LEU E 299 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 418 through 420 Processing sheet with id= AC, first strand: chain 'G' and resid 15 through 17 Processing sheet with id= AD, first strand: chain 'G' and resid 48 through 51 Processing sheet with id= AE, first strand: chain 'G' and resid 185 through 187 Processing sheet with id= AF, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.527A pdb=" N CYS G 372 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N GLU G 202 " --> pdb=" O CYS G 372 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ILE G 374 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE G 204 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU G 376 " --> pdb=" O ILE G 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'G' and resid 238 through 241 removed outlier: 6.523A pdb=" N VAL G 289 " --> pdb=" O VAL G 239 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N LEU G 241 " --> pdb=" O VAL G 289 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE G 291 " --> pdb=" O LEU G 241 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N THR G 310 " --> pdb=" O VAL G 290 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N THR G 292 " --> pdb=" O THR G 310 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE G 312 " --> pdb=" O THR G 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'G' and resid 351 through 355 Processing sheet with id= AI, first strand: chain 'G' and resid 407 through 409 Processing sheet with id= AJ, first strand: chain 'G' and resid 478 through 480 Processing sheet with id= AK, first strand: chain 'H' and resid 14 through 17 Processing sheet with id= AL, first strand: chain 'H' and resid 47 through 50 Processing sheet with id= AM, first strand: chain 'H' and resid 195 through 201 removed outlier: 6.590A pdb=" N CYS H 370 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N LYS H 198 " --> pdb=" O CYS H 370 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N PHE H 372 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N VAL H 200 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LEU H 374 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'H' and resid 214 through 217 Processing sheet with id= AO, first strand: chain 'H' and resid 237 through 240 removed outlier: 7.009A pdb=" N VAL H 288 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU H 240 " --> pdb=" O VAL H 288 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU H 290 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE H 309 " --> pdb=" O VAL H 289 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N SER H 291 " --> pdb=" O PHE H 309 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA H 311 " --> pdb=" O SER H 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'H' and resid 405 through 407 Processing sheet with id= AQ, first strand: chain 'H' and resid 475 through 478 Processing sheet with id= AR, first strand: chain 'Q' and resid 20 through 23 Processing sheet with id= AS, first strand: chain 'Q' and resid 54 through 57 Processing sheet with id= AT, first strand: chain 'Q' and resid 202 through 206 removed outlier: 6.623A pdb=" N SER Q 373 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N CYS Q 205 " --> pdb=" O SER Q 373 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ILE Q 375 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'Q' and resid 220 through 223 removed outlier: 3.570A pdb=" N THR Q 358 " --> pdb=" O VAL Q 355 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'Q' and resid 240 through 242 removed outlier: 6.123A pdb=" N MET Q 311 " --> pdb=" O VAL Q 291 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N THR Q 293 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL Q 313 " --> pdb=" O THR Q 293 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'Q' and resid 498 through 500 removed outlier: 3.908A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N VAL Q 147 " --> pdb=" O PRO Q 410 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id= AY, first strand: chain 'Z' and resid 12 through 15 removed outlier: 3.571A pdb=" N GLU Z 12 " --> pdb=" O ARG Z 523 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'Z' and resid 45 through 48 removed outlier: 3.541A pdb=" N LYS Z 45 " --> pdb=" O THR Z 57 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.937A pdb=" N VAL Z 372 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N MET Z 194 " --> pdb=" O VAL Z 372 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU Z 374 " --> pdb=" O MET Z 194 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N MET Z 196 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N ILE Z 376 " --> pdb=" O MET Z 196 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER Z 205 " --> pdb=" O LEU Z 375 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id= BC, first strand: chain 'Z' and resid 345 through 347 Processing sheet with id= BD, first strand: chain 'Z' and resid 407 through 409 Processing sheet with id= BE, first strand: chain 'Z' and resid 477 through 479 removed outlier: 3.621A pdb=" N MET Z 487 " --> pdb=" O GLY Z 478 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'a' and resid 9 through 13 Processing sheet with id= BG, first strand: chain 'a' and resid 43 through 46 Processing sheet with id= BH, first strand: chain 'a' and resid 180 through 182 Processing sheet with id= BI, first strand: chain 'a' and resid 196 through 201 removed outlier: 3.598A pdb=" N GLY a 379 " --> pdb=" O ALA a 200 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'a' and resid 213 through 216 Processing sheet with id= BK, first strand: chain 'a' and resid 346 through 348 removed outlier: 6.811A pdb=" N VAL a 285 " --> pdb=" O ALA a 235 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N LEU a 237 " --> pdb=" O VAL a 285 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU a 287 " --> pdb=" O LEU a 237 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N MET a 306 " --> pdb=" O ILE a 286 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N THR a 288 " --> pdb=" O MET a 306 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL a 308 " --> pdb=" O THR a 288 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'a' and resid 408 through 410 Processing sheet with id= BM, first strand: chain 'a' and resid 486 through 489 Processing sheet with id= BN, first strand: chain 'b' and resid 17 through 19 Processing sheet with id= BO, first strand: chain 'b' and resid 50 through 53 Processing sheet with id= BP, first strand: chain 'b' and resid 199 through 205 removed outlier: 6.268A pdb=" N CYS b 371 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N ILE b 202 " --> pdb=" O CYS b 371 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE b 373 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LYS b 204 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LEU b 375 " --> pdb=" O LYS b 204 " (cutoff:3.500A) No H-bonds generated for sheet with id= BP Processing sheet with id= BQ, first strand: chain 'b' and resid 218 through 220 Processing sheet with id= BR, first strand: chain 'b' and resid 344 through 346 removed outlier: 6.614A pdb=" N CYS b 289 " --> pdb=" O LEU b 238 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ALA b 240 " --> pdb=" O CYS b 289 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N ILE b 291 " --> pdb=" O ALA b 240 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N MET b 310 " --> pdb=" O PHE b 290 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N ASN b 292 " --> pdb=" O MET b 310 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE b 312 " --> pdb=" O ASN b 