Starting phenix.real_space_refine on Fri Dec 8 23:11:31 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfe_40439/12_2023/8sfe_40439_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfe_40439/12_2023/8sfe_40439.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfe_40439/12_2023/8sfe_40439.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfe_40439/12_2023/8sfe_40439.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfe_40439/12_2023/8sfe_40439_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sfe_40439/12_2023/8sfe_40439_updated.pdb" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.031 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 377 5.16 5 C 37846 2.51 5 N 10544 2.21 5 O 11713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "z ASP 107": "OD1" <-> "OD2" Residue "z GLU 112": "OE1" <-> "OE2" Residue "z TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ASP 389": "OD1" <-> "OD2" Residue "Z ASP 32": "OD1" <-> "OD2" Residue "Z ASP 389": "OD1" <-> "OD2" Residue "Z GLU 415": "OE1" <-> "OE2" Residue "a GLU 99": "OE1" <-> "OE2" Residue "b GLU 414": "OE1" <-> "OE2" Residue "e GLU 121": "OE1" <-> "OE2" Residue "e ASP 125": "OD1" <-> "OD2" Residue "g TYR 358": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 510": "OE1" <-> "OE2" Residue "h GLU 34": "OE1" <-> "OE2" Residue "h ASP 46": "OD1" <-> "OD2" Residue "h PHE 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ASP 387": "OD1" <-> "OD2" Residue "A PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 77": "OD1" <-> "OD2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 431": "OE1" <-> "OE2" Residue "D PHE 454": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 89": "OE1" <-> "OE2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "G GLU 113": "OE1" <-> "OE2" Residue "G PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 510": "OE1" <-> "OE2" Residue "H ASP 46": "OD1" <-> "OD2" Residue "H ASP 61": "OD1" <-> "OD2" Residue "H GLU 206": "OE1" <-> "OE2" Residue "H ASP 451": "OD1" <-> "OD2" Residue "H ASP 478": "OD1" <-> "OD2" Residue "H GLU 518": "OE1" <-> "OE2" Residue "Q PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 60512 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: "b" Number of atoms: 3590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 478, 3590 Classifications: {'peptide': 478} Link IDs: {'PTRANS': 8, 'TRANS': 469} Chain breaks: 1 Chain: "d" Number of atoms: 3673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 489, 3673 Classifications: {'peptide': 489} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 475} Chain breaks: 1 Chain: "e" Number of atoms: 3882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 3882 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 14, 'TRANS': 490} Chain breaks: 1 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: "B" Number of atoms: 3698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 492, 3698 Classifications: {'peptide': 492} Link IDs: {'PTRANS': 8, 'TRANS': 483} Chain breaks: 1 Chain: "D" Number of atoms: 3655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3655 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 473} Chain breaks: 1 Chain: "E" Number of atoms: 3863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3863 Classifications: {'peptide': 503} Link IDs: {'PTRANS': 14, 'TRANS': 488} Chain breaks: 1 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: "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: "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: "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: "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: "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} Time building chain proxies: 23.32, per 1000 atoms: 0.39 Number of scatterers: 60512 At special positions: 0 Unit cell: (187.266, 175.628, 190.44, 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 377 16.00 P 32 15.00 O 11713 8.00 N 10544 7.00 C 37846 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=2.03 Simple disulfide: pdb=" SG CYS H 326 " - pdb=" SG CYS H 345 " distance=2.03 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.14 Conformation dependent library (CDL) restraints added in 8.5 seconds 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14680 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 283 helices and 69 sheets defined 49.8% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.42 Creating SS restraints... Processing helix chain 'z' and resid 19 through 37 removed outlier: 4.729A pdb=" N THR z 36 " --> pdb=" O ASP z 32 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ASN z 37 " --> pdb=" O VAL z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 60 through 66 Processing helix chain 'z' and resid 72 through 85 Processing helix chain 'z' and resid 92 through 112 removed outlier: 3.623A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) removed outlier: 4.876A 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 157 Processing helix chain 'z' and resid 162 through 182 removed outlier: 4.144A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA z 171 " --> pdb=" O VAL z 167 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS z 181 " --> pdb=" O LEU z 177 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLN z 182 " --> pdb=" O ALA z 178 " (cutoff:3.500A) Processing helix chain 'z' and resid 253 through 258 Processing helix chain 'z' and resid 264 through 281 Processing helix chain 'z' and resid 299 through 308 removed outlier: 3.766A 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 414 through 425 Processing helix chain 'z' and resid 431 through 455 removed outlier: 4.156A pdb=" N GLN z 434 " --> pdb=" O GLY z 431 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE z 447 " --> pdb=" O LEU z 444 " (cutoff:3.500A) Proline residue: z 448 - end of helix Processing helix chain 'z' and resid 459 through 473 removed outlier: 3.884A 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 20 through 34 Processing helix chain 'Z' and resid 60 through 65 removed outlier: 5.042A pdb=" N HIS Z 65 " --> pdb=" O ASN Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 72 through 87 removed outlier: 5.173A pdb=" N ILE Z 87 " --> pdb=" O ALA Z 83 " (cutoff:3.500A) Processing helix chain 'Z' and resid 92 through 110 removed outlier: 3.867A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 116 through 137 removed outlier: 3.631A pdb=" N GLU Z 135 " --> pdb=" O LEU Z 131 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLU Z 136 " --> pdb=" O GLN Z 132 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL Z 137 " --> pdb=" O PHE Z 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 145 through 157 Processing helix chain 'Z' and resid 162 through 179 removed outlier: 3.816A pdb=" N ASP Z 166 " --> pdb=" O ALA Z 162 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL Z 167 " --> pdb=" O GLU Z 163 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU Z 168 " --> pdb=" O LEU Z 164 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU Z 170 " --> pdb=" O ASP Z 166 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA Z 171 " --> pdb=" O VAL Z 167 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER Z 175 " --> pdb=" O ALA Z 171 " (cutoff:3.500A) Processing helix chain 'Z' and resid 253 through 