Starting phenix.real_space_refine on Sat Dec 9 06:29:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgq_40464/12_2023/8sgq_40464_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgq_40464/12_2023/8sgq_40464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgq_40464/12_2023/8sgq_40464.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgq_40464/12_2023/8sgq_40464.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgq_40464/12_2023/8sgq_40464_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sgq_40464/12_2023/8sgq_40464_updated.pdb" } resolution = 3.7 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= 0.005 sd= 0.030 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: 5 Type Number sf(0) Gaussians P 32 5.49 5 S 384 5.16 5 C 38902 2.51 5 N 10842 2.21 5 O 12027 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "z PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z GLU 461": "OE1" <-> "OE2" Residue "Z TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ASP 61": "OD1" <-> "OD2" Residue "g ASP 87": "OD1" <-> "OD2" Residue "g ASP 149": "OD1" <-> "OD2" Residue "h ASP 14": "OD1" <-> "OD2" Residue "h TYR 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 38": "OE1" <-> "OE2" Residue "q GLU 117": "OE1" <-> "OE2" Residue "q TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 105": "OD1" <-> "OD2" Residue "A PHE 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 516": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "H TYR 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 114": "OE1" <-> "OE2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 518": "OD1" <-> "OD2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 46": "OD1" <-> "OD2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D ASP 268": "OD1" <-> "OD2" Residue "E PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 453": "OD1" <-> "OD2" Residue "b ASP 37": "OD1" <-> "OD2" Residue "b GLU 114": "OE1" <-> "OE2" Residue "b PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 93": "OE1" <-> "OE2" Residue "d PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 62187 Number of models: 1 Model: "" Number of chains: 32 Chain: "z" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3903 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 13, 'TRANS': 494} Chain: "Z" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3903 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 13, 'TRANS': 494} Chain: "a" Number of atoms: 3709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3709 Classifications: {'peptide': 490} Link IDs: {'PTRANS': 11, 'TRANS': 478} Chain breaks: 2 Chain: "g" Number of atoms: 3678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3678 Classifications: {'peptide': 477} Link IDs: {'PTRANS': 16, 'TRANS': 460} Chain breaks: 1 Chain: "h" Number of atoms: 3834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3834 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 14, 'TRANS': 485} Chain breaks: 1 Chain: "q" Number of atoms: 3692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3692 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 12, 'TRANS': 470} Chain breaks: 1 Chain: "A" Number of atoms: 3742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 494, 3742 Classifications: {'peptide': 494} Link IDs: {'PTRANS': 11, 'TRANS': 482} Chain breaks: 2 Chain: "G" Number of atoms: 3741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3741 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 16, 'TRANS': 468} Chain breaks: 1 Chain: "H" Number of atoms: 3825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3825 Classifications: {'peptide': 499} Link IDs: {'PTRANS': 14, 'TRANS': 484} Chain breaks: 1 Chain: "Q" Number of atoms: 3692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3692 Classifications: {'peptide': 483} Link IDs: {'PTRANS': 12, 'TRANS': 470} Chain breaks: 1 Chain: "B" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3952 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 10, 'TRANS': 515} Chain: "D" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3923 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "E" Number of atoms: 4132 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} Conformer: "C" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} bond proxies already assigned to first conformer: 4158 Chain: "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: "z" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N BPHE E 9 " occ=0.38 ... (20 atoms not shown) pdb=" CZ CPHE E 9 " occ=0.62 residue: pdb=" N APHE e 9 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE e 9 " occ=0.50 Time building chain proxies: 29.99, per 1000 atoms: 0.48 Number of scatterers: 62187 At special positions: 0 Unit cell: (183.034, 174.57, 188.324, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 384 16.00 P 32 15.00 O 12027 8.00 N 10842 7.00 C 38902 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS h 330 " - pdb=" SG CYS h 349 " distance=2.04 Simple disulfide: pdb=" SG CYS H 326 " - pdb=" SG CYS H 345 " distance=2.04 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.58 Conformation dependent library (CDL) restraints added in 10.6 seconds 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15086 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 283 helices and 70 sheets defined 49.4% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.15 Creating SS restraints... Processing helix chain 'z' and resid 19 through 33 Processing helix chain 'z' and resid 35 through 37 No H-bonds generated for 'chain 'z' and resid 35 through 37' Processing helix chain 'z' and resid 60 through 66 Processing helix chain 'z' and resid 72 through 85 Processing helix chain 'z' and resid 92 through 112 removed outlier: 3.587A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) removed outlier: 5.259A 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 156 Processing helix chain 'z' and resid 162 through 182 removed outlier: 4.089A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA z 171 " --> pdb=" O VAL z 167 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS z 181 " --> pdb=" O LEU z 177 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N GLN z 182 " --> pdb=" O ALA z 178 " (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 254 through 258 Processing helix chain 'z' and resid 264 through 281 Processing helix chain 'z' and resid 299 through 308 removed outlier: 3.800A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 318 through 327 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 404 Processing helix chain 'z' and resid 413 through 424 Processing helix chain 'z' and resid 426 through 428 No H-bonds generated for 'chain 'z' and resid 426 through 428' Processing helix chain 'z' and resid 433 through 455 removed outlier: 4.012A pdb=" N ILE z 446 " --> pdb=" O ASP z 442 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ILE z 447 " --> pdb=" O ALA z 443 " (cutoff:3.500A) Proline residue: z 448 - end of helix Processing helix chain 'z' and resid 459 through 473 removed outlier: 4.028A pdb=" N GLU z 472 " --> pdb=" O ALA z 468 " (cutoff:3.500A) 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 'Z' and resid 21 through 34 Processing helix chain 'Z' and resid 60 through 63 No H-bonds generated for 'chain 'Z' and resid 60 through 63' Processing helix chain 'Z' and resid 72 through 87 removed outlier: 4.474A pdb=" N ASP Z 86 " --> pdb=" O THR Z 82 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE Z 87 " --> pdb=" O ALA Z 83 " (cutoff:3.500A) Processing helix chain 'Z' and resid 92 through 110 removed outlier: 3.619A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 116 through 137 removed outlier: 3.968A pdb=" N GLU Z 135 " --> pdb=" O LEU Z 131 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLU Z 136 " --> pdb=" O GLN Z 132 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL Z 137 " --> pdb=" O PHE Z 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 145 through 157 removed outlier: 3.685A pdb=" N ASP Z 150 " --> pdb=" O GLU Z 146 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL Z 151 " --> pdb=" O THR Z 147 " (cutoff:3.500A) Processing helix chain 'Z' and resid 162 through 179 removed outlier: 3.737A pdb=" N VAL Z 167 " --> pdb=" O GLU Z 163 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N GLU Z 170 " --> pdb=" O ASP Z 166 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASP Z 174 " --> pdb=" O GLU Z 170 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER Z 175 " --> pdb=" O ALA Z 171 " (cutoff:3.500A) Processing helix chain 'Z' and resid 253 through 262 Processing helix chain 'Z' and resid 265 through 281 removed outlier: 4.721A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LYS Z 273 " --> pdb=" O ASP Z 269 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL Z 281 " --> pdb=" O LEU Z 277 " (cutoff:3.500A) Processing helix chain 'Z' and resid 299 through 307 Processing helix chain 'Z' and resid 320 through 327 removed outlier: 3.529A pdb=" N LEU Z 326 " --> pdb=" O GLU Z 322 " (cutoff:3.500A) Processing helix chain 'Z' and resid 381 through 403 removed outlier: 4.965A pdb=" N GLN Z 386 " --> pdb=" O HIS Z 382 " (cutoff:3.500A) Processing helix chain 'Z' and resid 413 through 424 Processing helix chain 'Z' and resid 431 through 455 removed outlier: 3.996A 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 472 removed outlier: 3.597A pdb=" N LEU Z 463 " --> pdb=" O LEU Z 459 