292 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'b' and resid 406 through 408 Processing sheet with id= BT, first strand: chain 'b' and resid 476 through 479 Processing sheet with id= BU, first strand: chain 'd' and resid 59 through 62 Processing sheet with id= BV, first strand: chain 'd' and resid 208 through 214 removed outlier: 6.631A pdb=" N VAL d 386 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N VAL d 211 " --> pdb=" O VAL d 386 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE d 388 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LYS d 213 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N VAL d 390 " --> pdb=" O LYS d 213 " (cutoff:3.500A) No H-bonds generated for sheet with id= BV Processing sheet with id= BW, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.593A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'd' and resid 357 through 359 removed outlier: 6.385A pdb=" N VAL d 297 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE d 249 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU d 299 " --> pdb=" O ILE d 249 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N MET d 323 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N ILE d 300 " --> pdb=" O MET d 323 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE d 325 " --> pdb=" O ILE d 300 " (cutoff:3.500A) Processing sheet with id= BY, first strand: chain 'd' and resid 421 through 423 Processing sheet with id= BZ, first strand: chain 'd' and resid 491 through 494 Processing sheet with id= CA, first strand: chain 'e' and resid 59 through 62 Processing sheet with id= CB, first strand: chain 'e' and resid 209 through 215 removed outlier: 7.034A pdb=" N VAL e 383 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N GLU e 212 " --> pdb=" O VAL e 383 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE e 385 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N LYS e 214 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE e 387 " --> pdb=" O LYS e 214 " (cutoff:3.500A) Processing sheet with id= CC, first strand: chain 'e' and resid 228 through 230 Processing sheet with id= CD, first strand: chain 'e' and resid 354 through 356 removed outlier: 7.001A pdb=" N LEU e 299 " --> pdb=" O ALA e 249 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU e 251 " --> pdb=" O LEU e 299 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N ILE e 301 " --> pdb=" O LEU e 251 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N CYS e 302 " --> pdb=" O PRO e 320 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL e 322 " --> pdb=" O CYS e 302 " (cutoff:3.500A) Processing sheet with id= CE, first strand: chain 'e' and resid 418 through 420 Processing sheet with id= CF, first strand: chain 'g' and resid 15 through 18 Processing sheet with id= CG, first strand: chain 'g' and resid 48 through 51 Processing sheet with id= CH, first strand: chain 'g' and resid 185 through 187 Processing sheet with id= CI, first strand: chain 'g' and resid 200 through 205 removed outlier: 4.031A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'g' and resid 218 through 220 Processing sheet with id= CK, first strand: chain 'g' and resid 238 through 241 removed outlier: 6.399A pdb=" N VAL g 289 " --> pdb=" O VAL g 239 " (cutoff:3.500A) removed outlier: 7.876A pdb=" N LEU g 241 " --> pdb=" O VAL g 289 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE g 291 " --> pdb=" O LEU g 241 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N THR g 310 " --> pdb=" O VAL g 290 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N THR g 292 " --> pdb=" O THR g 310 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE g 312 " --> pdb=" O THR g 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= CK Processing sheet with id= CL, first strand: chain 'g' and resid 407 through 409 Processing sheet with id= CM, first strand: chain 'g' and resid 478 through 481 removed outlier: 3.700A pdb=" N THR g 486 " --> pdb=" O ASN g 481 " (cutoff:3.500A) Processing sheet with id= CN, first strand: chain 'h' and resid 14 through 17 Processing sheet with id= CO, first strand: chain 'h' and resid 47 through 50 Processing sheet with id= CP, first strand: chain 'h' and resid 195 through 201 removed outlier: 6.469A pdb=" N CYS h 370 " --> pdb=" O GLY h 196 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LYS h 198 " --> pdb=" O CYS h 370 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHE h 372 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N VAL h 200 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU h 374 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR h 371 " --> pdb=" O VAL h 211 " (cutoff:3.500A) Processing sheet with id= CQ, first strand: chain 'h' and resid 214 through 217 Processing sheet with id= CR, first strand: chain 'h' and resid 237 through 240 removed outlier: 6.926A pdb=" N VAL h 288 " --> pdb=" O ALA h 238 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N LEU h 240 " --> pdb=" O VAL h 288 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU h 290 " --> pdb=" O LEU h 240 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N PHE h 309 " --> pdb=" O VAL h 289 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N SER h 291 " --> pdb=" O PHE h 309 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA h 311 " --> pdb=" O SER h 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= CR Processing sheet with id= CS, first strand: chain 'h' and resid 405 through 407 Processing sheet with id= CT, first strand: chain 'h' and resid 475 through 478 removed outlier: 3.521A pdb=" N ASP h 483 " --> pdb=" O ASP h 478 " (cutoff:3.500A) Processing sheet with id= CU, first strand: chain 'q' and resid 20 through 23 Processing sheet with id= CV, first strand: chain 'q' and resid 54 through 57 Processing sheet with id= CW, first strand: chain 'q' and resid 202 through 208 removed outlier: 6.799A pdb=" N SER q 373 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N CYS q 205 " --> pdb=" O SER q 373 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE q 375 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N ILE q 207 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LEU q 377 " --> pdb=" O ILE q 207 " (cutoff:3.500A) Processing sheet with id= CX, first strand: chain 'q' and resid 220 through 223 Processing sheet with id= CY, first strand: chain 'q' and resid 240 through 242 removed outlier: 6.074A pdb=" N MET q 311 " --> pdb=" O VAL q 291 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N THR q 293 " --> pdb=" O MET q 311 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL q 313 " --> pdb=" O THR q 293 " (cutoff:3.500A) Processing sheet with id= CZ, first strand: chain 'q' and resid 498 through 500 removed outlier: 3.877A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N VAL q 147 " --> pdb=" O PRO q 410 " (cutoff:3.500A) Processing sheet with id= DA, first strand: chain 'q' and resid 478 through 480 Processing sheet with id= DB, first strand: chain 'z' and resid 12 through 15 removed outlier: 3.577A pdb=" N GLU z 12 " --> pdb=" O ARG z 523 " (cutoff:3.500A) Processing sheet with id= DC, first strand: chain 'z' and resid 45 through 48 Processing sheet with id= DD, first strand: chain 'z' and resid 192 through 196 Processing sheet with id= DE, first strand: chain 'z' and resid 210 through 212 Processing sheet with id= DF, first strand: chain 'z' and resid 345 through 347 Processing sheet with id= DG, first strand: chain 'z' and resid 477 through 479 3398 hydrogen bonds defined for protein. 