281 removed outlier: 3.886A pdb=" N ARG Z 264 " --> pdb=" O VAL Z 260 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N PHE Z 266 " --> pdb=" O ALA Z 262 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ILE Z 267 " --> pdb=" O GLU Z 263 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LYS Z 273 " --> pdb=" O ASP Z 269 " (cutoff:3.500A) Processing helix chain 'Z' and resid 299 through 307 Processing helix chain 'Z' and resid 321 through 327 removed outlier: 4.249A pdb=" N LEU Z 326 " --> pdb=" O GLU Z 322 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA Z 327 " --> pdb=" O ARG Z 323 " (cutoff:3.500A) Processing helix chain 'Z' and resid 381 through 403 removed outlier: 4.630A pdb=" N GLN Z 386 " --> pdb=" O HIS Z 382 " (cutoff:3.500A) Processing helix chain 'Z' and resid 413 through 428 Proline residue: Z 427 - end of helix Processing helix chain 'Z' and resid 431 through 454 removed outlier: 3.596A pdb=" N GLN Z 434 " --> pdb=" O GLY Z 431 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE Z 447 " --> pdb=" O LEU Z 444 " (cutoff:3.500A) Proline residue: Z 448 - end of helix removed outlier: 3.520A pdb=" N ASN Z 454 " --> pdb=" O LEU Z 451 " (cutoff:3.500A) Processing helix chain 'Z' and resid 459 through 472 removed outlier: 3.716A pdb=" N LEU Z 463 " --> pdb=" O LEU Z 459 " (cutoff:3.500A) Processing helix chain 'Z' and resid 498 through 516 Processing helix chain 'a' and resid 17 through 35 removed outlier: 3.633A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N SER a 34 " --> pdb=" O ASN a 30 " (cutoff:3.500A) removed outlier: 5.893A 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: 3.526A pdb=" N VAL a 74 " --> pdb=" O PRO a 70 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 90 through 109 Processing helix chain 'a' and resid 114 through 134 removed outlier: 3.556A pdb=" N ASN a 133 " --> pdb=" O VAL a 129 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU a 134 " --> pdb=" O ARG a 130 " (cutoff:3.500A) Processing helix chain 'a' and resid 146 through 155 Processing helix chain 'a' and resid 160 through 177 removed outlier: 4.087A pdb=" N ILE a 163 " --> pdb=" O ILE a 160 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY a 165 " --> pdb=" O GLY a 162 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N ASP a 166 " --> pdb=" O ILE a 163 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE a 167 " --> pdb=" O ASN a 164 " (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 299 No H-bonds generated for 'chain 'a' and resid 296 through 299' Processing helix chain 'a' and resid 313 through 323 removed outlier: 3.594A pdb=" N ARG a 318 " --> pdb=" O ARG a 314 " (cutoff:3.500A) Processing helix chain 'a' and resid 386 through 403 removed outlier: 3.562A pdb=" N VAL a 402 " --> pdb=" O VAL a 398 " (cutoff:3.500A) Processing helix chain 'a' and resid 414 through 429 removed outlier: 3.630A pdb=" N GLU a 424 " --> pdb=" O SER a 420 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN a 425 " --> pdb=" O ILE a 421 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N SER a 429 " --> pdb=" O ASN a 425 " (cutoff:3.500A) Processing helix chain 'a' and resid 435 through 455 removed outlier: 3.989A pdb=" N LEU a 446 " --> pdb=" O ALA a 442 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N VAL a 447 " --> pdb=" O ARG a 443 " (cutoff:3.500A) removed outlier: 5.275A 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: 3.646A pdb=" N GLU a 473 " --> pdb=" O ALA a 469 " (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 479 through 481 No H-bonds generated for 'chain 'a' and resid 479 through 481' Processing helix chain 'a' and resid 507 through 525 Processing helix chain 'b' and resid 25 through 42 removed outlier: 3.630A pdb=" N VAL b 39 " --> pdb=" O ILE b 35 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N SER b 41 " --> pdb=" O ASP b 37 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N THR b 42 " --> pdb=" O LEU b 38 " (cutoff:3.500A) Processing helix chain 'b' and resid 68 through 73 removed outlier: 3.599A pdb=" N LYS b 72 " --> pdb=" O ALA b 68 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN b 73 " --> pdb=" O THR b 69 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 68 through 73' Processing helix chain 'b' and resid 79 through 93 Processing helix chain 'b' and resid 99 through 118 Processing helix chain 'b' and resid 123 through 143 removed outlier: 3.806A pdb=" N ALA b 136 " --> pdb=" O GLU b 132 " (cutoff:3.500A) Processing helix chain 'b' and resid 157 through 166 removed outlier: 3.706A pdb=" N THR b 166 " --> pdb=" O ILE b 162 " (cutoff:3.500A) Processing helix chain 'b' and resid 176 through 186 Processing helix chain 'b' and resid 264 through 283 Processing helix chain 'b' and resid 298 through 306 removed outlier: 3.987A pdb=" N LEU b 303 " --> pdb=" O TYR b 299 " (cutoff:3.500A) Processing helix chain 'b' and resid 317 through 326 Processing helix chain 'b' and resid 380 through 402 removed outlier: 3.967A pdb=" N ASP b 384 " --> pdb=" O GLN b 380 " (cutoff:3.500A) Processing helix chain 'b' and resid 412 through 425 Processing helix chain 'b' and resid 431 through 453 Proline residue: b 447 - end of helix Processing helix chain 'b' and resid 461 through 470 removed outlier: 3.931A pdb=" N SER b 470 " --> pdb=" O ARG b 466 " (cutoff:3.500A) 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 32 through 46 Processing helix chain 'd' and resid 49 through 51 No H-bonds generated for 'chain 'd' and resid 49 through 51' Processing helix chain 'd' and resid 74 through 80 Processing helix chain 'd' and resid 86 through 101 Processing helix chain 'd' and resid 106 through 125 removed outlier: 4.026A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU d 123 " --> pdb=" O SER d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 130 through 150 Processing helix chain 'd' and resid 160 through 170 Processing helix chain 'd' and resid 180 through 193 Proline residue: d 185 - end of helix 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 279 through 293 Processing helix chain 'd' and resid 311 through 318 removed outlier: 3.507A pdb=" N PHE d 316 " --> pdb=" O LEU d 312 " (cutoff:3.500A) Processing helix chain 'd' and resid 333 through 340 Processing helix chain 'd' and resid 348 through 350 No H-bonds generated for 'chain 'd' and resid 348 through 350' Processing helix chain 'd' and resid 353 through 355 No H-bonds generated for 'chain 'd' and resid 353 through 355' Processing helix chain 'd' and resid 396 through 417 removed outlier: 4.429A pdb=" N ALA d 401 " --> pdb=" O VAL d 397 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU d 402 " --> pdb=" O ILE d 398 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VAL d 416 " --> pdb=" O ILE d 412 " (cutoff:3.500A) Processing helix chain 'd' and resid 427 through 442 Processing helix chain 'd' and resid 446 through 468 removed outlier: 3.702A pdb=" N TYR d 449 " --> pdb=" O MET d 446 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL d 460 " --> pdb=" O ALA d 457 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ILE d 461 " --> pdb=" O MET d 458 " (cutoff:3.500A) Proline residue: d 462 - end of helix Processing helix chain 'd' and resid 473 through 486 Processing helix chain 'd' and resid 504 through 506 