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU Z 472 " --> pdb=" O ALA Z 468 " (cutoff:3.500A) Processing helix chain 'Z' and resid 499 through 516 removed outlier: 3.653A pdb=" N HIS Z 506 " --> pdb=" O LYS Z 502 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR Z 509 " --> pdb=" O LEU Z 505 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE Z 511 " --> pdb=" O SER Z 507 " (cutoff:3.500A) Processing helix chain 'a' and resid 17 through 35 removed outlier: 4.748A pdb=" N SER a 34 " --> pdb=" O ASN a 30 " (cutoff:3.500A) removed outlier: 5.442A 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: 3.607A pdb=" N GLU a 85 " --> pdb=" O LEU a 81 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 109 Processing helix chain 'a' and resid 114 through 133 removed outlier: 3.654A pdb=" N ASN a 133 " --> pdb=" O VAL a 129 " (cutoff:3.500A) Processing helix chain 'a' and resid 146 through 155 Processing helix chain 'a' and resid 160 through 178 removed outlier: 3.597A pdb=" N ASN a 164 " --> pdb=" O ILE a 161 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ASP a 166 " --> pdb=" O ILE a 163 " (cutoff:3.500A) Processing helix chain 'a' and resid 192 through 194 No H-bonds generated for 'chain 'a' and resid 192 through 194' 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 273 through 281 Processing helix chain 'a' and resid 296 through 302 removed outlier: 3.610A pdb=" N GLU a 302 " --> pdb=" O LYS a 298 " (cutoff:3.500A) Processing helix chain 'a' and resid 313 through 323 removed outlier: 3.684A pdb=" N ARG a 318 " --> pdb=" O ARG a 314 " (cutoff:3.500A) Processing helix chain 'a' and resid 386 through 403 Processing helix chain 'a' and resid 414 through 428 removed outlier: 3.616A pdb=" N GLU a 424 " --> pdb=" O SER a 420 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASN a 425 " --> pdb=" O ILE a 421 " (cutoff:3.500A) Processing helix chain 'a' and resid 435 through 446 removed outlier: 3.912A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) Processing helix chain 'a' and resid 448 through 455 Processing helix chain 'a' and resid 460 through 476 removed outlier: 3.806A pdb=" N GLU a 473 " --> pdb=" O ALA a 469 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA a 474 " --> pdb=" O PHE a 470 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN a 475 " --> pdb=" O HIS a 471 " (cutoff:3.500A) Processing helix chain 'a' and resid 478 through 484 removed outlier: 4.744A pdb=" N ASN a 482 " --> pdb=" O GLU a 479 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS a 484 " --> pdb=" O LYS a 481 " (cutoff:3.500A) Processing helix chain 'a' and resid 507 through 525 Processing helix chain 'g' and resid 18 through 34 removed outlier: 3.558A pdb=" N VAL g 21 " --> pdb=" O GLY g 18 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR g 31 " --> pdb=" O ALA g 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 68 Processing helix chain 'g' and resid 74 through 90 removed outlier: 3.822A pdb=" N GLU g 88 " --> pdb=" O ARG g 84 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU g 89 " --> pdb=" O THR g 85 " (cutoff:3.500A) Processing helix chain 'g' and resid 96 through 113 removed outlier: 4.533A pdb=" N HIS g 110 " --> pdb=" O SER g 106 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE g 111 " --> pdb=" O VAL g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 139 removed outlier: 3.534A pdb=" N SER g 134 " --> pdb=" O ASP g 130 " (cutoff:3.500A) Processing helix chain 'g' and resid 148 through 158 Processing helix chain 'g' and resid 165 through 180 removed outlier: 4.194A pdb=" N SER g 168 " --> pdb=" O SER g 165 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N SER g 169 " --> pdb=" O ARG g 166 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU g 170 " --> pdb=" O TRP g 167 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL g 179 " --> pdb=" O LEU g 176 " (cutoff:3.500A) Processing helix chain 'g' and resid 208 through 210 No H-bonds generated for 'chain 'g' and resid 208 through 210' Processing helix chain 'g' and resid 276 through 283 removed outlier: 4.409A pdb=" N ILE g 282 " --> pdb=" O CYS g 278 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N GLN g 283 " --> pdb=" O GLU g 279 " (cutoff:3.500A) Processing helix chain 'g' and resid 297 through 305 Processing helix chain 'g' and resid 316 through 326 removed outlier: 4.122A pdb=" N ARG g 321 " --> pdb=" O THR g 317 " (cutoff:3.500A) Processing helix chain 'g' and resid 383 through 402 Processing helix chain 'g' and resid 412 through 424 Processing helix chain 'g' and resid 431 through 454 Proline residue: g 435 - end of helix removed outlier: 3.981A pdb=" N VAL g 439 " --> pdb=" O TYR g 436 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE g 446 " --> pdb=" O LEU g 443 " (cutoff:3.500A) Proline residue: g 447 - end of helix removed outlier: 3.720A pdb=" N ASN g 453 " --> pdb=" O LEU g 450 " (cutoff:3.500A) Processing helix chain 'g' and resid 458 through 471 removed outlier: 3.702A pdb=" N GLN g 471 " --> pdb=" O ALA g 467 " (cutoff:3.500A) Processing helix chain 'g' and resid 489 through 492 No H-bonds generated for 'chain 'g' and resid 489 through 492' Processing helix chain 'g' and resid 498 through 517 Processing helix chain 'h' and resid 19 through 36 removed outlier: 3.609A pdb=" N ALA h 35 " --> pdb=" O VAL h 31 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL h 36 " --> pdb=" O ILE h 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 62 through 68 removed outlier: 3.790A pdb=" N LEU h 68 " --> pdb=" O THR h 64 " (cutoff:3.500A) Processing helix chain 'h' and resid 78 through 93 removed outlier: 4.241A pdb=" N ILE h 86 " --> pdb=" O THR h 82 " (cutoff:3.500A) Processing helix chain 'h' and resid 99 through 116 Proline residue: h 114 - end of helix Processing helix chain 'h' and resid 122 through 143 Processing helix chain 'h' and resid 157 through 167 removed outlier: 3.685A pdb=" N THR h 165 " --> pdb=" O LYS h 161 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ALA h 166 " --> pdb=" O CYS h 162 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU h 167 " --> pdb=" O ALA h 163 " (cutoff:3.500A) Processing helix chain 'h' and resid 173 through 188 removed outlier: 4.251A pdb=" N ALA h 177 " --> pdb=" O SER h 173 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N PHE h 178 " --> pdb=" O GLN h 174 " (cutoff:3.500A) Processing helix chain 'h' and resid 267 through 282 removed outlier: 3.831A pdb=" N LEU h 282 " --> pdb=" O LEU h 278 " (cutoff:3.500A) Processing helix chain 'h' and resid 304 through 307 No H-bonds generated for 'chain 'h' and resid 304 through 307' Processing helix chain 'h' and resid 320 through 329 Processing helix chain 'h' and resid 383 through 405 removed outlier: 3.868A pdb=" N MET h 386 " --> pdb=" O GLU h 383 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU h 387 " --> pdb=" O GLN h 384 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU h 393 " --> pdb=" O GLU h 390 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N HIS h 394 " --> pdb=" O ARG h 391 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS h 405 " --> pdb=" O ARG h 402 " (cutoff:3.500A) Processing helix chain 'h' and resid 416 through 430 removed outlier: 3.827A pdb=" N ARG h 429 " --> pdb=" O ARG h 425 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR h 430 " --> pdb=" O ASP h 426 " (cutoff:3.500A) Processing helix chain 'h' and resid 434 through 457 removed outlier: 3.601A pdb=" N LEU h 437 " --> pdb=" O LYS h 434 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU h 447 " --> pdb=" O LYS h 444 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE h 449 " --> pdb=" O LEU h 446 " (cutoff:3.500A) Proline residue: h 450 - end of helix Processing helix chain 'h' and resid 461 through 473 Processing helix chain 'h' and resid 491 through 494 No H-bonds generated for 'chain 'h' and resid 491 through 494' Processing helix chain 'h' and resid 500 through 518 Processing helix chain 'q' and resid 30 through 44 removed outlier: 3.667A pdb=" N THR q 43 " --> pdb=" O LEU q 39 " (cutoff:3.500A) Processing helix chain 'q' and resid 69 through 75 removed outlier: 3.635A pdb=" N ARG q 74 " --> pdb=" O ALA q 70 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU q 75 " --> pdb=" O THR q 71 " (cutoff:3.500A) Processing helix chain 'q' and resid 81 through 96 Processing helix chain 'q' and resid 101 through 121 Processing helix chain 'q' and resid 125 through 146 Proline residue: q 144 - end of helix Processing helix chain 'q' and resid 157 through 171 removed outlier: 3.502A pdb=" N ARG q 165 " --> pdb=" O SER q 161 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N SER q 167 " --> pdb=" O LEU q 163 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ILE q 168 " --> pdb=" O LEU q 164 " (cutoff:3.500A) Processing helix chain 'q' and resid 177 through 191 removed outlier: 3.838A pdb=" N LEU q 182 " --> pdb=" O PHE q 178 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N CYS q 187 " --> pdb=" O ILE q 183 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE q 190 " --> pdb=" O ALA q 186 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N PHE q 191 " --> pdb=" O CYS q 187 " (cutoff:3.500A) 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 263 through 283 Processing helix chain 'q' and resid 299 through 307 Processing helix chain 'q' and resid 320 through 328 Processing helix chain 'q' and resid 385 through 404 removed outlier: 3.772A pdb=" N THR q 