8952 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: 31.18 Time building geometry restraints manager: 23.49 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: 22222 1.34 - 1.46: 9077 1.46 - 1.58: 34747 1.58 - 1.69: 48 1.69 - 1.81: 722 Bond restraints: 66816 Sorted by residual: bond pdb=" F2 AF3 z 603 " pdb="AL AF3 z 603 " ideal model delta sigma weight residual 1.637 1.799 -0.162 2.00e-02 2.50e+03 6.52e+01 bond pdb=" F2 AF3 Z 603 " pdb="AL AF3 Z 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.41e+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 6.41e+01 bond pdb=" F2 AF3 a 603 " pdb="AL AF3 a 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.37e+01 bond pdb=" F2 AF3 H 603 " pdb="AL AF3 H 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.34e+01 ... (remaining 66811 not shown) Histogram of bond angle deviations from ideal: 98.02 - 105.72: 1142 105.72 - 113.42: 39064 113.42 - 121.12: 32971 121.12 - 128.82: 16759 128.82 - 136.52: 289 Bond angle restraints: 90225 Sorted by residual: angle pdb=" N ALA Z 162 " pdb=" CA ALA Z 162 " pdb=" C ALA Z 162 " ideal model delta sigma weight residual 110.97 115.09 -4.12 1.09e+00 8.42e-01 1.43e+01 angle pdb=" N GLY Q 209 " pdb=" CA GLY Q 209 " pdb=" C GLY Q 209 " ideal model delta sigma weight residual 113.18 121.09 -7.91 2.37e+00 1.78e-01 1.11e+01 angle pdb=" N GLY q 209 " pdb=" CA GLY q 209 " pdb=" C GLY q 209 " ideal model delta sigma weight residual 113.18 120.82 -7.64 2.37e+00 1.78e-01 1.04e+01 angle pdb=" N LEU g 8 " pdb=" CA LEU g 8 " pdb=" C LEU g 8 " ideal model delta sigma weight residual 110.91 114.59 -3.68 1.17e+00 7.31e-01 9.91e+00 angle pdb=" C ALA q 151 " pdb=" N LYS q 152 " pdb=" CA LYS q 152 " ideal model delta sigma weight residual 121.54 127.37 -5.83 1.91e+00 2.74e-01 9.32e+00 ... (remaining 90220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.64: 40645 34.64 - 69.28: 580 69.28 - 103.92: 69 103.92 - 138.56: 8 138.56 - 173.20: 9 Dihedral angle restraints: 41311 sinusoidal: 16609 harmonic: 24702 Sorted by residual: 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 -60.00 113.20 -173.20 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP g 601 " pdb=" O3A ADP g 601 " pdb=" PA ADP g 601 " pdb=" PB ADP g 601 " ideal model delta sinusoidal sigma weight residual -60.00 109.99 -169.99 1 2.00e+01 2.50e-03 4.76e+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 300.00 130.38 169.62 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 41308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 7295 0.034 - 0.068: 2323 0.068 - 0.101: 707 0.101 - 0.135: 415 0.135 - 0.169: 17 Chirality restraints: 10757 Sorted by residual: chirality pdb=" CB ILE G 363 " pdb=" CA ILE G 363 " pdb=" CG1 ILE G 363 " pdb=" CG2 ILE G 363 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" CA ILE b 11 " pdb=" N ILE b 11 " pdb=" C ILE b 11 " pdb=" CB ILE b 11 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.20e-01 chirality pdb=" CA GLU a 77 " pdb=" N GLU a 77 " pdb=" C GLU a 77 " pdb=" CB GLU a 77 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 10754 not shown) Planarity restraints: 11514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 14 " -0.053 5.00e-02 4.00e+02 8.12e-02 1.06e+01 pdb=" N PRO E 15 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO E 15 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 15 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN a 477 " 0.050 5.00e-02 4.00e+02 7.57e-02 9.17e+00 pdb=" N PRO a 478 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO a 478 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO a 478 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 231 " -0.013 2.00e-02 2.50e+03 2.73e-02 7.47e+00 pdb=" CG ASP E 231 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASP E 231 " -0.017 2.00e-02 2.50e+03 pdb=" OD2 ASP E 231 " -0.016 2.00e-02 2.50e+03 ... (remaining 11511 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 517 2.52 - 3.12: 50218 3.12 - 3.71: 103588 3.71 - 4.31: 147473 4.31 - 4.90: 252491 Nonbonded interactions: 554287 Sorted by model distance: nonbonded pdb="MG MG e 602 " pdb=" F1 AF3 e 603 " model vdw 1.928 2.120 nonbonded pdb="MG MG B 602 " pdb=" F1 AF3 B 603 " model vdw 1.932 2.120 nonbonded pdb="MG MG D 602 " pdb=" F2 AF3 D 603 " model vdw 1.948 2.120 nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.957 2.120 nonbonded pdb="MG MG G 602 " pdb=" F2 AF3 G 603 " model vdw 1.976 2.120 ... (remaining 554282 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 535 or resid 601 through 603)) selection = chain 'a' } ncs_group { reference = (chain 'B' and (resid 2 through 526 or resid 601 through 603)) selection = chain 'b' } ncs_group { reference = (chain 'D' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 538 or resid 601 through 603)) selection = chain 'd' } ncs_group { reference = (chain 'E' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) selection = (chain 'e' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) } ncs_group { reference = (chain 'G' and (resid 5 through 528 or resid 601 through 603)) selection = (chain 'g' and (resid 5 through 528 or resid 601 through 603)) } ncs_group { reference = (chain 'H' and (resid 1 through 525 or resid 601 through 603)) selection = chain 'h' } ncs_group { reference = (chain 'Q' and (resid 2 through 534 or resid 601 through 603)) selection = chain 'q' } ncs_group { reference = chain 'Z' selection = (chain 'z' and (resid 2 through 526 or resid 601 through 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 8.120 Check model and map are aligned: 0.700 Set scattering table: 0.450 Process input model: 146.050 Find NCS groups from input model: 6.650 Set up NCS constraints: 0.660 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 176.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 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 0.162 66816 Z= 0.272 Angle : 0.543 7.910 90225 Z= 0.267 Chirality : 0.041 0.169 10757 Planarity : 0.003 0.081 11514 Dihedral : 13.798 173.199 25313 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.29 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: 1.61 (0.09), residues: 8548 helix: 2.26 (0.08), residues: 4378 sheet: 0.36 (0.16), residues: 1169 loop : -0.41 (0.11), residues: 3001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP q 319 HIS 0.011 0.001 HIS z 161 PHE 0.030 0.001 PHE b 12 TYR 0.017 0.001 TYR G 437 ARG 0.008 0.000 ARG z 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 7151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 596 time to evaluate : 5.709 Fit side-chains REVERT: N 223 ASP cc_start: 0.8945 (t70) cc_final: 0.8684 (t70) REVERT: N 268 MET cc_start: 0.8650 (mpp) cc_final: 0.8373 (mpp) REVERT: D 65 LYS cc_start: 0.9322 (ptpp) cc_final: 0.8751 (ptmm) REVERT: D 67 ASP cc_start: 0.8287 (m-30) cc_final: 0.7846 (m-30) REVERT: D 332 ASP cc_start: 0.8782 (m-30) cc_final: 0.8576 (m-30) REVERT: E 21 ASP cc_start: 0.8148 (t70) cc_final: 0.7568 (t0) REVERT: Q 34 GLN cc_start: 0.8168 (tp-100) cc_final: 0.7802 (tp-100) REVERT: e 60 MET cc_start: 0.9014 (ttm) cc_final: 0.8809 (ttp) REVERT: g 182 MET cc_start: 0.8992 (ptp) cc_final: 0.8789 (ptp) REVERT: h 185 MET cc_start: 0.8479 (mtp) cc_final: 0.8123 (mtm) REVERT: h 519 THR cc_start: 0.8876 (m) cc_final: 0.8665 (m) REVERT: q 41 GLN cc_start: 0.8478 (tp-100) cc_final: 0.7937 (tp-100) REVERT: z 415 GLU cc_start: 0.8596 (mp0) cc_final: 0.8353 (mp0) outliers start: 0 outliers final: 2 residues processed: 596 average time/residue: 1.5401 time to fit residues: 1178.8782 Evaluate side-chains 460 residues out of total 7151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 458 time to evaluate : 5.