No H-bonds generated for 'chain 'd' and resid 504 through 506' Processing helix chain 'd' and resid 512 through 531 Processing helix chain 'e' and resid 30 through 44 Processing helix chain 'e' and resid 49 through 51 No H-bonds generated for 'chain 'e' and resid 49 through 51' Processing helix chain 'e' and resid 74 through 80 Processing helix chain 'e' and resid 86 through 101 Processing helix chain 'e' and resid 106 through 126 removed outlier: 4.599A pdb=" N GLN e 122 " --> pdb=" O GLU e 118 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU e 123 " --> pdb=" O GLU e 119 " (cutoff:3.500A) Processing helix chain 'e' and resid 130 through 150 Processing helix chain 'e' and resid 162 through 168 removed outlier: 3.579A pdb=" N ILE e 166 " --> pdb=" O THR e 162 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN e 167 " --> pdb=" O GLU e 163 " (cutoff:3.500A) Processing helix chain 'e' and resid 170 through 173 No H-bonds generated for 'chain 'e' and resid 170 through 173' Processing helix chain 'e' and resid 178 through 180 No H-bonds generated for 'chain 'e' and resid 178 through 180' Processing helix chain 'e' and resid 182 through 195 Processing helix chain 'e' and resid 273 through 288 removed outlier: 4.047A pdb=" N GLU e 287 " --> pdb=" O GLU e 283 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N MET e 288 " --> pdb=" O LYS e 284 " (cutoff:3.500A) Processing helix chain 'e' and resid 308 through 317 Processing helix chain 'e' and resid 329 through 333 Processing helix chain 'e' and resid 392 through 414 Processing helix chain 'e' and resid 424 through 439 removed outlier: 3.868A pdb=" N ASP e 438 " --> pdb=" O SER e 434 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LYS e 439 " --> pdb=" O GLN e 435 " (cutoff:3.500A) Processing helix chain 'e' and resid 442 through 466 removed outlier: 3.728A pdb=" N VAL e 457 " --> pdb=" O ASP e 453 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ILE e 458 " --> pdb=" O ALA e 454 " (cutoff:3.500A) Proline residue: e 459 - end of helix Processing helix chain 'e' and resid 472 through 483 Processing helix chain 'e' and resid 501 through 504 No H-bonds generated for 'chain 'e' and resid 501 through 504' Processing helix chain 'e' and resid 510 through 529 Processing helix chain 'g' and resid 19 through 35 Processing helix chain 'g' and resid 62 through 68 Processing helix chain 'g' and resid 74 through 90 Processing helix chain 'g' and resid 94 through 113 removed outlier: 3.635A pdb=" N ILE g 98 " --> pdb=" O THR g 94 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLU g 109 " --> pdb=" O LEU g 105 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N HIS g 110 " --> pdb=" O SER g 106 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N PHE g 111 " --> pdb=" O VAL g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 139 Processing helix chain 'g' and resid 148 through 158 Processing helix chain 'g' and resid 168 through 180 removed outlier: 3.718A pdb=" N ASN g 173 " --> pdb=" O SER g 169 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS g 180 " --> 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 275 through 283 removed outlier: 4.204A pdb=" N ILE g 282 " --> pdb=" O CYS g 278 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLN g 283 " --> pdb=" O GLU g 279 " (cutoff:3.500A) Processing helix chain 'g' and resid 297 through 306 Processing helix chain 'g' and resid 316 through 326 removed outlier: 4.152A pdb=" N ARG g 321 " --> pdb=" O THR g 317 " (cutoff:3.500A) Processing helix chain 'g' and resid 354 through 356 No H-bonds generated for 'chain 'g' and resid 354 through 356' Processing helix chain 'g' and resid 380 through 402 removed outlier: 3.681A pdb=" N SER g 384 " --> pdb=" O LYS g 380 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLU g 385 " --> pdb=" O GLU g 381 " (cutoff:3.500A) Processing helix chain 'g' and resid 412 through 427 removed outlier: 3.650A pdb=" N LYS g 426 " --> pdb=" O THR g 422 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ALA g 427 " --> pdb=" O GLU g 423 " (cutoff:3.500A) Processing helix chain 'g' and resid 431 through 454 removed outlier: 3.908A pdb=" N TRP g 434 " --> pdb=" O VAL g 431 " (cutoff:3.500A) Proline residue: g 435 - end of helix removed outlier: 3.980A pdb=" N VAL g 439 " --> pdb=" O TYR g 436 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU g 444 " --> pdb=" O GLN g 441 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL g 445 " --> pdb=" O ALA g 442 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE g 446 " --> pdb=" O LEU g 443 " (cutoff:3.500A) Proline residue: g 447 - end of helix removed outlier: 3.889A pdb=" N ASN g 453 " --> pdb=" O LEU g 450 " (cutoff:3.500A) Processing helix chain 'g' and resid 458 through 470 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 35 removed outlier: 3.577A pdb=" N ALA h 35 " --> pdb=" O VAL h 31 " (cutoff:3.500A) Processing helix chain 'h' and resid 37 through 39 No H-bonds generated for 'chain 'h' and resid 37 through 39' Processing helix chain 'h' and resid 62 through 68 Processing helix chain 'h' and resid 78 through 93 removed outlier: 4.172A pdb=" N ILE h 86 " --> pdb=" O THR h 82 " (cutoff:3.500A) Processing helix chain 'h' and resid 99 through 115 Proline residue: h 114 - end of helix Processing helix chain 'h' and resid 122 through 142 removed outlier: 3.564A pdb=" N LYS h 141 " --> pdb=" O VAL h 137 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLU h 142 " --> pdb=" O ASN h 138 " (cutoff:3.500A) Processing helix chain 'h' and resid 157 through 167 removed outlier: 4.661A pdb=" N THR h 165 " --> pdb=" O LYS h 161 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ALA h 166 " --> pdb=" O CYS h 162 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LEU h 167 " --> pdb=" O ALA h 163 " (cutoff:3.500A) Processing helix chain 'h' and resid 176 through 190 Processing helix chain 'h' and resid 269 through 284 removed outlier: 4.032A pdb=" N LEU h 282 " --> pdb=" O LEU h 278 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU h 283 " --> pdb=" O TYR h 279 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LYS h 284 " --> pdb=" O ASP h 280 " (cutoff:3.500A) Processing helix chain 'h' and resid 301 through 310 removed outlier: 5.062A pdb=" N GLN h 305 " --> pdb=" O VAL h 302 " (cutoff:3.500A) Processing helix chain 'h' and resid 320 through 329 Processing helix chain 'h' and resid 383 through 405 removed outlier: 3.931A pdb=" N MET h 386 " --> pdb=" O GLU h 383 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU h 387 " --> pdb=" O GLN h 384 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N LEU h 393 " --> pdb=" O GLU h 390 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N HIS h 394 " --> pdb=" O ARG h 391 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS h 405 " --> pdb=" O ARG h 402 " (cutoff:3.500A) Processing helix chain 'h' and resid 415 through 428 Processing helix chain 'h' and resid 434 through 456 removed outlier: 3.684A pdb=" N LEU h 438 " --> pdb=" O LYS h 434 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU h 447 " --> pdb=" O ALA h 443 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ILE h 448 " --> pdb=" O LYS h 444 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ILE h 449 " --> pdb=" O ALA h 445 " (cutoff:3.500A) Proline residue: h 450 - end of helix Processing helix chain 'h' and resid 461 through 474 Processing helix chain 'h' and resid 500 through 518 Processing helix chain 'q' and resid 30 through 44 removed outlier: 3.863A pdb=" N THR q 43 " --> pdb=" O LEU q 39 " (cutoff:3.500A) Processing helix chain 'q' and resid 69 through 75 Processing helix chain 'q' and resid 81 through 96 removed outlier: 3.587A pdb=" N MET q 85 " --> pdb=" O PRO q 81 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE q 86 " --> pdb=" O ALA q 82 " (cutoff:3.500A) Processing helix chain 'q' and resid 101 through 121 Processing helix chain 'q' and resid 125 through 145 removed outlier: 3.549A pdb=" N GLU q 141 " --> pdb=" O ARG q 137 " (cutoff:3.500A) Proline residue: q 144 - end of helix Processing helix chain 'q' and resid 157 through 171 removed outlier: 4.964A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 5.605A pdb=" N SER q 167 " --> pdb=" O LEU q 163 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE q 168 " --> pdb=" O LEU q 164 " (cutoff:3.500A) Processing helix chain 'q' and resid 177 through 191 removed outlier: 3.950A pdb=" N LEU q 182 " --> pdb=" O PHE q 178 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N CYS q 187 " --> pdb=" O ILE q 183 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL q 188 " --> pdb=" O ALA q 184 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE q 190 " --> pdb=" O ALA q 186 " (cutoff:3.500A) removed outlier: 5.124A 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 308 Processing helix chain 'q' and resid 320 through 328 Processing helix chain 'q' and resid 383 through 404 removed outlier: 3.925A pdb=" N ASP q 387 " --> pdb=" O ASN q 383 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N THR q 398 " --> pdb=" O ASP q 394 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ARG q 404 " --> pdb=" O LYS q 400 " (cutoff:3.500A) Processing helix chain 'q' and resid 414 through 428 removed outlier: 4.100A pdb=" N GLU q 428 " --> pdb=" O THR q 424 " (cutoff:3.500A) Processing helix chain 'q' and resid 435 through 456 removed outlier: 3.522A pdb=" N ALA q 447 " --> pdb=" O GLU q 443 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE q 448 " --> pdb=" O ALA q 444 " (cutoff:3.500A) Proline residue: q 449 - end of helix removed outlier: 4.211A pdb=" N SER q 456 " --> pdb=" O LEU q 452 " (cutoff:3.500A) Processing helix chain 'q' and resid 460 through 473 removed outlier: 3.763A pdb=" N GLN q 472 " --> pdb=" O TYR q 468 " (cutoff:3.500A) removed outlier: 4.335A 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 35 removed outlier: 4.543A pdb=" N SER A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N SER A 35 " --> pdb=" O ILE A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 70 through 85 Processing helix chain 'A' and resid 90 through 110 removed outlier: 3.609A pdb=" N GLN A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 134 removed outlier: 3.542A pdb=" N ARG A 130 " --> pdb=" O LYS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 162 through 178 removed outlier: 4.099A pdb=" N ASP A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N PHE A 167 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP A 174 " --> pdb=" O ASN A 170 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA A 175 " --> pdb=" O MET A 171 " (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 Processing helix chain 'A' and resid 313 through 321 Processing helix chain 'A' and resid 386 through 403 Processing helix chain 'A' and resid 414 through 430 removed outlier: 3.567A pdb=" N ASN A 425 " --> pdb=" O ILE A 421 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 455 removed outlier: 4.159A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL A 447 " --> pdb=" O ARG A 443 " (cutoff:3.500A) removed outlier: 5.044A 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: 3.585A pdb=" N ALA A 474 " --> pdb=" O PHE A 470 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN A 475 " --> pdb=" O HIS A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 501 No H-bonds generated for 'chain 'A' and resid 498 through 501' Processing helix chain 'A' and resid 507 through 526 Processing helix chain 'B' and resid 23 through 40 Processing helix chain 'B' and resid 67 through 73 Processing helix chain 'B' and resid 79 through 94 Processing helix chain 'B' and resid 99 through 119 Processing helix chain 'B' and resid 123 through 144 removed outlier: 3.845A pdb=" N GLU B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 166 removed outlier: 3.634A pdb=" N THR B 166 " --> pdb=" O ILE B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 264 through 285 removed outlier: 4.104A pdb=" N LYS B 284 " --> pdb=" O GLU B 280 " (cutoff:3.500A) removed outlier: 5.474A 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 325 Processing helix chain 'B' and resid 380 through 402 removed outlier: 4.735A pdb=" N ALA B 386 " --> pdb=" O LEU B 383 " (cutoff:3.500A) 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: 3.561A pdb=" N ASN B 453 " --> pdb=" O ILE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 471 removed outlier: 4.019A pdb=" N GLU B 471 " --> pdb=" O ALA B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 491 No H-bonds generated for 'chain 'B' and resid 488 through 491' Processing helix chain 'B' and resid 497 through 515 Processing helix chain 'D' and resid 31 through 51 removed outlier: 3.656A pdb=" N SER D 36 " --> pdb=" O GLN D 32 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) removed outlier: 6.412A 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: 3.795A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 150 Processing helix chain 'D' and resid 160 through 171 Processing helix chain 'D' and resid 180 through 193 Proline residue: D 185 - end of helix 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 285 through 293 Processing helix chain 'D' and resid 311 through 316 Processing helix chain 'D' and resid 330 through 340 removed outlier: 4.413A pdb=" N GLU D 334 " --> pdb=" O GLU D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 355 No H-bonds generated for 'chain 'D' and resid 353 through 355' Processing helix chain 'D' and resid 396 through 417 removed outlier: 4.245A pdb=" N ALA D 401 " --> pdb=" O VAL D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 427 through 442 removed outlier: 3.826A pdb=" N THR D 437 " --> pdb=" O ALA D 433 " (cutoff:3.500A) Processing helix chain 'D' and resid 446 through 467 removed outlier: 3.595A pdb=" N TYR D 449 " --> pdb=" O MET D 446 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL D 460 " --> pdb=" O ALA D 457 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE D 461 " --> pdb=" O MET D 458 " (cutoff:3.500A) Proline residue: D 462 - end of helix Processing helix chain 'D' and resid 473 through 485 Processing helix chain 'D' and resid 503 through 506 No H-bonds generated for 'chain 'D' and resid 503 through 506' Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'E' and resid 30 through 50 removed outlier: 3.535A pdb=" N ARG E 49 " --> pdb=" O ASN E 46 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N THR E 50 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 74 through 80 Processing helix chain 'E' and resid 86 