398 " --> pdb=" O ASP q 394 " (cutoff:3.500A) Processing helix chain 'q' and resid 414 through 429 removed outlier: 3.903A pdb=" N GLU q 428 " --> pdb=" O THR q 424 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 456 removed outlier: 3.636A pdb=" N TYR q 436 " --> pdb=" O LEU q 433 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE q 448 " --> pdb=" O PHE q 445 " (cutoff:3.500A) Proline residue: q 449 - end of helix removed outlier: 4.161A pdb=" N ASN q 455 " --> pdb=" O LEU q 452 " (cutoff:3.500A) Processing helix chain 'q' and resid 460 through 473 removed outlier: 3.920A pdb=" N GLN q 472 " --> pdb=" O TYR q 468 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLU q 473 " --> pdb=" O ALA q 469 " (cutoff:3.500A) Processing helix chain 'q' and resid 492 through 495 No H-bonds generated for 'chain 'q' and resid 492 through 495' Processing helix chain 'q' and resid 501 through 519 Processing helix chain 'A' and resid 17 through 33 removed outlier: 3.691A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 64 removed outlier: 3.970A pdb=" N LEU A 64 " --> pdb=" O THR A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 86 Processing helix chain 'A' and resid 90 through 109 Processing helix chain 'A' and resid 114 through 132 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 165 through 178 removed outlier: 3.727A pdb=" N VAL A 173 " --> pdb=" O ALA A 169 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP A 174 " --> pdb=" O ASN A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 194 No H-bonds generated for 'chain 'A' and resid 192 through 194' 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 273 through 281 Processing helix chain 'A' and resid 296 through 303 Processing helix chain 'A' and resid 313 through 322 Processing helix chain 'A' and resid 384 through 403 removed outlier: 4.130A pdb=" N GLU A 387 " --> pdb=" O MET A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 430 removed outlier: 3.543A pdb=" N ASN A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 455 removed outlier: 3.925A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 5.133A 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 removed outlier: 3.743A pdb=" N GLU A 473 " --> pdb=" O ALA A 469 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A 474 " --> pdb=" O PHE A 470 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 525 Processing helix chain 'G' and resid 18 through 36 removed outlier: 3.543A pdb=" N VAL G 21 " --> pdb=" O GLY G 18 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ASP G 34 " --> pdb=" O THR G 31 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE G 35 " --> pdb=" O ILE G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 68 Processing helix chain 'G' and resid 74 through 87 Processing helix chain 'G' and resid 94 through 113 removed outlier: 4.226A pdb=" N HIS G 110 " --> pdb=" O SER G 106 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE G 111 " --> pdb=" O VAL G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 139 removed outlier: 3.603A pdb=" N LYS G 137 " --> pdb=" O ILE G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 157 Processing helix chain 'G' and resid 168 through 178 Processing helix chain 'G' and resid 208 through 210 No H-bonds generated for 'chain 'G' and resid 208 through 210' Processing helix chain 'G' and resid 275 through 284 Processing helix chain 'G' and resid 297 through 305 Processing helix chain 'G' and resid 316 through 326 removed outlier: 4.745A pdb=" N ARG G 321 " --> pdb=" O THR G 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 383 through 402 Processing helix chain 'G' and resid 412 through 426 removed outlier: 3.779A pdb=" N LYS G 426 " --> pdb=" O THR G 422 " (cutoff:3.500A) Processing helix chain 'G' and resid 431 through 454 Proline residue: G 435 - end of helix removed outlier: 4.436A pdb=" N VAL G 439 " --> pdb=" O TYR G 436 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU G 444 " --> pdb=" O GLN G 441 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL G 445 " --> pdb=" O ALA G 442 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE G 446 " --> pdb=" O LEU G 443 " (cutoff:3.500A) Proline residue: G 447 - end of helix removed outlier: 3.729A pdb=" N ASN G 453 " --> pdb=" O LEU G 450 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 471 removed outlier: 3.788A pdb=" N GLN G 471 " --> pdb=" O ALA G 467 " (cutoff:3.500A) Processing helix chain 'G' and resid 489 through 492 No H-bonds generated for 'chain 'G' and resid 489 through 492' Processing helix chain 'G' and resid 498 through 516 Processing helix chain 'H' and resid 18 through 36 removed outlier: 3.573A 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 74 through 89 removed outlier: 3.563A pdb=" N GLU H 89 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 112 Proline residue: H 110 - end of helix Processing helix chain 'H' and resid 118 through 135 Processing helix chain 'H' and resid 153 through 163 removed outlier: 3.614A pdb=" N ALA H 162 " --> pdb=" O CYS H 158 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU H 163 " --> pdb=" O ALA H 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 186 removed outlier: 4.249A pdb=" N GLN H 170 " --> pdb=" O LEU H 167 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA H 173 " --> pdb=" O GLN H 170 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET H 185 " --> pdb=" O ALA H 182 " (cutoff:3.500A) 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 263 through 284 removed outlier: 5.176A pdb=" N ASP H 268 " --> pdb=" O GLN H 264 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ALA H 269 " --> pdb=" O ALA H 265 " (cutoff:3.500A) Processing helix chain 'H' and resid 304 through 306 No H-bonds generated for 'chain 'H' and resid 304 through 306' Processing helix chain 'H' and resid 316 through 320 Processing helix chain 'H' and resid 382 through 401 removed outlier: 4.511A pdb=" N ASP H 391 " --> pdb=" O ARG H 387 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA H 392 " --> pdb=" O SER H 388 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE H 393 " --> pdb=" O LEU H 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 426 removed outlier: 3.722A pdb=" N ARG H 425 " --> pdb=" O ARG H 421 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N THR H 426 " --> pdb=" O ASP H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 431 through 453 removed outlier: 4.140A pdb=" N GLU H 443 " --> pdb=" O ALA H 439 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ILE H 444 " --> pdb=" O LYS H 440 " (cutoff:3.500A) removed outlier: 5.837A 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 30 through 46 removed outlier: 3.595A pdb=" N THR Q 43 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) removed outlier: 5.531A 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 97 removed outlier: 3.822A pdb=" N GLU Q 96 " --> pdb=" O MET Q 92 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 121 removed outlier: 3.624A pdb=" N GLU Q 117 " --> pdb=" O GLU Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 145 Proline residue: Q 144 - end of helix Processing helix chain 'Q' and resid 157 through 171 removed outlier: 3.565A pdb=" N ARG Q 165 " --> pdb=" O SER Q 161 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE Q 168 " --> pdb=" O LEU Q 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 177 through 188 removed outlier: 3.989A pdb=" N LEU Q 182 " --> pdb=" O PHE Q 178 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N CYS Q 187 " --> pdb=" O ILE Q 183 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL Q 188 " --> pdb=" O ALA Q 184 " (cutoff:3.500A) 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 263 through 283 Processing helix chain 'Q' and resid 285 through 287 No H-bonds generated for 'chain 'Q' and resid 285 through 287' Processing helix chain 'Q' and resid 299 through 307 Processing helix chain 'Q' and resid 318 through 328 removed outlier: 4.243A pdb=" N LEU Q 321 " --> pdb=" O LYS Q 318 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ARG Q 322 " --> pdb=" O TRP Q 319 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU Q 324 " --> pdb=" O LEU Q 321 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL Q 328 " --> pdb=" O CYS Q 325 " (cutoff:3.500A) Processing helix chain 'Q' and resid 355 through 357 No H-bonds generated for 'chain 'Q' and resid 355 through 357' Processing helix chain 'Q' and resid 382 through 404 removed outlier: 4.001A pdb=" N ASP Q 387 " --> pdb=" O ASN Q 383 " (cutoff:3.500A) Processing helix chain 'Q' and resid 414 through 429 removed outlier: 4.276A pdb=" N GLU Q 428 " --> pdb=" O THR Q 424 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 456 removed outlier: 3.667A pdb=" N TYR Q 436 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) Proline residue: Q 449 - end of helix Processing helix chain 'Q' and resid 460 through 472 removed outlier: 3.915A pdb=" N GLN Q 472 " --> pdb=" O TYR Q 468 " (cutoff:3.500A) Processing helix chain 'Q' and resid 502 through 520 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 removed outlier: 3.622A pdb=" N SER B 144 " --> pdb=" O ALA B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 168 Processing helix chain 'B' and resid 171 through 189 removed outlier: 4.171A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ASP B 177 " --> pdb=" O HIS B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 198 No H-bonds generated for 'chain 'B' and