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 311 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 718 optimal weight: 10.0000 chunk 645 optimal weight: 2.9990 chunk 357 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 chunk 435 optimal weight: 9.9990 chunk 344 optimal weight: 7.9990 chunk 667 optimal weight: 6.9990 chunk 258 optimal weight: 0.7980 chunk 405 optimal weight: 9.9990 chunk 496 optimal weight: 7.9990 chunk 772 optimal weight: 7.9990 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN A 164 ASN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 426 ASN b 498 GLN ** d 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 468 ASN ** g 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 396 GLN g 400 ASN h 331 GLN q 4 HIS q 303 HIS ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS z 346 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 66816 Z= 0.476 Angle : 0.652 9.400 90225 Z= 0.324 Chirality : 0.045 0.192 10757 Planarity : 0.005 0.062 11514 Dihedral : 7.756 171.405 9291 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.79 % Favored : 96.20 % Rotamer: Outliers : 1.08 % Allowed : 7.06 % Favored : 91.86 % 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: 8548 helix: 1.81 (0.08), residues: 4397 sheet: 0.22 (0.16), residues: 1129 loop : -0.56 (0.11), residues: 3022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 222 HIS 0.011 0.001 HIS z 161 PHE 0.022 0.002 PHE b 12 TYR 0.026 0.002 TYR E 420 ARG 0.009 0.001 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 7151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 475 time to evaluate : 5.769 Fit side-chains REVERT: N 223 ASP cc_start: 0.8996 (t70) cc_final: 0.8644 (t70) REVERT: N 268 MET cc_start: 0.8601 (mpp) cc_final: 0.8324 (mpp) REVERT: D 65 LYS cc_start: 0.9359 (ptpp) cc_final: 0.8812 (ptmm) REVERT: D 67 ASP cc_start: 0.8246 (m-30) cc_final: 0.7940 (m-30) REVERT: E 21 ASP cc_start: 0.8375 (t70) cc_final: 0.7770 (t0) REVERT: G 21 LYS cc_start: 0.8579 (mmmm) cc_final: 0.8256 (mmtt) REVERT: H 185 MET cc_start: 0.8197 (mtp) cc_final: 0.7955 (mtp) REVERT: Q 34 GLN cc_start: 0.8232 (tp-100) cc_final: 0.7949 (tp40) REVERT: a 156 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8439 (mtp) REVERT: b 445 MET cc_start: 0.8723 (tpp) cc_final: 0.8491 (tpp) REVERT: g 15 LYS cc_start: 0.8579 (mtmm) cc_final: 0.8268 (mtmt) REVERT: h 2 MET cc_start: 0.8169 (OUTLIER) cc_final: 0.7480 (mmp) REVERT: h 30 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7907 (mt0) REVERT: h 185 MET cc_start: 0.8560 (mtp) cc_final: 0.8307 (mtp) REVERT: h 356 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.7924 (mt-10) REVERT: q 41 GLN cc_start: 0.8531 (tp-100) cc_final: 0.8031 (tp-100) REVERT: z 364 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8113 (mt-10) REVERT: z 415 GLU cc_start: 0.8580 (mp0) cc_final: 0.8348 (mp0) outliers start: 77 outliers final: 27 residues processed: 509 average time/residue: 1.4590 time to fit residues: 969.1917 Evaluate side-chains 481 residues out of total 7151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 450 time to evaluate : 5.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Z residue 20 LEU Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 325 THR Chi-restraints excluded: chain Z residue 374 LEU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain g residue 111 HIS Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 30 GLN Chi-restraints excluded: chain h residue 356 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 117 GLU Chi-restraints excluded: chain z residue 246 SER Chi-restraints excluded: chain z residue 418 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 429 optimal weight: 2.9990 chunk 239 optimal weight: 0.9980 chunk 643 optimal weight: 3.9990 chunk 526 optimal weight: 8.9990 chunk 213 optimal weight: 9.9990 chunk 774 optimal weight: 2.9990 chunk 836 optimal weight: 6.9990 chunk 689 optimal weight: 10.0000 chunk 767 optimal weight: 9.9990 chunk 263 optimal weight: 0.9990 chunk 621 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 205 ASN N 228 GLN N 272 GLN A 164 ASN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN ** d 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 474 ASN g 526 HIS ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 66816 Z= 0.241 Angle : 0.543 8.697 90225 Z= 0.269 Chirality : 0.042 0.161 10757 Planarity : 0.004 0.060 11514 Dihedral : 7.540 173.314 9289 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.21 % Favored : 96.78 % Rotamer: Outliers : 1.13 % Allowed : 8.75 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.09), residues: 8548 helix: 1.88 (0.08), residues: 4386 sheet: 0.23 (0.16), residues: 1137 loop : -0.48 (0.11), residues: 3025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 222 HIS 0.013 0.001 HIS z 161 PHE 0.020 0.001 PHE h 455 TYR 0.020 0.001 TYR A 181 ARG 0.006 0.000 ARG a 185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 7151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 492 time to evaluate : 5.899 Fit side-chains revert: symmetry clash REVERT: N 223 ASP cc_start: 0.8936 (t70) cc_final: 0.8607 (t0) REVERT: N 268 MET cc_start: 0.8556 (mpp) cc_final: 0.8237 (mpp) REVERT: B 415 MET cc_start: 0.9350 (mmm) cc_final: 0.9108 (mmp) REVERT: D 65 LYS cc_start: 0.9347 (ptpp) cc_final: 0.8749 (ptmm) REVERT: D 67 ASP cc_start: 0.8214 (m-30) cc_final: 0.7812 (m-30) REVERT: E 21 ASP cc_start: 0.8308 (t70) cc_final: 0.7646 (t0) REVERT: G 21 LYS cc_start: 0.8488 (mmmm) cc_final: 0.8195 (mmtm) REVERT: H 227 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8167 (mpt) REVERT: H 394 MET cc_start: 0.8910 (mmm) cc_final: 0.8540 (mmm) REVERT: Q 34 GLN cc_start: 0.8113 (tp-100) cc_final: 0.7837 (tp40) REVERT: Q 61 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8261 (mp0) REVERT: Q 387 ASP cc_start: 0.8444 (t0) cc_final: 0.7910 (m-30) REVERT: a 77 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7678 (mp0) REVERT: a 156 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8310 (mtp) REVERT: b 445 MET cc_start: 0.8640 (tpp) cc_final: 0.8398 (tpp) REVERT: d 429 GLU cc_start: 0.8257 (mp0) cc_final: 0.7835 (mp0) REVERT: e 4 MET cc_start: 0.4611 (mpp) cc_final: 0.3369 (mmt) REVERT: g 15 LYS cc_start: 0.8548 (mtmm) cc_final: 0.8218 (mtmt) REVERT: g 229 MET cc_start: 0.9225 (mtt) cc_final: 0.8942 (mtt) REVERT: h 2 MET cc_start: 0.8115 (OUTLIER) cc_final: 0.7464 (mmp) REVERT: h 455 PHE cc_start: 0.7957 (m-80) cc_final: 0.7661 (m-80) REVERT: q 41 GLN cc_start: 0.8508 (tp-100) cc_final: 0.7990 (tp-100) REVERT: z 364 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8111 (mt-10) REVERT: z 415 GLU cc_start: 0.8514 (mp0) cc_final: 0.8236 (mp0) outliers start: 81 outliers final: 26 residues processed: 534 average time/residue: 1.4559 time to fit residues: 1016.9314 Evaluate side-chains 493 residues out of total 7151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 462 time to evaluate : 5.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 374 LEU Chi-restraints excluded: chain a residue 77 GLU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 164 ASN Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain b residue 310 MET Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 377 THR Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 117 GLU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 463 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 764 optimal weight: 5.9990 chunk 582 optimal weight: 9.9990 chunk 401 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 369 optimal weight: 1.9990 chunk 519 optimal weight: 5.9990 chunk 776 optimal weight: 0.6980 chunk 822 optimal weight: 0.8980 chunk 405 optimal weight: 9.9990 chunk 736 optimal weight: 9.9990 chunk 221 optimal weight: 5.