through 98 removed outlier: 3.886A pdb=" N SER E 97 " --> pdb=" O GLU E 93 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N GLN E 98 " --> pdb=" O LEU E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 126 removed outlier: 3.952A pdb=" N ARG E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 151 Processing helix chain 'E' and resid 162 through 172 removed outlier: 3.516A pdb=" N ILE E 166 " --> pdb=" O THR E 162 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN E 167 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 177 through 194 removed outlier: 3.574A pdb=" N HIS E 182 " --> pdb=" O ASN E 179 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ARG E 183 " --> pdb=" O SER E 180 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N ALA E 186 " --> pdb=" O ARG E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'E' and resid 272 through 295 Processing helix chain 'E' and resid 308 through 316 Processing helix chain 'E' and resid 330 through 336 removed outlier: 3.766A pdb=" N ALA E 336 " --> pdb=" O LEU E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 352 No H-bonds generated for 'chain 'E' and resid 350 through 352' Processing helix chain 'E' and resid 392 through 414 Processing helix chain 'E' and resid 424 through 437 Processing helix chain 'E' and resid 443 through 465 removed outlier: 4.042A pdb=" N GLU E 456 " --> pdb=" O ASP E 453 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE E 458 " --> pdb=" O LEU E 455 " (cutoff:3.500A) Proline residue: E 459 - end of helix removed outlier: 3.584A pdb=" N ASN E 465 " --> pdb=" O LEU E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 483 Processing helix chain 'E' and resid 501 through 504 No H-bonds generated for 'chain 'E' and resid 501 through 504' Processing helix chain 'E' and resid 510 through 529 Processing helix chain 'G' and resid 18 through 33 removed outlier: 3.651A pdb=" N VAL G 21 " --> pdb=" O GLY G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 68 Processing helix chain 'G' and resid 74 through 90 Processing helix chain 'G' and resid 94 through 112 removed outlier: 3.814A pdb=" N GLU G 109 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N HIS G 110 " --> pdb=" O SER G 106 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N PHE G 111 " --> pdb=" O VAL G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 139 Processing helix chain 'G' and resid 148 through 157 Processing helix chain 'G' and resid 168 through 180 removed outlier: 4.174A pdb=" N ASN G 173 " --> pdb=" O SER G 169 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N LYS G 180 " --> 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 275 through 284 removed outlier: 3.512A pdb=" N GLN G 283 " --> pdb=" O GLU G 279 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU G 284 " --> pdb=" O ASP G 280 " (cutoff:3.500A) Processing helix chain 'G' and resid 297 through 305 Processing helix chain 'G' and resid 316 through 326 removed outlier: 4.231A pdb=" N ARG G 321 " --> pdb=" O THR G 317 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 341 No H-bonds generated for 'chain 'G' and resid 339 through 341' Processing helix chain 'G' and resid 380 through 402 removed outlier: 3.742A pdb=" N SER G 384 " --> pdb=" O LYS G 380 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N GLU G 385 " --> pdb=" O GLU G 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 424 Processing helix chain 'G' and resid 431 through 454 removed outlier: 3.979A pdb=" N TRP G 434 " --> pdb=" O VAL G 431 " (cutoff:3.500A) Proline residue: G 435 - end of helix removed outlier: 3.722A pdb=" N VAL G 439 " --> pdb=" O TYR G 436 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU G 444 " --> pdb=" O GLN G 441 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ILE G 446 " --> pdb=" O LEU G 443 " (cutoff:3.500A) Proline residue: G 447 - end of helix removed outlier: 3.987A pdb=" N ASN G 453 " --> pdb=" O LEU G 450 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 470 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 18 through 34 Processing helix chain 'H' and resid 37 through 39 No H-bonds generated for 'chain 'H' and resid 37 through 39' Processing helix chain 'H' and resid 62 through 68 Processing helix chain 'H' and resid 74 through 89 removed outlier: 3.741A pdb=" N GLU H 89 " --> pdb=" O SER H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 113 removed outlier: 4.323A pdb=" N THR H 98 " --> pdb=" O THR H 95 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LEU H 99 " --> pdb=" O SER H 96 " (cutoff:3.500A) Proline residue: H 110 - end of helix Processing helix chain 'H' and resid 118 through 138 removed outlier: 3.817A pdb=" N LYS H 137 " --> pdb=" O VAL H 133 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU H 138 " --> pdb=" O ASN H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 163 removed outlier: 3.619A pdb=" N LEU H 163 " --> pdb=" O MET H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 185 removed outlier: 4.003A pdb=" N GLN H 170 " --> pdb=" O LEU H 167 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA H 173 " --> pdb=" O GLN H 170 " (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 267 through 284 removed outlier: 3.926A pdb=" N ILE H 281 " --> pdb=" O LYS H 277 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N HIS H 282 " --> pdb=" O LEU H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 306 removed outlier: 5.830A pdb=" N GLN H 301 " --> pdb=" O VAL H 298 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG H 306 " --> pdb=" O PHE H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 316 through 323 Processing helix chain 'H' and resid 353 through 355 No H-bonds generated for 'chain 'H' and resid 353 through 355' Processing helix chain 'H' and resid 379 through 386 Processing helix chain 'H' and resid 390 through 401 Processing helix chain 'H' and resid 411 through 426 removed outlier: 3.811A pdb=" N ARG H 425 " --> pdb=" O ARG H 421 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N THR H 426 " --> pdb=" O ASP H 422 " (cutoff:3.500A) Processing helix chain 'H' and resid 430 through 453 removed outlier: 4.295A pdb=" N ILE H 445 " --> pdb=" O LEU H 442 " (cutoff:3.500A) Proline residue: H 446 - end of helix Processing helix chain 'H' and resid 457 through 470 Processing helix chain 'H' and resid 496 through 515 Processing helix chain 'Q' and resid 30 through 44 removed outlier: 3.684A pdb=" N THR Q 43 " --> pdb=" O LEU Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 75 Processing helix chain 'Q' and resid 81 through 97 Processing helix chain 'Q' and resid 101 through 121 Processing helix chain 'Q' and resid 125 through 145 removed outlier: 3.533A pdb=" N GLU Q 141 " --> pdb=" O ARG Q 137 " (cutoff:3.500A) Proline residue: Q 144 - end of helix Processing helix chain 'Q' and resid 157 through 171 removed outlier: 3.736A pdb=" N SER Q 162 " --> pdb=" O ASP Q 158 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE Q 168 " --> pdb=" O LEU Q 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 191 removed outlier: 4.531A pdb=" N LYS Q 181 " --> pdb=" O PHE Q 178 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA Q 186 " --> pdb=" O ILE Q 183 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N CYS Q 187 " --> pdb=" O ALA