resid 196 through 198' Processing helix chain 'B' and resid 209 through 211 No H-bonds generated for 'chain 'B' and resid 209 through 211' Processing helix chain 'B' and resid 261 through 285 removed outlier: 4.068A pdb=" N HIS B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 307 Processing helix chain 'B' and resid 317 through 327 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 380 through 402 Processing helix chain 'B' and resid 412 through 426 Processing helix chain 'B' and resid 431 through 452 Proline residue: B 447 - end of helix Processing helix chain 'B' and resid 459 through 470 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 516 Processing helix chain 'D' and resid 29 through 51 removed outlier: 4.884A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 6.371A 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: 3.536A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE D 111 " --> pdb=" O THR D 107 " (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 178 through 193 removed outlier: 4.352A pdb=" N LEU D 182 " --> pdb=" O GLN D 178 " (cutoff:3.500A) Proline residue: D 185 - end of helix Processing helix chain 'D' and resid 205 through 207 No H-bonds generated for 'chain 'D' and resid 205 through 207' Processing helix chain 'D' and resid 218 through 220 No H-bonds generated for 'chain 'D' and resid 218 through 220' Processing helix chain 'D' and resid 271 through 293 removed outlier: 3.636A 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 333 through 340 Processing helix chain 'D' and resid 395 through 417 Processing helix chain 'D' and resid 427 through 441 Processing helix chain 'D' and resid 446 through 468 removed outlier: 4.288A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL D 460 " --> pdb=" O ASP D 456 " (cutoff:3.500A) removed outlier: 5.494A 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 531 Processing helix chain 'E' and resid 31 through 51 removed outlier: 4.966A pdb=" N THR E 50 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N SER E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 79 Processing helix chain 'E' and resid 86 through 101 Processing helix chain 'E' and resid 106 through 126 removed outlier: 3.681A pdb=" N VAL E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 151 removed outlier: 3.799A pdb=" N ILE E 151 " --> pdb=" O HIS E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 175 removed outlier: 4.508A pdb=" N SER E 175 " --> pdb=" O THR E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 195 removed outlier: 4.098A pdb=" N SER E 180 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS E 182 " --> pdb=" O ASN E 179 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ARG E 183 " --> pdb=" O SER E 180 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR E 195 " --> pdb=" O ALA E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 221 No H-bonds generated for 'chain 'E' and resid 219 through 221' Processing helix chain 'E' and resid 271 through 295 removed outlier: 4.266A pdb=" N THR E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 316 Processing helix chain 'E' and resid 327 through 337 Processing helix chain 'E' and resid 345 through 347 No H-bonds generated for 'chain 'E' and resid 345 through 347' Processing helix chain 'E' and resid 392 through 414 Processing helix chain 'E' and resid 424 through 438 Processing helix chain 'E' and resid 442 through 466 removed outlier: 4.301A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N VAL E 457 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ILE E 458 " --> pdb=" O ALA E 454 " (cutoff:3.500A) Proline residue: E 459 - end of helix removed outlier: 3.763A pdb=" N SER E 466 " --> pdb=" O LEU E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 471 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 'b' and resid 21 through 39 Processing helix chain 'b' and resid 67 through 72 Processing helix chain 'b' and resid 79 through 94 Processing helix chain 'b' and resid 99 through 118 Processing helix chain 'b' and resid 123 through 144 Processing helix chain 'b' and resid 152 through 168 Processing helix chain 'b' and resid 171 through 174 removed outlier: 4.004A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 171 through 174' Processing helix chain 'b' and resid 176 through 190 removed outlier: 3.923A pdb=" N LEU b 190 " --> pdb=" O ALA b 186 " (cutoff:3.500A) Processing helix chain 'b' and resid 209 through 211 No H-bonds generated for 'chain 'b' and resid 209 through 211' Processing helix chain 'b' and resid 261 through 285 removed outlier: 4.053A pdb=" N HIS b 285 " --> pdb=" O ARG b 281 " (cutoff:3.500A) Processing helix chain 'b' and resid 298 through 307 Processing helix chain 'b' and resid 317 through 327 Processing helix chain 'b' and resid 338 through 340 No H-bonds generated for 'chain 'b' and resid 338 through 340' Processing helix chain 'b' and resid 380 through 402 Processing helix chain 'b' and resid 412 through 427 Processing helix chain 'b' and resid 431 through 454 Proline residue: b 447 - end of helix removed outlier: 4.331A pdb=" N ALA b 454 " --> pdb=" O ILE b 450 " (cutoff:3.500A) Processing helix chain 'b' and resid 459 through 471 Processing helix chain 'b' and resid 497 through 515 Processing helix chain 'd' and resid 29 through 47 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: 3.782A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 132 through 151 Processing helix chain 'd' and resid 160 through 173 removed outlier: 4.063A pdb=" N SER d 173 " --> pdb=" O THR d 169 " (cutoff:3.500A) Processing helix chain 'd' and resid 183 through 194 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 269 through 293 removed outlier: 3.589A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 4.338A 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 331 through 339 removed outlier: 4.121A pdb=" N PHE d 335 " --> pdb=" O GLU d 331 " (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 395 through 416 Processing helix chain 'd' and resid 427 through 442 Processing helix chain 'd' and resid 445 through 466 removed outlier: 3.911A pdb=" N ILE d 461 " --> pdb=" O MET d 458 " (cutoff:3.500A) Proline residue: d 462 - end of helix removed outlier: 3.644A pdb=" N LEU d 465 " --> pdb=" O PRO d 462 " (cutoff:3.500A) Processing helix chain 'd' and resid 473 through 486 Processing helix chain 'd' and resid 512 through 530 removed outlier: 4.846A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 31 through 51 removed outlier: 4.822A pdb=" N THR e 50 " --> pdb=" O ASN e 46 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N SER e 51 " --> pdb=" O THR e 47 " (cutoff:3.500A) Processing helix chain 'e' and resid 74 through 78 Processing helix chain 'e' and resid 86 through 101 Processing helix chain 'e' and resid 106 through 125 removed outlier: 3.841A pdb=" N VAL e 110 " --> pdb=" O THR e 106 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN e 122 " --> pdb=" O GLU e 118 " (cutoff:3.500A) Processing helix chain 'e' and resid 130 through 150 Processing helix chain 'e' and resid 163 through 175 removed outlier: 4.129A pdb=" N SER e 175 " --> pdb=" O THR e 171 " (cutoff:3.500A) Processing helix chain 'e' and resid 177 through 195 removed outlier: 4.083A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS e 182 " --> pdb=" O ASN e 179 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ARG e 183 " --> pdb=" O SER e 180 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET e 185 " --> pdb=" O HIS e 182 " (cutoff:3.500A) Processing helix chain 'e' and resid 219 through 221 No H-bonds generated for 'chain 'e' and resid 219 through 221' Processing helix chain 'e' and resid 271 through 295 removed outlier: 3.939A pdb=" N THR e 295 " --> pdb=" O GLN e 291 " (cutoff:3.500A) Processing helix chain 'e' and resid 308 through 317 Processing helix chain 'e' and resid 327 through 337 Processing helix chain 'e' and resid 345 through 347 No H-bonds generated for 'chain 'e' and resid 345 through 347' Processing helix chain 'e' and resid 350 through 352 No H-bonds generated for 'chain 'e' and resid 350 through 352' Processing helix chain 'e' and resid 392 through 414 Processing helix chain 'e' and resid 424 through 438 Processing helix chain 'e' and resid 443 through 466 removed outlier: 3.994A pdb=" N TYR e 446 " --> pdb=" O LEU e 443 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE e 458 " --> pdb=" O LEU e 455 " (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 502 through 504 No H-bonds generated for 'chain 'e' and resid 502 through 504' Processing helix chain 'e' and resid 510 through 529 Processing sheet with id= A, first strand: chain 'z' and resid 45 through 48 Processing sheet with id= B, first strand: chain 'z' and resid 191 through 194 removed outlier: 7.103A pdb=" N VAL z 372 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N MET z 194 " --> pdb=" O VAL z 372 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU z 374 " --> pdb=" O MET z 194 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'z' and resid 210 through 212 removed outlier: 3.670A pdb=" N THR z 361 " --> pdb=" O LEU z 212 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU z 358 " --> pdb=" O LEU z 355 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'z' and resid 345 through 347 removed outlier: 6.236A pdb=" N GLY z 288 " --> pdb=" O TYR z 229 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'Z' and resid 45 through 