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 66816 Z= 0.295 Angle : 0.560 9.120 90225 Z= 0.275 Chirality : 0.042 0.154 10757 Planarity : 0.004 0.062 11514 Dihedral : 7.436 178.710 9287 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.57 % Favored : 96.42 % Rotamer: Outliers : 1.44 % Allowed : 9.94 % Favored : 88.62 % 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: 1.20 (0.09), residues: 8548 helix: 1.84 (0.08), residues: 4382 sheet: 0.23 (0.16), residues: 1137 loop : -0.48 (0.11), residues: 3029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 222 HIS 0.012 0.001 HIS z 161 PHE 0.018 0.001 PHE h 455 TYR 0.019 0.001 TYR N 174 ARG 0.007 0.000 ARG a 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 7151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 476 time to evaluate : 5.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 223 ASP cc_start: 0.8957 (t70) cc_final: 0.8608 (t0) REVERT: N 268 MET cc_start: 0.8569 (mpp) cc_final: 0.8314 (mpt) REVERT: A 189 ARG cc_start: 0.7868 (mtm110) cc_final: 0.7559 (ptp-110) REVERT: D 65 LYS cc_start: 0.9358 (ptpp) cc_final: 0.8764 (ptmm) REVERT: D 67 ASP cc_start: 0.8215 (m-30) cc_final: 0.7849 (m-30) REVERT: E 21 ASP cc_start: 0.8315 (t70) cc_final: 0.7714 (t0) REVERT: E 29 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7101 (mtm) REVERT: E 526 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8748 (ttm) REVERT: G 21 LYS cc_start: 0.8512 (mmmm) cc_final: 0.8187 (mmtm) REVERT: H 227 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8162 (mpt) REVERT: H 394 MET cc_start: 0.8891 (mmm) cc_final: 0.8533 (mmm) REVERT: Q 34 GLN cc_start: 0.8154 (tp-100) cc_final: 0.7890 (tp40) REVERT: Q 61 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8161 (mp0) REVERT: Q 387 ASP cc_start: 0.8461 (t0) cc_final: 0.7918 (m-30) REVERT: a 77 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7677 (mp0) REVERT: a 156 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8294 (mtp) REVERT: d 429 GLU cc_start: 0.8248 (mp0) cc_final: 0.7811 (mp0) REVERT: e 4 MET cc_start: 0.4635 (mpp) cc_final: 0.3433 (mmt) REVERT: g 15 LYS cc_start: 0.8604 (mtmm) cc_final: 0.8240 (mtmt) REVERT: g 527 LYS cc_start: 0.8917 (mmmt) cc_final: 0.8700 (mmmm) REVERT: h 2 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7494 (mmp) REVERT: h 356 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7875 (mt-10) REVERT: h 455 PHE cc_start: 0.7960 (m-80) cc_final: 0.7646 (m-80) REVERT: q 41 GLN cc_start: 0.8514 (tp-100) cc_final: 0.8016 (tp-100) REVERT: z 210 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8910 (mp) REVERT: z 364 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8147 (mt-10) REVERT: z 415 GLU cc_start: 0.8504 (mp0) cc_final: 0.8171 (mp0) outliers start: 103 outliers final: 41 residues processed: 533 average time/residue: 1.4414 time to fit residues: 1007.5027 Evaluate side-chains 517 residues out of total 7151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 467 time to evaluate : 5.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 526 MET Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 28 ASN Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 236 ASP Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Q residue 296 LYS Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 374 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 77 GLU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain e residue 229 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 356 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 117 GLU Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 210 LEU Chi-restraints excluded: chain z residue 463 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 685 optimal weight: 0.9980 chunk 466 optimal weight: 7.9990 chunk 11 optimal weight: 50.0000 chunk 612 optimal weight: 4.9990 chunk 339 optimal weight: 0.9990 chunk 701 optimal weight: 0.0030 chunk 568 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 420 optimal weight: 10.0000 chunk 738 optimal weight: 1.9990 chunk 207 optimal weight: 1.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 228 GLN N 272 GLN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN G 390 ASN G 481 ASN H 352 GLN a 135 ASN ** d 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 303 HIS ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 66816 Z= 0.154 Angle : 0.512 10.175 90225 Z= 0.250 Chirality : 0.040 0.165 10757 Planarity : 0.003 0.062 11514 Dihedral : 7.128 178.504 9287 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.15 % Favored : 96.84 % Rotamer: Outliers : 1.08 % Allowed : 10.94 % Favored : 87.99 % 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: 1.37 (0.09), residues: 8548 helix: 2.02 (0.08), residues: 4357 sheet: 0.24 (0.16), residues: 1141 loop : -0.41 (0.11), residues: 3050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 222 HIS 0.013 0.001 HIS z 161 PHE 0.014 0.001 PHE h 455 TYR 0.025 0.001 TYR A 181 ARG 0.008 0.000 ARG G 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 7151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 515 time to evaluate : 5.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 223 ASP cc_start: 0.8852 (t70) cc_final: 0.8505 (t0) REVERT: N 268 MET cc_start: 0.8581 (mpp) cc_final: 0.8338 (mpt) REVERT: A 156 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8190 (mmm) REVERT: A 181 TYR cc_start: 0.8604 (p90) cc_final: 0.8377 (p90) REVERT: B 408 TYR cc_start: 0.8842 (m-80) cc_final: 0.8491 (m-80) REVERT: D 65 LYS cc_start: 0.9335 (ptpp) cc_final: 0.8804 (ptmm) REVERT: D 67 ASP cc_start: 0.8180 (m-30) cc_final: 0.7905 (m-30) REVERT: D 120 CYS cc_start: 0.8750 (m) cc_final: 0.8395 (m) REVERT: E 21 ASP cc_start: 0.8262 (t70) cc_final: 0.7522 (t0) REVERT: G 47 MET cc_start: 0.8976 (mmm) cc_final: 0.8704 (mmm) REVERT: H 227 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8175 (mpt) REVERT: Q 34 GLN cc_start: 0.7999 (tp-100) cc_final: 0.7728 (tp40) REVERT: Q 61 GLU cc_start: 0.8333 (mp0) cc_final: 0.8077 (mp0) REVERT: Q 387 ASP cc_start: 0.8446 (t0) cc_final: 0.8050 (m-30) REVERT: a 77 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7537 (mp0) REVERT: a 156 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8106 (mtp) REVERT: b 445 MET cc_start: 0.8500 (tpp) cc_final: 0.8299 (tpp) REVERT: d 429 GLU cc_start: 0.8235 (mp0) cc_final: 0.7814 (mp0) REVERT: e 84 ASP cc_start: 0.8794 (t70) cc_final: 0.8369 (m-30) REVERT: g 15 LYS cc_start: 0.8616 (mtmm) cc_final: 0.8276 (mtmt) REVERT: g 527 LYS cc_start: 0.8928 (mmmt) cc_final: 0.8705 (mmmm) REVERT: h 2 MET cc_start: 0.8166 (OUTLIER) cc_final: 0.7535 (mmp) REVERT: h 57 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8716 (p) REVERT: h 185 MET cc_start: 0.8499 (mtp) cc_final: 0.8215 (mtp) REVERT: q 41 GLN cc_start: 0.8481 (tp-100) cc_final: 0.7937 (tp-100) REVERT: z 210 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8897 (mp) REVERT: z 364 GLU cc_start: 0.8399 (mt-10) cc_final: 0.8131 (mt-10) outliers start: 77 outliers final: 26 residues processed: 557 average time/residue: 1.4417 time to fit residues: 1054.1884 Evaluate side-chains 509 residues out of total 7151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 476 time to evaluate : 5.