Q 184 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER Q 189 " --> pdb=" O ALA Q 186 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE Q 190 " --> pdb=" O CYS Q 187 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE Q 191 " --> pdb=" O VAL Q 188 " (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 287 removed outlier: 5.523A pdb=" N THR Q 286 " --> pdb=" O ALA Q 282 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N GLY Q 287 " --> pdb=" O ILE Q 283 " (cutoff:3.500A) Processing helix chain 'Q' and resid 299 through 307 Processing helix chain 'Q' and resid 321 through 328 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: 4.328A pdb=" N ASP Q 386 " --> pdb=" O ASN Q 383 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ASP Q 387 " --> pdb=" O LEU Q 384 " (cutoff:3.500A) Processing helix chain 'Q' and resid 414 through 427 Processing helix chain 'Q' and resid 433 through 456 removed outlier: 3.863A pdb=" N TYR Q 436 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) Proline residue: Q 449 - end of helix removed outlier: 3.632A pdb=" N ASN Q 455 " --> pdb=" O LEU Q 452 " (cutoff:3.500A) Processing helix chain 'Q' and resid 460 through 472 removed outlier: 3.815A pdb=" N GLN Q 472 " --> pdb=" O TYR Q 468 " (cutoff:3.500A) Processing helix chain 'Q' and resid 501 through 519 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 193 removed outlier: 6.966A pdb=" N VAL z 372 " --> pdb=" O GLU z 192 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'z' and resid 209 through 212 removed outlier: 3.963A pdb=" N THR z 361 " --> pdb=" O LEU z 212 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU z 358 " --> pdb=" O LEU z 355 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'z' and resid 288 through 290 Processing sheet with id= E, first strand: chain 'z' and resid 407 through 409 Processing sheet with id= F, first strand: chain 'Z' and resid 45 through 48 Processing sheet with id= G, first strand: chain 'Z' and resid 349 through 353 Processing sheet with id= H, first strand: chain 'Z' and resid 478 through 480 removed outlier: 3.997A pdb=" N GLU Z 485 " --> pdb=" O ASP Z 480 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'a' and resid 195 through 199 removed outlier: 7.650A pdb=" N ALA a 373 " --> pdb=" O ASN a 196 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N LEU a 198 " --> pdb=" O ALA a 373 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE a 375 " --> pdb=" O LEU a 198 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'a' and resid 346 through 348 removed outlier: 4.008A pdb=" N GLY a 346 " --> pdb=" O ILE a 234 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL a 285 " --> pdb=" O ALA a 235 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'a' and resid 350 through 355 removed outlier: 3.954A pdb=" N GLU a 350 " --> pdb=" O LYS a 365 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS a 365 " --> pdb=" O GLU a 350 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL a 352 " --> pdb=" O LEU a 363 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU a 363 " --> pdb=" O VAL a 352 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU a 354 " --> pdb=" O LEU a 361 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU a 361 " --> pdb=" O GLU a 354 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'a' and resid 408 through 410 Processing sheet with id= M, first strand: chain 'a' and resid 486 through 489 removed outlier: 3.788A pdb=" N LYS a 494 " --> pdb=" O ASP a 489 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'b' and resid 200 through 205 removed outlier: 3.657A pdb=" N LYS b 204 " --> pdb=" O LEU b 375 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'b' and resid 289 through 292 removed outlier: 5.589A pdb=" N MET b 310 " --> pdb=" O PHE b 290 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ASN b 292 " --> pdb=" O MET b 310 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N ILE b 312 " --> pdb=" O ASN b 292 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'b' and resid 406 through 408 Processing sheet with id= Q, first strand: chain 'b' and resid 476 through 479 removed outlier: 3.594A pdb=" N THR b 484 " --> pdb=" O ASP b 479 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'd' and resid 212 through 214 removed outlier: 5.904A pdb=" N VAL d 390 " --> pdb=" O LYS d 213 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'd' and resid 361 through 363 removed outlier: 4.368A pdb=" N LEU d 361 " --> pdb=" O THR d 377 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR d 377 " --> pdb=" O LEU d 361 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU d 363 " --> pdb=" O LYS d 375 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS d 375 " --> pdb=" O GLU d 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'd' and resid 421 through 423 Processing sheet with id= U, first strand: chain 'd' and resid 491 through 494 removed outlier: 3.914A pdb=" N GLY d 492 " --> pdb=" O SER d 501 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER d 501 " --> pdb=" O GLY d 492 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'e' and resid 59 through 62 Processing sheet with id= W, first strand: chain 'e' and resid 248 through 250 removed outlier: 5.905A pdb=" N LEU e 299 " --> pdb=" O ALA e 249 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'g' and resid 47 through 50 Processing sheet with id= Y, first strand: chain 'g' and resid 199 through 204 removed outlier: 3.929A pdb=" N GLY g 377 " --> pdb=" O ILE g 203 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'g' and resid 237 through 239 removed outlier: 7.499A pdb=" N VAL g 288 " --> pdb=" O VAL g 238 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'g' and resid 348 through 352 removed outlier: 3.563A pdb=" N LEU g 348 " --> pdb=" O THR g 363 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LYS g 352 " --> pdb=" O PHE g 359 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N PHE g 359 " --> pdb=" O LYS g 352 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'g' and resid 406 through 408 Processing sheet with id= AC, first strand: chain 'h' and resid 47 through 50 Processing sheet with id= AD, first strand: chain 'h' and resid 213 through 215 removed outlier: 3.704A pdb=" N GLN h 213 " --> pdb=" O ILE h 377 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'h' and resid 241 through 244 removed outlier: 7.034A pdb=" N VAL h 292 " --> pdb=" O ALA h 242 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU h 244 " --> pdb=" O VAL h 292 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N LEU h 294 " --> pdb=" O LEU h 244 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N PHE h 313 " --> pdb=" O VAL h 293 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N SER h 295 " --> pdb=" O PHE h 313 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA h 315 " --> pdb=" O SER h 295 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'h' and resid 353 through 357 removed outlier: 3.658A pdb=" N THR h 355 " --> pdb=" O TYR h 362 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'h' and resid 409 through 411 Processing sheet with id= AH, first strand: chain 'h' and resid 479 through 482 removed outlier: 3.693A pdb=" N ALA h 489 " --> pdb=" O GLY h 480 