48 Processing sheet with id= F, first strand: chain 'Z' and resid 204 through 207 removed outlier: 3.847A pdb=" N SER Z 205 " --> pdb=" O LEU Z 375 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'Z' and resid 224 through 226 Processing sheet with id= H, first strand: chain 'Z' and resid 345 through 347 removed outlier: 7.128A pdb=" N VAL Z 290 " --> pdb=" O LEU Z 231 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N CYS Z 233 " --> pdb=" O VAL Z 290 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE Z 292 " --> pdb=" O CYS Z 233 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'Z' and resid 478 through 480 removed outlier: 4.111A pdb=" N GLU Z 485 " --> pdb=" O ASP Z 480 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'a' and resid 197 through 201 removed outlier: 6.434A pdb=" N ILE a 375 " --> pdb=" O LEU a 198 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N ALA a 200 " --> pdb=" O ILE a 375 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU a 377 " --> pdb=" O ALA a 200 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'a' and resid 215 through 217 removed outlier: 3.626A pdb=" N LEU a 216 " --> pdb=" O ILE a 362 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU a 361 " --> pdb=" O GLU a 354 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLU a 354 " --> pdb=" O LEU a 361 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS a 365 " --> pdb=" O GLU a 350 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLU a 350 " --> pdb=" O LYS a 365 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'a' and resid 234 through 237 removed outlier: 6.803A pdb=" N VAL a 285 " --> pdb=" O ALA a 235 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU a 237 " --> pdb=" O VAL a 285 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU a 287 " --> pdb=" O LEU a 237 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'a' and resid 408 through 410 removed outlier: 3.599A pdb=" N GLU a 505 " --> pdb=" O VAL a 409 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'a' and resid 486 through 489 removed outlier: 3.600A pdb=" N LYS a 494 " --> pdb=" O ASP a 489 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'g' and resid 47 through 50 Processing sheet with id= P, first strand: chain 'g' and resid 199 through 204 removed outlier: 3.660A pdb=" N GLY g 377 " --> pdb=" O ILE g 203 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'g' and resid 406 through 408 Processing sheet with id= R, first strand: chain 'g' and resid 477 through 479 Processing sheet with id= S, first strand: chain 'h' and resid 213 through 215 removed outlier: 3.738A pdb=" N GLN h 213 " --> pdb=" O ILE h 377 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'h' and resid 333 through 335 removed outlier: 6.898A pdb=" N VAL h 292 " --> pdb=" O ALA h 242 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU h 244 " --> pdb=" O VAL h 292 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N LEU h 294 " --> pdb=" O LEU h 244 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N PHE h 313 " --> pdb=" O VAL h 293 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N SER h 295 " --> pdb=" O PHE h 313 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA h 315 " --> pdb=" O SER h 295 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'h' and resid 409 through 411 Processing sheet with id= V, first strand: chain 'h' and resid 479 through 482 Processing sheet with id= W, first strand: chain 'q' and resid 54 through 56 Processing sheet with id= X, first strand: chain 'q' and resid 204 through 208 removed outlier: 5.687A pdb=" N ILE q 375 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE q 207 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N LEU q 377 " --> pdb=" O ILE q 207 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'q' and resid 221 through 224 Processing sheet with id= Z, first strand: chain 'q' and resid 239 through 242 removed outlier: 7.207A pdb=" N VAL q 290 " --> pdb=" O ALA q 240 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N TYR q 242 " --> pdb=" O VAL q 290 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL q 292 " --> pdb=" O TYR q 242 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'q' and resid 408 through 410 Processing sheet with id= AB, first strand: chain 'q' and resid 478 through 480 Processing sheet with id= AC, first strand: chain 'A' and resid 43 through 45 removed outlier: 3.558A pdb=" N THR A 55 " --> pdb=" O LYS A 43 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'A' and resid 195 through 199 removed outlier: 6.999A pdb=" N ALA A 373 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LEU A 198 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE A 375 " --> pdb=" O LEU A 198 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'A' and resid 214 through 216 removed outlier: 3.658A pdb=" N TYR A 214 " --> pdb=" O ILE A 364 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 216 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 363 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL A 352 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 350 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'A' and resid 408 through 410 Processing sheet with id= AG, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.570A pdb=" N ARG A 496 " --> pdb=" O GLY A 487 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 489 " --> pdb=" O LYS A 494 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS A 494 " --> pdb=" O ASP A 489 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'G' and resid 47 through 49 removed outlier: 3.898A pdb=" N THR G 59 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU G 49 " --> pdb=" O VAL G 57 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'G' and resid 199 through 204 removed outlier: 3.913A pdb=" N GLY G 377 " --> pdb=" O ILE G 203 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'G' and resid 237 through 239 removed outlier: 7.556A pdb=" N VAL G 288 " --> pdb=" O VAL G 238 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N THR G 309 " --> pdb=" O VAL G 289 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'G' and resid 348 through 350 Processing sheet with id= AL, first strand: chain 'G' and resid 406 through 408 Processing sheet with id= AM, first strand: chain 'H' and resid 196 through 201 removed outlier: 3.556A pdb=" N PHE H 372 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS H 198 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLY H 376 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'H' and resid 329 through 331 removed outlier: 6.633A pdb=" N VAL H 288 " --> pdb=" O ALA H 238 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LEU H 240 " --> pdb=" O VAL H 288 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N LEU H 290 " --> pdb=" O LEU H 240 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'H' and resid 475 through 477 Processing sheet with id= AP, first strand: chain 'Q' and resid 202 through 205 removed outlier: 6.338A pdb=" N SER Q 373 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N CYS Q 205 " --> pdb=" O SER Q 373 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ILE Q 375 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'Q' and resid 221 through 223 removed outlier: 3.581A pdb=" N TYR Q 351 " --> pdb=" O VAL Q 362 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS Q 364 " --> pdb=" O SER Q 349 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'Q' and resid 239 through 241 removed outlier: 8.021A pdb=" N VAL Q 290 " --> pdb=" O ALA Q 240 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N MET Q 311 " --> pdb=" O VAL Q 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'B' and resid 199 through 201 removed outlier: 5.928A pdb=" N CYS B 371 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR B 372 " --> pdb=" O ASP B 215 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'B' and resid 218 through 220 removed outlier: 3.662A pdb=" N ASP B 357 " --> pdb=" O ILE B 354 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'B' and resid 237 through 240 removed outlier: 6.965A pdb=" N CYS B 289 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ALA B 240 " --> pdb=" O CYS B 289 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ILE B 291 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET B 310 " --> pdb=" O PHE B 290 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ASN B 292 " --> pdb=" O MET B 310 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE B 312 " --> pdb=" O ASN B 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= AU Processing sheet with id= AV, first strand: chain 'B' and resid 476 through 478 Processing sheet with id= AW, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.832A pdb=" N VAL D 386 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N VAL D 211 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ILE D 388 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N LYS D 213 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N VAL D 390 " --> pdb=" O LYS D 213 " (cutoff:3.500A) No H-bonds generated for sheet with id= AW Processing sheet with id= AX, first strand: chain 'D' and resid 227 through 229 Processing sheet with id= AY, first strand: chain 'D' and resid 297 through 299 removed outlier: 6.262A pdb=" N MET D 323 " --> pdb=" O LEU D 298 " (cutoff:3.500A) No H-bonds generated for sheet with id= AY Processing sheet with id= AZ, first strand: chain 