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 61 ASN Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain a residue 77 GLU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 255 ASP Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain q residue 256 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 210 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 276 optimal weight: 4.9990 chunk 740 optimal weight: 10.0000 chunk 162 optimal weight: 9.9990 chunk 482 optimal weight: 10.0000 chunk 203 optimal weight: 0.9990 chunk 823 optimal weight: 10.0000 chunk 683 optimal weight: 10.0000 chunk 381 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 272 optimal weight: 0.9990 chunk 432 optimal weight: 0.6980 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN G 390 ASN ** d 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 65 HIS ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 66816 Z= 0.221 Angle : 0.530 12.597 90225 Z= 0.258 Chirality : 0.041 0.161 10757 Planarity : 0.003 0.059 11514 Dihedral : 7.077 178.749 9287 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.42 % Favored : 96.57 % Rotamer: Outliers : 1.31 % Allowed : 11.55 % Favored : 87.13 % 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: 1.38 (0.09), residues: 8548 helix: 2.01 (0.08), residues: 4364 sheet: 0.24 (0.16), residues: 1164 loop : -0.39 (0.11), residues: 3020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 222 HIS 0.003 0.001 HIS A 113 PHE 0.013 0.001 PHE a 167 TYR 0.020 0.001 TYR N 174 ARG 0.013 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 7151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 480 time to evaluate : 5.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 223 ASP cc_start: 0.8870 (t70) cc_final: 0.8503 (t0) REVERT: N 264 MET cc_start: 0.7601 (mmm) cc_final: 0.7218 (mmm) REVERT: A 156 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8221 (mmm) REVERT: A 344 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.8059 (mtp) REVERT: B 408 TYR cc_start: 0.8867 (m-80) cc_final: 0.8515 (m-80) REVERT: D 65 LYS cc_start: 0.9341 (ptpp) cc_final: 0.8808 (ptmm) REVERT: D 67 ASP cc_start: 0.8194 (m-30) cc_final: 0.7916 (m-30) REVERT: D 90 MET cc_start: 0.9061 (mmm) cc_final: 0.8840 (mtt) REVERT: E 21 ASP cc_start: 0.8276 (t70) cc_final: 0.7532 (t0) REVERT: E 29 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.7066 (mtm) REVERT: G 47 MET cc_start: 0.9006 (mmm) cc_final: 0.8732 (mmm) REVERT: H 227 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8188 (mpt) REVERT: H 350 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8603 (tt0) REVERT: H 382 MET cc_start: 0.9130 (mtm) cc_final: 0.8908 (mtm) REVERT: Q 34 GLN cc_start: 0.8025 (tp-100) cc_final: 0.7819 (tp40) REVERT: Q 61 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8125 (mp0) REVERT: Q 387 ASP cc_start: 0.8445 (t0) cc_final: 0.7990 (m-30) REVERT: Z 415 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.7816 (mp0) REVERT: a 77 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: a 156 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8183 (mtp) REVERT: b 445 MET cc_start: 0.8575 (tpp) cc_final: 0.8334 (tpp) REVERT: d 429 GLU cc_start: 0.8242 (mp0) cc_final: 0.7900 (mp0) REVERT: e 4 MET cc_start: 0.4697 (mpp) cc_final: 0.3415 (mmt) REVERT: g 15 LYS cc_start: 0.8636 (mtmm) cc_final: 0.8291 (mtmt) REVERT: g 105 MET cc_start: 0.8715 (OUTLIER) cc_final: 0.8311 (mmt) REVERT: g 527 LYS cc_start: 0.8957 (mmmt) cc_final: 0.8721 (mmmm) REVERT: h 2 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7614 (mmp) REVERT: h 57 THR cc_start: 0.9191 (OUTLIER) cc_final: 0.8785 (p) REVERT: q 41 GLN cc_start: 0.8497 (tp-100) cc_final: 0.7950 (tp-100) REVERT: z 210 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8889 (mp) outliers start: 94 outliers final: 48 residues processed: 535 average time/residue: 1.4505 time to fit residues: 1018.5816 Evaluate side-chains 534 residues out of total 7151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 473 time to evaluate : 5.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 250 THR Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 61 ASN Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 296 LYS 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 415 GLU Chi-restraints excluded: chain a residue 77 GLU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 217 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 377 THR Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 229 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 105 MET Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 117 GLU Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain q residue 256 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 210 LEU Chi-restraints excluded: chain z residue 463 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 793 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 469 optimal weight: 6.9990 chunk 601 optimal weight: 6.9990 chunk 465 optimal weight: 1.9990 chunk 693 optimal weight: 5.9990 chunk 459 optimal weight: 2.9990 chunk 820 optimal weight: 0.4980 chunk 513 optimal weight: 2.9990 chunk 500 optimal weight: 9.9990 chunk 378 optimal weight: 10.0000 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN H 501 ASN d 301 GLN z 65 HIS ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 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 : 0.004 0.050 66816 Z= 0.276 Angle : 0.551 12.955 90225 Z= 0.269 Chirality : 0.042 0.173 10757 Planarity : 0.004 0.059 11514 Dihedral : 7.095 178.742 9287 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.44 % Favored : 96.55 % Rotamer: Outliers : 1.36 % Allowed : 11.94 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.09), residues: 8548 helix: 1.98 (0.08), residues: 4364 sheet: 0.21 (0.16), residues: 1171 loop : -0.40 (0.11), residues: 3013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 222 HIS 0.005 0.001 HIS N 234 PHE 0.014 0.001 PHE a 167 TYR 0.020 0.001 TYR N 174 ARG 0.010 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 7151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 477 time to evaluate : 5.874 Fit side-chains revert: symmetry clash REVERT: N 223 ASP cc_start: 0.8889 (t70) cc_final: 0.8530 (t0) REVERT: N 244 ASP cc_start: 0.7104 (t0) cc_final: 0.6890 (t0) REVERT: N 264 MET cc_start: 0.7706 (mmm) cc_final: 0.7264 (mmm) REVERT: A 156 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8228 (mmm) REVERT: A 344 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8012 (mtp) REVERT: B 408 TYR cc_start: 0.8882 (m-80) cc_final: 0.8532 (m-80) REVERT: D 65 LYS cc_start: 0.9347 (ptpp) cc_final: 0.8803 (ptmm) REVERT: D 67 ASP cc_start: 0.8202 (m-30) cc_final: 0.7909 (m-30) REVERT: D 90 MET cc_start: 0.9038 (mmm) cc_final: 0.8828 (mtt) REVERT: E 21 ASP cc_start: 0.8344 (t70) cc_final: 0.7607 (t0) REVERT: E 29 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.6931 (mtm) REVERT: G 47 MET cc_start: 0.9032 (mmm) cc_final: 0.8680 (mmm) REVERT: H 227 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.8182 (mpt) REVERT: Q 276 MET cc_start: 0.8770 (tpt) cc_final: 0.7903 (tpt) REVERT: Q 387 ASP cc_start: 0.8490 (t0) cc_final: 0.8005 (m-30) REVERT: a 77 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: a 156 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8251 (mtp) REVERT: d 429 GLU cc_start: 0.8247 (mp0) cc_final: 0.7900 (mp0) REVERT: g 15 LYS cc_start: 0.8616 (mtmm) cc_final: 0.8264 (mtmt) REVERT: g 105 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8221 (mmt) REVERT: g 527 LYS cc_start: 0.8975 (mmmt) cc_final: 0.8729 (mmmm) REVERT: h 2 MET cc_start: 0.8197 (OUTLIER) cc_final: 0.7675 (mmp) REVERT: h 57 THR cc_start: 0.9162 (OUTLIER) cc_final: 0.8783 (p) REVERT: h 185 MET cc_start: 0.8473 (mtp) cc_final: 0.8223 (mtp) REVERT: q 41 GLN cc_start: 0.8510 (tp-100) cc_final: 0.7957 (tp-100) REVERT: z 210 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8891 (mp) outliers start: 97 outliers final: 53 residues processed: 540 average time/residue: 1.5071 time to fit residues: 1077.7155 Evaluate side-chains 528 residues out of total 7151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 465 time to evaluate : 5.