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP h 487 " --> pdb=" O ASP h 482 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'q' and resid 54 through 56 Processing sheet with id= AJ, first strand: chain 'q' and resid 202 through 208 removed outlier: 6.364A pdb=" N SER q 373 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 7.971A pdb=" N CYS q 205 " --> pdb=" O SER q 373 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ILE q 375 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N ILE q 207 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LEU q 377 " --> pdb=" O ILE q 207 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'q' and resid 221 through 223 removed outlier: 3.573A pdb=" N PHE q 223 " --> pdb=" O VAL q 361 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'q' and resid 239 through 242 removed outlier: 7.288A pdb=" N VAL q 290 " --> pdb=" O ALA q 240 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N TYR q 242 " --> pdb=" O VAL q 290 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N VAL q 292 " --> pdb=" O TYR q 242 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N MET q 311 " --> pdb=" O VAL q 291 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N THR q 293 " --> pdb=" O MET q 311 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N VAL q 313 " --> pdb=" O THR q 293 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'q' and resid 408 through 410 Processing sheet with id= AN, first strand: chain 'q' and resid 478 through 480 Processing sheet with id= AO, first strand: chain 'A' and resid 197 through 199 removed outlier: 6.046A pdb=" N ILE A 375 " --> pdb=" O LEU A 198 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'A' and resid 350 through 352 removed outlier: 3.773A pdb=" N GLU A 350 " --> pdb=" O LYS A 365 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'A' and resid 408 through 410 Processing sheet with id= AR, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.588A pdb=" N LYS A 494 " --> pdb=" O ASP A 489 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'B' and resid 50 through 52 removed outlier: 4.100A pdb=" N MET B 62 " --> pdb=" O LEU B 52 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'B' and resid 201 through 205 removed outlier: 6.205A pdb=" N ILE B 373 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N LYS B 204 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU B 375 " --> pdb=" O LYS B 204 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 374 " --> pdb=" O TYR B 213 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR B 213 " --> pdb=" O VAL B 374 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'B' and resid 406 through 408 Processing sheet with id= AV, first strand: chain 'B' and resid 476 through 479 removed outlier: 3.522A pdb=" N THR B 484 " --> pdb=" O ASP B 479 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'D' and resid 246 through 249 removed outlier: 6.828A pdb=" N VAL D 297 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ILE D 249 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU D 299 " --> pdb=" O ILE D 249 " (cutoff:3.500A) No H-bonds generated for sheet with id= AW Processing sheet with id= AX, first strand: chain 'D' and resid 362 through 367 removed outlier: 4.237A pdb=" N GLU D 363 " --> pdb=" O LYS D 375 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS D 375 " --> pdb=" O GLU D 363 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 365 " --> pdb=" O LEU D 373 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.672A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'E' and resid 59 through 62 Processing sheet with id= BA, first strand: chain 'E' and resid 248 through 251 removed outlier: 5.836A pdb=" N LEU E 299 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU E 251 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE E 301 " --> pdb=" O LEU E 251 " (cutoff:3.500A) No H-bonds generated for sheet with id= BA Processing sheet with id= BB, first strand: chain 'G' and resid 47 through 50 removed outlier: 3.572A pdb=" N THR G 59 " --> pdb=" O LYS G 47 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU G 49 " --> pdb=" O VAL G 57 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'G' and resid 199 through 204 removed outlier: 3.849A pdb=" N GLY G 377 " --> pdb=" O ILE G 203 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'G' and resid 216 through 219 removed outlier: 3.682A pdb=" N LEU G 348 " --> pdb=" O THR G 363 " (cutoff:3.500A) Processing sheet with id= BE, first strand: chain 'G' and resid 237 through 239 removed outlier: 7.262A pdb=" N VAL G 288 " --> pdb=" O VAL G 238 " (cutoff:3.500A) No H-bonds generated for sheet with id= BE Processing sheet with id= BF, first strand: chain 'G' and resid 406 through 408 Processing sheet with id= BG, first strand: chain 'H' and resid 47 through 49 removed outlier: 4.105A pdb=" N LYS H 47 " --> pdb=" O SER H 59 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER H 59 " --> pdb=" O LYS H 47 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'H' and resid 195 through 201 removed outlier: 6.875A pdb=" N CYS H 370 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N LYS H 198 " --> pdb=" O CYS H 370 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N PHE H 372 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL H 200 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LEU H 374 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing sheet with id= BI, first strand: chain 'H' and resid 288 through 291 removed outlier: 6.877A pdb=" N SER H 329 " --> pdb=" O LEU H 239 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'H' and resid 405 through 407 Processing sheet with id= BK, first strand: chain 'H' and resid 475 through 477 Processing sheet with id= BL, first strand: chain 'Q' and resid 54 through 57 Processing sheet with id= BM, first strand: chain 'Q' and resid 202 through 208 removed outlier: 6.225A pdb=" N SER Q 373 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N CYS Q 205 " --> pdb=" O SER Q 373 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE Q 375 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE Q 207 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N LEU Q 377 " --> pdb=" O ILE Q 207 " (cutoff:3.500A) No H-bonds generated for sheet with id= BM Processing sheet with id= BN, first strand: chain 'Q' and resid 221 through 223 removed outlier: 3.896A pdb=" N TYR Q 351 " --> pdb=" O VAL Q 362 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS Q 364 " --> pdb=" O SER Q 349 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER Q 349 " --> pdb=" O LYS Q 364 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'Q' and resid 290 through 292 removed outlier: 6.542A pdb=" N MET Q 311 " --> pdb=" O VAL Q 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= BO Processing sheet with id= BP, first strand: chain 'Q' and resid 408 through 410 Processing sheet with id= BQ, first strand: chain 'Q' and resid 478 through 480 2711 hydrogen bonds defined for protein. 7014 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: 19.16 Time building geometry restraints manager: 20.