'D' and resid 421 through 423 Processing sheet with id= BA, first strand: chain 'D' and resid 491 through 493 removed outlier: 3.588A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'E' and resid 223 through 225 removed outlier: 4.187A pdb=" N LYS E 223 " --> pdb=" O PHE E 386 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE E 386 " --> pdb=" O LYS E 223 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'E' and resid 353 through 355 removed outlier: 6.815A pdb=" N LEU E 299 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'E' and resid 358 through 362 removed outlier: 3.964A pdb=" N MET E 371 " --> pdb=" O ILE E 362 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'b' and resid 50 through 52 Processing sheet with id= BF, first strand: chain 'b' and resid 213 through 215 Processing sheet with id= BG, first strand: chain 'b' and resid 218 through 220 removed outlier: 3.789A pdb=" N ASP b 357 " --> pdb=" O ILE b 354 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ILE b 354 " --> pdb=" O ASP b 357 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'b' and resid 237 through 239 removed outlier: 7.526A pdb=" N CYS b 289 " --> pdb=" O LEU b 238 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N MET b 310 " --> pdb=" O PHE b 290 " (cutoff:3.500A) No H-bonds generated for sheet with id= BH Processing sheet with id= BI, first strand: chain 'b' and resid 476 through 479 Processing sheet with id= BJ, first strand: chain 'd' and resid 209 through 212 Processing sheet with id= BK, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.658A pdb=" N LEU d 374 " --> pdb=" O LEU d 229 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'd' and resid 246 through 249 removed outlier: 6.342A pdb=" N VAL d 297 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ILE d 249 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU d 299 " --> pdb=" O ILE d 249 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N MET d 323 " --> pdb=" O LEU d 298 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ILE d 300 " --> pdb=" O MET d 323 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE d 325 " --> pdb=" O ILE d 300 " (cutoff:3.500A) No H-bonds generated for sheet with id= BL Processing sheet with id= BM, first strand: chain 'd' and resid 421 through 423 Processing sheet with id= BN, first strand: chain 'd' and resid 491 through 494 Processing sheet with id= BO, first strand: chain 'e' and resid 59 through 62 Processing sheet with id= BP, first strand: chain 'e' and resid 223 through 225 Processing sheet with id= BQ, first strand: chain 'e' and resid 227 through 230 removed outlier: 3.533A pdb=" N MET e 371 " --> pdb=" O ILE e 362 " (cutoff:3.500A) Processing sheet with id= BR, first strand: chain 'e' and resid 354 through 356 removed outlier: 7.210A pdb=" N LEU e 299 " --> pdb=" O ALA e 249 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N LEU e 251 " --> pdb=" O LEU e 299 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ILE e 301 " --> pdb=" O LEU e 251 " (cutoff:3.500A) 2859 hydrogen bonds defined for protein. 7629 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: 20.36 Time building geometry restraints manager: 22.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 16089 1.33 - 1.46: 10140 1.46 - 1.58: 36011 1.58 - 1.70: 48 1.70 - 1.82: 632 Bond restraints: 62920 Sorted by residual: bond pdb=" C LYS E 439 " pdb=" N CYS E 440 " ideal model delta sigma weight residual 1.331 1.378 -0.047 1.59e-02 3.96e+03 8.63e+00 bond pdb=" CG ARG E 478 " pdb=" CD ARG E 478 " ideal model delta sigma weight residual 1.520 1.481 0.039 3.00e-02 1.11e+03 1.67e+00 bond pdb=" CA GLY Z 345 " pdb=" C GLY Z 345 " ideal model delta sigma weight residual 1.520 1.512 0.009 7.30e-03 1.88e+04 1.38e+00 bond pdb=" N MET h 231 " pdb=" CA MET h 231 " ideal model delta sigma weight residual 1.457 1.472 -0.015 1.29e-02 6.01e+03 1.34e+00 bond pdb=" C4 ADP Q5000 " pdb=" C5 ADP Q5000 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.32e+00 ... (remaining 62915 not shown) Histogram of bond angle deviations from ideal: 97.17 - 105.00: 896 105.00 - 112.82: 35672 112.82 - 120.65: 27472 120.65 - 128.48: 20662 128.48 - 136.31: 281 Bond angle restraints: 84983 Sorted by residual: angle pdb=" N VAL Z 62 " pdb=" CA VAL Z 62 " pdb=" C VAL Z 62 " ideal model delta sigma weight residual 112.96 109.21 3.75 1.00e+00 1.00e+00 1.40e+01 angle pdb=" C GLU E 121 " pdb=" N GLN E 122 " pdb=" CA GLN E 122 " ideal model delta sigma weight residual 121.58 114.39 7.19 1.95e+00 2.63e-01 1.36e+01 angle pdb=" C VAL E 477 " pdb=" N ARG E 478 " pdb=" CA ARG E 478 " ideal model delta sigma weight residual 121.14 115.05 6.09 1.75e+00 3.27e-01 1.21e+01 angle pdb=" CA GLN E 122 " pdb=" CB GLN E 122 " pdb=" CG GLN E 122 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.14e+01 angle pdb=" CA LYS a 111 " pdb=" CB LYS a 111 " pdb=" CG LYS a 111 " ideal model delta sigma weight residual 114.10 120.83 -6.73 2.00e+00 2.50e-01 1.13e+01 ... (remaining 84978 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.00: 37686 31.00 - 62.00: 1113 62.00 - 93.00: 94 93.00 - 124.00: 13 124.00 - 155.00: 9 Dihedral angle restraints: 38915 sinusoidal: 15629 harmonic: 23286 Sorted by residual: dihedral pdb=" C5' ADP q5000 " pdb=" O5' ADP q5000 " pdb=" PA ADP q5000 " pdb=" O2A ADP q5000 " ideal model delta sinusoidal sigma weight residual -60.00 95.00 -155.00 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" O2A ADP b 601 " pdb=" O3A ADP b 601 " pdb=" PA ADP b 601 " pdb=" PB ADP b 601 " ideal model delta sinusoidal sigma weight residual 300.00 154.95 145.05 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" O2A ADP e 601 " pdb=" O3A ADP e 601 " pdb=" PA ADP e 601 " pdb=" PB ADP e 601 " ideal model delta sinusoidal sigma weight residual 300.00 162.01 137.99 1 2.00e+01 2.50e-03 4.18e+01 ... (remaining 38912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 8288 0.055 - 0.110: 1652 0.110 - 0.165: 217 0.165 - 0.219: 10 0.219 - 0.274: 1 Chirality restraints: 10168 Sorted by residual: chirality pdb=" CB ILE A 531 " pdb=" CA ILE A 531 " pdb=" CG1 ILE A 531 " pdb=" CG2 ILE A 531 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB ILE Q 497 " pdb=" CA ILE Q 497 " pdb=" CG1 ILE Q 497 " pdb=" CG2 ILE Q 497 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CG LEU A 530 " pdb=" CB LEU A 530 " pdb=" CD1 LEU A 530 " pdb=" CD2 LEU A 530 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 10165 not shown) Planarity restraints: 10833 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO Q 338 " 0.054 5.00e-02 4.00e+02 8.12e-02 1.05e+01 pdb=" N PRO Q 339 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO Q 339 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO Q 339 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.040 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO e 441 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU b 108 " -0.011 2.00e-02 2.50e+03 2.10e-02 4.42e+00 pdb=" C GLU b 108 " 0.036 2.00e-02 2.50e+03 pdb=" O GLU b 108 " -0.014 2.00e-02 2.50e+03 pdb=" N LEU b 109 " -0.012 2.00e-02 2.50e+03 ... (remaining 10830 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 942 2.60 - 3.18: 58259 3.18 - 3.75: 104043 3.75 - 4.33: 134802 4.33 - 4.90: 216472 Nonbonded interactions: 514518 Sorted by model distance: nonbonded pdb=" OG1 THR D 69 " pdb=" OE1 GLN D 80 " model vdw 2.031 2.440 nonbonded pdb=" O ASN g 156 " pdb=" OG1 THR g 160 " model vdw 2.145 2.440 nonbonded pdb=" OG1 THR D 71 " pdb=" OE1 GLU D 400 " model vdw 2.157 2.440 nonbonded pdb=" NH2 ARG G 229 " pdb=" OD1 ASN G 307 " model vdw 2.168 2.520 nonbonded pdb=" O LYS Q 400 " pdb=" OG1 THR Q 403 " model vdw 2.177 2.440 ... (remaining 514513 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 13 through 528 or resid 601)) selection = chain 'a' } ncs_group { reference = (chain 'B' and (resid 2 through 526 or resid 601)) 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)) selection = chain 'd' } ncs_group { reference = (chain 'E' and (resid 2 through 8 or resid 10 through 536 or resid 601)) selection = (chain 'e' and (resid 2 through 8 or resid 10 through 536 or resid 601)) } ncs_group { reference = (chain 'G' and (resid 17 through 241 or resid 274 through 525 or resid 601)) selection = chain 'g' } ncs_group { reference = chain 'H' selection = (chain 'h' and (resid 12 through 250 or resid 266 through 529 or resid 601)) } ncs_group { reference = chain 'Q' selection = chain 'q' } ncs_group { reference = chain 'Z' selection = chain 'z' } 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 group one per residue 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: 1.310 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: 8.510 Check model and map are aligned: 0.710 Set scattering table: 0.420 Process input model: 138.170 Find NCS groups from input model: 5.810 Set up NCS constraints: 0.550 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 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 : 0.003 0.047 62920 Z= 0.177 Angle : 0.645 10.183 84983 Z= 0.325 Chirality : 0.043 0.274 10168 Planarity : 0.003 0.081 10833 Dihedral : 14.793 155.001 23823 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.34 % Favored : 94.64 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.10), residues: 8047 helix: 1.38 (0.08), residues: 4072 sheet: -1.01 (0.22), residues: 622 loop : -1.34 (0.11), residues: 3353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 506 HIS 0.009 0.001 HIS E 182 PHE 0.025 0.001 PHE B 317 TYR 0.025 0.001 TYR h 267 ARG 0.006 0.000 ARG E 400 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 558 time to evaluate : 5.