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 250 THR Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 266 MET Chi-restraints excluded: chain Q residue 296 LYS Chi-restraints excluded: chain Q residue 358 THR Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 77 GLU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 217 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 377 THR Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 229 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain g residue 105 MET Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 117 GLU Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain q residue 256 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 210 LEU Chi-restraints excluded: chain z residue 463 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 507 optimal weight: 3.9990 chunk 327 optimal weight: 9.9990 chunk 489 optimal weight: 9.9990 chunk 247 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 521 optimal weight: 10.0000 chunk 558 optimal weight: 0.5980 chunk 405 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 644 optimal weight: 9.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 228 GLN N 234 HIS N 272 GLN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 501 ASN z 65 HIS ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 66816 Z= 0.293 Angle : 0.563 14.368 90225 Z= 0.275 Chirality : 0.042 0.168 10757 Planarity : 0.004 0.058 11514 Dihedral : 7.113 177.749 9287 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.49 % Favored : 96.50 % Rotamer: Outliers : 1.22 % Allowed : 12.38 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.09), residues: 8548 helix: 1.92 (0.08), residues: 4374 sheet: 0.24 (0.16), residues: 1155 loop : -0.43 (0.11), residues: 3019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 222 HIS 0.010 0.001 HIS z 161 PHE 0.013 0.001 PHE a 167 TYR 0.021 0.001 TYR N 174 ARG 0.009 0.000 ARG G 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 561 residues out of total 7151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 474 time to evaluate : 6.000 Fit side-chains revert: symmetry clash REVERT: N 223 ASP cc_start: 0.8921 (t70) cc_final: 0.8581 (t70) REVERT: N 244 ASP cc_start: 0.7167 (t0) cc_final: 0.6961 (t0) REVERT: N 264 MET cc_start: 0.7766 (mmm) cc_final: 0.7433 (tpp) REVERT: A 156 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8223 (mmm) REVERT: A 344 MET cc_start: 0.8769 (OUTLIER) cc_final: 0.7986 (mtp) REVERT: B 408 TYR cc_start: 0.8880 (m-80) cc_final: 0.8532 (m-80) REVERT: D 65 LYS cc_start: 0.9353 (ptpp) cc_final: 0.8805 (ptmm) REVERT: D 67 ASP cc_start: 0.8203 (m-30) cc_final: 0.7917 (m-30) REVERT: E 21 ASP cc_start: 0.8343 (t70) cc_final: 0.7602 (t0) REVERT: E 29 MET cc_start: 0.7479 (OUTLIER) cc_final: 0.6890 (mtm) REVERT: G 47 MET cc_start: 0.8960 (mmm) cc_final: 0.8662 (mmm) REVERT: H 227 MET cc_start: 0.9154 (OUTLIER) cc_final: 0.8179 (mpt) REVERT: H 394 MET cc_start: 0.8898 (mmm) cc_final: 0.8559 (mmm) REVERT: Q 65 VAL cc_start: 0.9204 (OUTLIER) cc_final: 0.8868 (m) REVERT: Q 387 ASP cc_start: 0.8514 (t0) cc_final: 0.8008 (m-30) REVERT: a 77 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7654 (mp0) REVERT: a 156 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8284 (mtp) REVERT: a 246 MET cc_start: 0.8867 (mmm) cc_final: 0.8620 (mmt) REVERT: b 452 ASP cc_start: 0.8274 (m-30) cc_final: 0.7910 (m-30) REVERT: d 429 GLU cc_start: 0.8252 (mp0) cc_final: 0.7890 (mp0) REVERT: g 15 LYS cc_start: 0.8584 (mtmm) cc_final: 0.8229 (mtmt) REVERT: g 527 LYS cc_start: 0.8968 (mmmt) cc_final: 0.8719 (mmmm) REVERT: h 57 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8783 (p) REVERT: h 356 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.7831 (mt-10) REVERT: q 41 GLN cc_start: 0.8526 (tp-100) cc_final: 0.7976 (tp-100) outliers start: 87 outliers final: 54 residues processed: 530 average time/residue: 1.4716 time to fit residues: 1026.4848 Evaluate side-chains 528 residues out of total 7151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 465 time to evaluate : 5.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 61 ASN Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 266 MET Chi-restraints excluded: chain Q residue 296 LYS Chi-restraints excluded: chain Q residue 358 THR Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 67 VAL Chi-restraints excluded: chain a residue 77 GLU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 217 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 377 THR Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 229 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 356 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 117 GLU Chi-restraints excluded: chain q residue 256 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 463 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 746 optimal weight: 0.0070 chunk 785 optimal weight: 3.9990 chunk 716 optimal weight: 6.9990 chunk 764 optimal weight: 0.9990 chunk 460 optimal weight: 1.9990 chunk 332 optimal weight: 7.9990 chunk 600 optimal weight: 6.9990 chunk 234 optimal weight: 7.9990 chunk 690 optimal weight: 5.9990 chunk 722 optimal weight: 6.9990 chunk 761 optimal weight: 0.7980 overall best weight: 1.5604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN G 390 ASN H 21 GLN z 65 HIS ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 66816 Z= 0.178 Angle : 0.532 13.863 90225 Z= 0.259 Chirality : 0.041 0.170 10757 Planarity : 0.003 0.058 11514 Dihedral : 6.964 177.255 9287 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.27 % Favored : 96.72 % Rotamer: Outliers : 1.05 % Allowed : 12.64 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.09), residues: 8548 helix: 2.01 (0.08), residues: 4364 sheet: 0.23 (0.16), residues: 1167 loop : -0.38 (0.11), residues: 3017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 222 HIS 0.014 0.001 HIS z 161 PHE 0.012 0.001 PHE a 167 TYR 0.023 0.001 TYR A 181 ARG 0.013 0.000 ARG a 185 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 7151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 492 time to evaluate : 5.979 Fit side-chains revert: symmetry clash REVERT: N 223 ASP cc_start: 0.8874 (t70) cc_final: 0.8495 (t0) REVERT: N 264 MET cc_start: 0.7720 (mmm) cc_final: 0.7488 (mmm) REVERT: A 156 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8204 (mmm) REVERT: A 344 MET cc_start: 0.8755 (OUTLIER) cc_final: 0.8022 (mtp) REVERT: B 408 TYR cc_start: 0.8840 (m-80) cc_final: 0.8506 (m-80) REVERT: D 65 LYS cc_start: 0.9342 (ptpp) cc_final: 0.8766 (ptmm) REVERT: D 67 ASP cc_start: 0.8177 (m-30) cc_final: 0.7810 (m-30) REVERT: D 120 CYS cc_start: 0.8779 (m) cc_final: 0.8418 (m) REVERT: E 21 ASP cc_start: 0.8303 (t70) cc_final: 0.7539 (t0) REVERT: E 29 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.6919 (mtm) REVERT: G 47 MET cc_start: 0.9147 (mmm) cc_final: 0.8794 (mmm) REVERT: H 227 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8333 (mpp) REVERT: H 394 MET cc_start: 0.8903 (mmm) cc_final: 0.8539 (mmm) REVERT: Q 65 VAL cc_start: 0.9172 (OUTLIER) cc_final: 0.8839 (m) REVERT: Q 387 ASP cc_start: 0.8464 (t0) cc_final: 0.7991 (m-30) REVERT: b 452 ASP cc_start: 0.8232 (m-30) cc_final: 0.7863 (m-30) REVERT: d 429 GLU cc_start: 0.8237 (mp0) cc_final: 0.7891 (mp0) REVERT: g 15 LYS cc_start: 0.8582 (mtmm) cc_final: 0.8225 (mtmt) REVERT: g 527 LYS cc_start: 0.8957 (mmmt) cc_final: 0.8698 (mmmm) REVERT: h 57 THR cc_start: 0.9158 (OUTLIER) cc_final: 0.8751 (p) REVERT: h 185 MET cc_start: 0.8216 (mtp) cc_final: 0.7975 (mtp) REVERT: h 356 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7816 (mt-10) REVERT: q 41 GLN cc_start: 0.8478 (tp-100) cc_final: 0.7912 (tp-100) REVERT: z 210 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8886 (mp) REVERT: z 357 GLU cc_start: 0.7675 (tp30) cc_final: 0.7439 (tp30) outliers start: 75 outliers final: 43 residues processed: 544 average time/residue: 1.4949 time to fit residues: 1070.8331 Evaluate side-chains 522 residues out of total 7151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 471 time to evaluate : 5.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 296 LYS Chi-restraints excluded: chain Q residue 358 THR Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 217 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 377 THR Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 229 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 356 GLU Chi-restraints excluded: chain q residue 117 GLU Chi-restraints excluded: chain q residue 256 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 210 LEU Chi-restraints excluded: chain z residue 463 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 501 optimal weight: 5.9990 chunk 808 optimal weight: 0.9990 chunk 493 optimal weight: 10.0000 chunk 383 optimal weight: 10.0000 chunk 561 optimal weight: 6.9990 chunk 847 optimal weight: 1.9990 chunk 780 optimal weight: 0.9990 chunk 675 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 521 optimal weight: 0.9980 chunk 413 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN H 21 GLN z 65 HIS ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 66816 Z= 0.196 Angle : 0.536 13.851 90225 Z= 0.261 Chirality : 0.041 0.182 10757 Planarity : 0.003 0.058 11514 Dihedral : 6.871 175.748 9287 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.36 % Favored : 96.63 % Rotamer: Outliers : 0.81 % Allowed : 13.10 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.09), residues: 8548 helix: 2.03 (0.08), residues: 4361 sheet: 0.24 (0.16), residues: 1156 loop : -0.39 (0.11), residues: 3031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 222 HIS 0.003 0.001 HIS A 113 PHE 0.011 0.001 PHE a 167 TYR 0.022 0.001 TYR N 174 ARG 0.011 0.000 ARG a 185 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 7151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 485 time to evaluate : 5.805 Fit side-chains revert: symmetry clash REVERT: N 223 ASP cc_start: 0.8891 (t70) cc_final: 0.8554 (t70) REVERT: N 264 MET cc_start: 0.7743 (mmm) cc_final: 0.7439 (tpp) REVERT: A 156 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8211 (mmm) REVERT: A 344 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8029 (mtp) REVERT: B 408 TYR cc_start: 0.8843 (m-80) cc_final: 0.8509 (m-80) REVERT: D 65 LYS cc_start: 0.9342 (ptpp) cc_final: 0.8812 (ptmm) REVERT: D 67 ASP cc_start: 0.8182 (m-30) cc_final: 0.7902 (m-30) REVERT: D 90 MET cc_start: 0.9064 (mmm) cc_final: 0.8829 (mtt) REVERT: E 21 ASP cc_start: 0.8283 (t70) cc_final: 0.7510 (t0) REVERT: E 64 LYS cc_start: 0.8960 (pttm) cc_final: 0.8650 (ptmm) REVERT: G 47 MET cc_start: 0.9010 (mmm) cc_final: 0.8695 (mmm) REVERT: H 227 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8180 (mpt) REVERT: H 350 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8630 (tt0) REVERT: H 394 MET cc_start: 0.8880 (mmm) cc_final: 0.8496 (mmm) REVERT: Q 65 VAL cc_start: 0.9180 (OUTLIER) cc_final: 0.8844 (m) REVERT: Q 249 MET cc_start: 0.7826 (pmt) cc_final: 0.7557 (pmt) REVERT: Q 387 ASP cc_start: 0.8481 (t0) cc_final: 0.8009 (m-30) REVERT: a 206 MET cc_start: 0.9064 (mpp) cc_final: 0.8799 (mmm) REVERT: a 480 ARG cc_start: 0.7852 (mmm-85) cc_final: 0.7293 (mmm-85) REVERT: b 244 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8414 (mtm) REVERT: b 452 ASP cc_start: 0.8247 (m-30) cc_final: 0.7882 (m-30) REVERT: d 429 GLU cc_start: 0.8238 (mp0) cc_final: 0.7806 (mp0) REVERT: g 15 LYS cc_start: 0.8591 (mtmm) cc_final: 0.8236 (mtmt) REVERT: g 527 LYS cc_start: 0.8963 (mmmt) cc_final: 0.8686 (mmmm) REVERT: h 57 THR cc_start: 0.9178 (OUTLIER) cc_final: 0.8774 (p) REVERT: h 185 MET cc_start: 0.8267 (mtp) cc_final: 0.8044 (mtp) REVERT: h 245 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7874 (mt-10) REVERT: h 356 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7820 (mt-10) REVERT: q 41 GLN cc_start: 0.8471 (tp-100) cc_final: 0.7902 (tp-100) REVERT: z 210 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8889 (mp) outliers start: 58 outliers final: 41 residues processed: 526 average time/residue: 1.4737 time to fit residues: 1015.7139 Evaluate side-chains 524 residues out of total 7151 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 474 time to evaluate : 5.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 170 SER Chi-restraints excluded: chain D residue 273 ASP Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain D residue 366 ASN Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 307 ASP Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 61 ASN Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 340 ASP Chi-restraints excluded: chain H residue 350 GLU Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 296 LYS Chi-restraints excluded: chain Q residue 358 THR Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 244 MET Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 217 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 377 THR Chi-restraints excluded: chain e residue 229 ILE Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 356 GLU Chi-restraints excluded: chain q residue 256 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 210 LEU Chi-restraints excluded: chain z residue 463 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 536 optimal weight: 9.9990 chunk 719 optimal weight: 3.9990 chunk 206 optimal weight: 6.9990 chunk 622 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 187 optimal weight: 9.9990 chunk 676 optimal weight: 9.9990 chunk 282 optimal weight: 0.8980 chunk 694 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN G 390 ASN H 21 GLN H 501 ASN z 65 HIS ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.074531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.062787 restraints weight = 156141.757| |-----------------------------------------------------------------------------| r_work (start): 0.2791 rms_B_bonded: 2.68 r_work: 0.2657 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2534 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2536 r_free = 0.2536 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 66816 Z= 0.285 Angle : 0.565 15.661 90225 Z= 0.275 Chirality : 0.042 0.176 10757 Planarity : 0.003 0.058 11514 Dihedral : 6.913 175.513 9287 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.43 % Favored : 96.56 % Rotamer: Outliers : 0.94 % Allowed : 13.06 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.09), residues: 8548 helix: 1.98 (0.08), residues: 4371 sheet: 0.24 (0.16), residues: 1158 loop : -0.43 (0.11), residues: 3019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 222 HIS 0.003 0.001 HIS A 113 PHE 0.013 0.001 PHE a 167 TYR 0.024 0.001 TYR A 181 ARG 0.009 0.000 ARG a 185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17178.53 seconds wall clock time: 301 minutes 54.36 seconds (18114.36 seconds total)