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 558 average time/residue: 0.5564 time to fit residues: 547.8804 Evaluate side-chains 443 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 443 time to evaluate : 6.029 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.1162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 678 optimal weight: 0.5980 chunk 608 optimal weight: 10.0000 chunk 337 optimal weight: 10.0000 chunk 207 optimal weight: 0.8980 chunk 410 optimal weight: 20.0000 chunk 325 optimal weight: 6.9990 chunk 629 optimal weight: 9.9990 chunk 243 optimal weight: 10.0000 chunk 382 optimal weight: 1.9990 chunk 468 optimal weight: 0.9980 chunk 729 optimal weight: 40.0000 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 37 ASN ** z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 453 GLN ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 114 GLN g 319 ASN ** q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 365 HIS ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 426 ASN D 32 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 ASN ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 403 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 62920 Z= 0.181 Angle : 0.616 12.332 84983 Z= 0.303 Chirality : 0.043 0.255 10168 Planarity : 0.004 0.080 10833 Dihedral : 7.714 158.718 8763 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.46 % Favored : 94.50 % Rotamer: Outliers : 0.73 % Allowed : 7.67 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.10), residues: 8047 helix: 1.25 (0.08), residues: 4088 sheet: -1.09 (0.22), residues: 632 loop : -1.35 (0.11), residues: 3327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP g 477 HIS 0.012 0.001 HIS Q 365 PHE 0.042 0.001 PHE e 364 TYR 0.021 0.001 TYR d 439 ARG 0.006 0.000 ARG h 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 479 time to evaluate : 6.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 27 residues processed: 506 average time/residue: 0.5513 time to fit residues: 494.2312 Evaluate side-chains 464 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 437 time to evaluate : 5.380 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.4380 time to fit residues: 29.8033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 405 optimal weight: 10.0000 chunk 226 optimal weight: 50.0000 chunk 606 optimal weight: 5.9990 chunk 496 optimal weight: 6.9990 chunk 201 optimal weight: 0.9980 chunk 730 optimal weight: 50.0000 chunk 789 optimal weight: 30.0000 chunk 650 optimal weight: 30.0000 chunk 724 optimal weight: 20.0000 chunk 249 optimal weight: 9.9990 chunk 586 optimal weight: 5.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 436 GLN h 484 ASN ** q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 HIS ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 32 ASN ** Q 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 461 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 289 GLN ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 72 ASN ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 317 ASN ** E 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 290 GLN e 403 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 62920 Z= 0.305 Angle : 0.678 11.693 84983 Z= 0.336 Chirality : 0.044 0.251 10168 Planarity : 0.004 0.078 10833 Dihedral : 7.890 169.611 8763 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 20.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.12 % Favored : 93.84 % Rotamer: Outliers : 1.10 % Allowed : 11.89 % Favored : 87.01 % 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: -0.27 (0.09), residues: 8047 helix: 0.96 (0.08), residues: 4081 sheet: -1.29 (0.23), residues: 563 loop : -1.39 (0.11), residues: 3403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 324 HIS 0.010 0.001 HIS G 469 PHE 0.031 0.002 PHE d 351 TYR 0.029 0.002 TYR d 439 ARG 0.006 0.000 ARG B 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 451 time to evaluate : 5.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 74 outliers final: 33 residues processed: 505 average time/residue: 0.5973 time to fit residues: 538.7707 Evaluate side-chains 449 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 416 time to evaluate : 5.564 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.5234 time to fit residues: 40.0646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 721 optimal weight: 5.9990 chunk 549 optimal weight: 5.9990 chunk 379 optimal weight: 5.9990 chunk 80 optimal weight: 8.9990 chunk 348 optimal weight: 9.9990 chunk 490 optimal weight: 10.0000 chunk 733 optimal weight: 30.0000 chunk 776 optimal weight: 0.9990 chunk 383 optimal weight: 0.5980 chunk 694 optimal weight: 10.0000 chunk 209 optimal weight: 5.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 23 ASN ** z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 114 GLN ** q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 461 ASN ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 161 ASN ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 62920 Z= 0.223 Angle : 0.628 11.841 84983 Z= 0.307 Chirality : 0.043 0.381 10168 Planarity : 0.004 0.078 10833 Dihedral : 7.759 171.153 8763 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.83 % Favored : 94.13 % Rotamer: Outliers : 1.14 % Allowed : 14.34 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.10), residues: 8047 helix: 1.01 (0.08), residues: 4076 sheet: -1.38 (0.23), residues: 556 loop : -1.35 (0.11), residues: 3415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 324 HIS 0.007 0.001 HIS G 469 PHE 0.022 0.001 PHE d 351 TYR 0.030 0.001 TYR d 439 ARG 0.006 0.000 ARG h 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 451 time to evaluate : 6.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 77 outliers final: 32 residues processed: 508 average time/residue: 0.5610 time to fit residues: 508.7223 Evaluate side-chains 450 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 418 time to evaluate : 5.494 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.4595 time to fit residues: 35.7433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 646 optimal weight: 40.0000 chunk 440 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 577 optimal weight: 4.9990 chunk 320 optimal weight: 2.9990 chunk 662 optimal weight: 30.0000 chunk 536 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 396 optimal weight: 1.9990 chunk 696 optimal weight: 9.9990 chunk 195 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 470 HIS ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 522 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 95 GLN ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 122 GLN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 62920 Z= 0.180 Angle : 0.617 14.011 84983 Z= 0.299 Chirality : 0.042 0.332 10168 Planarity : 0.004 0.079 10833 Dihedral : 7.625 172.650 8763 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 18.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.79 % Favored : 94.18 % Rotamer: Outliers : 0.85 % Allowed : 16.40 % Favored : 82.75 % 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: -0.14 (0.10), residues: 8047 helix: 1.11 (0.08), residues: 4075 sheet: -1.41 (0.22), residues: 575 loop : -1.34 (0.11), residues: 3397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 495 HIS 0.007 0.001 HIS a 113 PHE 0.036 0.001 PHE e 364 TYR 0.027 0.001 TYR d 439 ARG 0.005 0.000 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 452 time to evaluate : 5.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 57 outliers final: 19 residues processed: 491 average time/residue: 0.5654 time to fit residues: 494.4280 Evaluate side-chains 444 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 425 time to evaluate : 5.535 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.4896 time to fit residues: 24.9227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 261 optimal weight: 7.9990 chunk 698 optimal weight: 5.9990 chunk 153 optimal weight: 2.9990 chunk 455 optimal weight: 0.7980 chunk 191 optimal weight: 5.9990 chunk 776 optimal weight: 10.0000 chunk 644 optimal weight: 6.9990 chunk 359 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 257 optimal weight: 7.9990 chunk 407 optimal weight: 7.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 164 ASN ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 510 GLN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 62920 Z= 0.242 Angle : 0.654 11.182 84983 Z= 0.318 Chirality : 0.043 0.338 10168 Planarity : 0.004 0.080 10833 Dihedral : 7.663 176.606 8763 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 19.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.15 % Favored : 93.82 % Rotamer: Outliers : 0.95 % Allowed : 17.75 % Favored : 81.30 % 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: -0.27 (0.10), residues: 8047 helix: 1.00 (0.08), residues: 4071 sheet: -1.45 (0.22), residues: 582 loop : -1.39 (0.11), residues: 3394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 495 HIS 0.007 0.001 HIS G 469 PHE 0.025 0.001 PHE d 137 TYR 0.025 0.001 TYR d 439 ARG 0.005 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 438 time to evaluate : 5.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 27 residues processed: 485 average time/residue: 0.5667 time to fit residues: 489.3156 Evaluate side-chains 441 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 414 time to evaluate : 5.480 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.4672 time to fit residues: 31.6617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 749 optimal weight: 20.0000 chunk 87 optimal weight: 2.9990 chunk 442 optimal weight: 7.9990 chunk 567 optimal weight: 7.9990 chunk 439 optimal weight: 7.9990 chunk 654 optimal weight: 10.0000 chunk 433 optimal weight: 6.9990 chunk 773 optimal weight: 5.9990 chunk 484 optimal weight: 5.9990 chunk 471 optimal weight: 8.9990 chunk 357 optimal weight: 9.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 485 ASN q 32 ASN ** q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 504 GLN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 32 GLN d 72 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 62920 Z= 0.306 Angle : 0.703 10.562 84983 Z= 0.347 Chirality : 0.045 0.355 10168 Planarity : 0.004 0.079 10833 Dihedral : 7.820 179.318 8763 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 22.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.77 % Favored : 93.19 % Rotamer: Outliers : 0.93 % Allowed : 18.80 % Favored : 80.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.09), residues: 8047 helix: 0.75 (0.08), residues: 4076 sheet: -1.37 (0.22), residues: 586 loop : -1.49 (0.11), residues: 3385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 324 HIS 0.010 0.001 HIS G 469 PHE 0.031 0.002 PHE e 364 TYR 0.025 0.002 TYR d 439 ARG 0.007 0.000 ARG D 34 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 429 time to evaluate : 5.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 25 residues processed: 473 average time/residue: 0.5791 time to fit residues: 486.8835 Evaluate side-chains 437 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 412 time to evaluate : 5.452 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.4719 time to fit residues: 29.9824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 478 optimal weight: 3.9990 chunk 309 optimal weight: 7.9990 chunk 462 optimal weight: 9.9990 chunk 233 optimal weight: 10.0000 chunk 152 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 492 optimal weight: 7.9990 chunk 527 optimal weight: 5.9990 chunk 382 optimal weight: 0.2980 chunk 72 optimal weight: 6.9990 chunk 608 optimal weight: 20.0000 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 477 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 GLN G 220 ASN ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 477 ASN ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 406 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 62920 Z= 0.263 Angle : 0.679 10.483 84983 Z= 0.333 Chirality : 0.044 0.264 10168 Planarity : 0.004 0.079 10833 Dihedral : 7.756 179.141 8763 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.48 % Favored : 93.48 % Rotamer: Outliers : 0.67 % Allowed : 19.72 % Favored : 79.61 % 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: -0.50 (0.09), residues: 8047 helix: 0.78 (0.08), residues: 4075 sheet: -1.38 (0.22), residues: 599 loop : -1.50 (0.11), residues: 3373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 324 HIS 0.009 0.001 HIS a 69 PHE 0.028 0.002 PHE e 364 TYR 0.020 0.001 TYR d 439 ARG 0.010 0.000 ARG B 281 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 427 time to evaluate : 5.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 20 residues processed: 456 average time/residue: 0.5760 time to fit residues: 467.5280 Evaluate side-chains 431 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 411 time to evaluate : 5.468 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.5120 time to fit residues: 26.4749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 704 optimal weight: 9.9990 chunk 741 optimal weight: 0.0040 chunk 676 optimal weight: 0.0970 chunk 721 optimal weight: 50.0000 chunk 434 optimal weight: 0.0000 chunk 314 optimal weight: 50.0000 chunk 566 optimal weight: 9.9990 chunk 221 optimal weight: 0.0870 chunk 651 optimal weight: 8.9990 chunk 682 optimal weight: 9.9990 chunk 718 optimal weight: 2.9990 overall best weight: 0.6374 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 103 ASN ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 32 ASN ** q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 HIS E 516 GLN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 157 GLN b 161 ASN ** b 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 62920 Z= 0.163 Angle : 0.657 13.643 84983 Z= 0.316 Chirality : 0.043 0.273 10168 Planarity : 0.004 0.078 10833 Dihedral : 7.440 178.867 8763 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 17.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.05 % Favored : 94.91 % Rotamer: Outliers : 0.42 % Allowed : 20.01 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.10), residues: 8047 helix: 1.02 (0.08), residues: 4072 sheet: -1.39 (0.22), residues: 580 loop : -1.46 (0.10), residues: 3395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP h 497 HIS 0.007 0.001 HIS a 113 PHE 0.041 0.001 PHE h 385 TYR 0.017 0.001 TYR G 302 ARG 0.005 0.000 ARG d 527 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 472 time to evaluate : 5.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 10 residues processed: 488 average time/residue: 0.5736 time to fit residues: 495.5666 Evaluate side-chains 441 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 431 time to evaluate : 5.437 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.4780 time to fit residues: 16.7267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 473 optimal weight: 30.0000 chunk 762 optimal weight: 5.9990 chunk 465 optimal weight: 10.0000 chunk 361 optimal weight: 10.0000 chunk 530 optimal weight: 0.0670 chunk 799 optimal weight: 8.9990 chunk 736 optimal weight: 5.9990 chunk 637 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 492 optimal weight: 9.9990 chunk 390 optimal weight: 0.5980 overall best weight: 3.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 522 ASN ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 GLN ** E 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 182 HIS ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 161 ASN ** b 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 62920 Z= 0.229 Angle : 0.679 15.671 84983 Z= 0.330 Chirality : 0.044 0.405 10168 Planarity : 0.004 0.082 10833 Dihedral : 7.429 175.002 8763 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 19.58 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.86 % Favored : 94.09 % Rotamer: Outliers : 0.28 % Allowed : 20.53 % Favored : 79.19 % 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: -0.31 (0.10), residues: 8047 helix: 0.99 (0.08), residues: 4074 sheet: -1.31 (0.21), residues: 615 loop : -1.49 (0.11), residues: 3358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 324 HIS 0.016 0.001 HIS E 129 PHE 0.032 0.001 PHE h 385 TYR 0.017 0.001 TYR G 302 ARG 0.008 0.000 ARG D 34 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16094 Ramachandran restraints generated. 8047 Oldfield, 0 Emsley, 8047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 429 time to evaluate : 5.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 5 residues processed: 445 average time/residue: 0.5844 time to fit residues: 462.5454 Evaluate side-chains 424 residues out of total 6735 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 419 time to evaluate : 5.509 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.4692 time to fit residues: 12.1238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 803 random chunks: chunk 506 optimal weight: 8.9990 chunk 678 optimal weight: 9.9990 chunk 195 optimal weight: 4.9990 chunk 587 optimal weight: 0.6980 chunk 94 optimal weight: 9.9990 chunk 177 optimal weight: 40.0000 chunk 638 optimal weight: 8.9990 chunk 267 optimal weight: 50.0000 chunk 655 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 117 optimal weight: 30.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.118072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.083056 restraints weight = 306504.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.084449 restraints weight = 187359.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.087036 restraints weight = 131727.173| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3765 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3765 r_free = 0.3765 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3765 r_free = 0.3765 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3765 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 62920 Z= 0.271 Angle : 0.708 13.964 84983 Z= 0.345 Chirality : 0.045 0.468 10168 Planarity : 0.004 0.080 10833 Dihedral : 7.516 173.643 8763 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 21.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.27 % Favored : 93.68 % Rotamer: Outliers : 0.36 % Allowed : 20.57 % Favored : 79.07 % 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: -0.47 (0.09), residues: 8047 helix: 0.84 (0.08), residues: 4079 sheet: -1.37 (0.21), residues: 630 loop : -1.55 (0.11), residues: 3338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 324 HIS 0.014 0.001 HIS E 129 PHE 0.032 0.002 PHE h 385 TYR 0.016 0.001 TYR G 302 ARG 0.013 0.000 ARG G 215 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11197.53 seconds wall clock time: 200 minutes 42.76 seconds (12042.76 seconds total)