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 20351 1.34 - 1.46: 9744 1.46 - 1.58: 30446 1.58 - 1.70: 48 1.70 - 1.82: 618 Bond restraints: 61207 Sorted by residual: bond pdb=" CA PRO Q 192 " pdb=" CB PRO Q 192 " ideal model delta sigma weight residual 1.531 1.519 0.012 6.20e-03 2.60e+04 4.06e+00 bond pdb=" C4 ADP Q5000 " pdb=" C5 ADP Q5000 " ideal model delta sigma weight residual 1.490 1.462 0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" C4 ADP G 601 " pdb=" C5 ADP G 601 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.63e+00 bond pdb=" C ARG H 152 " pdb=" O ARG H 152 " ideal model delta sigma weight residual 1.236 1.254 -0.019 1.47e-02 4.63e+03 1.60e+00 bond pdb=" C4 ADP q5000 " pdb=" C5 ADP q5000 " ideal model delta sigma weight residual 1.490 1.465 0.025 2.00e-02 2.50e+03 1.52e+00 ... (remaining 61202 not shown) Histogram of bond angle deviations from ideal: 97.16 - 105.06: 873 105.06 - 112.96: 35175 112.96 - 120.86: 28726 120.86 - 128.77: 17617 128.77 - 136.67: 273 Bond angle restraints: 82664 Sorted by residual: angle pdb=" N ILE E 159 " pdb=" CA ILE E 159 " pdb=" C ILE E 159 " ideal model delta sigma weight residual 111.62 107.61 4.01 7.90e-01 1.60e+00 2.58e+01 angle pdb=" N VAL h 147 " pdb=" CA VAL h 147 " pdb=" C VAL h 147 " ideal model delta sigma weight residual 113.20 108.90 4.30 9.60e-01 1.09e+00 2.01e+01 angle pdb=" N THR a 371 " pdb=" CA THR a 371 " pdb=" C THR a 371 " ideal model delta sigma weight residual 114.75 109.21 5.54 1.26e+00 6.30e-01 1.93e+01 angle pdb=" C GLN H 151 " pdb=" N ARG H 152 " pdb=" CA ARG H 152 " ideal model delta sigma weight residual 122.31 129.69 -7.38 2.00e+00 2.50e-01 1.36e+01 angle pdb=" C VAL D 508 " pdb=" N VAL D 509 " pdb=" CA VAL D 509 " ideal model delta sigma weight residual 121.97 128.59 -6.62 1.80e+00 3.09e-01 1.35e+01 ... (remaining 82659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 37108 35.93 - 71.86: 658 71.86 - 107.79: 52 107.79 - 143.72: 14 143.72 - 179.65: 4 Dihedral angle restraints: 37836 sinusoidal: 15184 harmonic: 22652 Sorted by residual: dihedral pdb=" C5' ADP D 601 " pdb=" O5' ADP D 601 " pdb=" PA ADP D 601 " pdb=" O2A ADP D 601 " ideal model delta sinusoidal sigma weight residual 300.00 120.35 179.65 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O1B ADP z 601 " pdb=" O3A ADP z 601 " pdb=" PB ADP z 601 " pdb=" PA ADP z 601 " ideal model delta sinusoidal sigma weight residual -60.00 111.88 -171.88 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O1B ADP Q5000 " pdb=" O3A ADP Q5000 " pdb=" PB ADP Q5000 " pdb=" PA ADP Q5000 " ideal model delta sinusoidal sigma weight residual 300.00 152.23 147.77 1 2.00e+01 2.50e-03 4.43e+01 ... (remaining 37833 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 7166 0.043 - 0.086: 2013 0.086 - 0.129: 685 0.129 - 0.172: 43 0.172 - 0.215: 7 Chirality restraints: 9914 Sorted by residual: chirality pdb=" CB ILE h 172 " pdb=" CA ILE h 172 " pdb=" CG1 ILE h 172 " pdb=" CG2 ILE h 172 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CB ILE E 209 " pdb=" CA ILE E 209 " pdb=" CG1 ILE E 209 " pdb=" CG2 ILE E 209 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" CA MET g 304 " pdb=" N MET g 304 " pdb=" C MET g 304 " pdb=" CB MET g 304 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.17e-01 ... (remaining 9911 not shown) Planarity restraints: 10525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO Q 338 " 0.054 5.00e-02 4.00e+02 8.14e-02 1.06e+01 pdb=" N PRO Q 339 " -0.141 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 GLU Z 184 " 0.036 5.00e-02 4.00e+02 5.43e-02 4.72e+00 pdb=" N PRO Z 185 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO Z 185 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO Z 185 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS e 535 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO e 536 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO e 536 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO e 536 " -0.028 5.00e-02 4.00e+02 ... (remaining 10522 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 1013 2.64 - 3.20: 59903 3.20 - 3.77: 99095 3.77 - 4.33: 129094 4.33 - 4.90: 207041 Nonbonded interactions: 496146 Sorted by model distance: nonbonded pdb=" OH TYR d 449 " pdb=" OE1 GLU E 456 " model vdw 2.072 2.440 nonbonded pdb=" OH TYR a 181 " pdb=" OG1 THR a 371 " model vdw 2.093 2.440 nonbonded pdb=" OE2 GLU Q 273 " pdb=" OH TYR Q 304 " model vdw 2.097 2.440 nonbonded pdb=" OG SER q 215 " pdb=" O VAL q 376 " model vdw 2.113 2.440 nonbonded pdb=" O LYS q 400 " pdb=" OG1 THR q 403 " model vdw 2.132 2.440 ... (remaining 496141 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 24 through 243 or resid 263 through 520 or resid 601)) selection = chain 'b' } ncs_group { reference = chain 'D' selection = (chain 'd' and (resid 30 through 256 or resid 280 through 539 or resid 601)) } ncs_group { reference = (chain 'E' and (resid 25 through 540 or resid 601)) selection = (chain 'e' and (resid 25 through 540 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 7.850 Check model and map are aligned: 0.690 Set scattering table: 0.410 Process input model: 124.150 Find NCS groups from input model: 5.800 Set up NCS constraints: 0.500 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:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 143.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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 0.043 61207 Z= 0.215 Angle : 0.653 10.398 82664 Z= 0.325 Chirality : 0.044 0.215 9914 Planarity : 0.003 0.081 10525 Dihedral : 14.918 179.654 23150 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.56 % Favored : 93.36 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.39 (0.10), residues: 7817 helix: 1.20 (0.08), residues: 3955 sheet: -1.45 (0.24), residues: 506 loop : -1.92 (0.10), residues: 3356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP b 130 HIS 0.010 0.001 HIS z 214 PHE 0.024 0.001 PHE Q 223 TYR 0.024 0.001 TYR A 131 ARG 0.011 0.000 ARG d 539 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 6557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 548 time to evaluate : 5.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 548 average time/residue: 0.5218 time to fit residues: 504.1803 Evaluate side-chains 446 residues out of total 6557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 446 time to evaluate : 5.112 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.0294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 658 optimal weight: 0.0770 chunk 591 optimal weight: 1.9990 chunk 328 optimal weight: 5.9990 chunk 201 optimal weight: 8.9990 chunk 398 optimal weight: 1.9990 chunk 315 optimal weight: 6.9990 chunk 611 optimal weight: 50.0000 chunk 236 optimal weight: 0.8980 chunk 371 optimal weight: 40.0000 chunk 455 optimal weight: 10.0000 chunk 708 optimal weight: 30.0000 overall best weight: 2.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: z 214 HIS ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 110 GLN b 292 ASN ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 406 HIS ** e 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 384 GLN h 526 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 523 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.0708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 61207 Z= 0.198 Angle : 0.616 10.140 82664 Z= 0.301 Chirality : 0.043 0.266 9914 Planarity : 0.004 0.081 10525 Dihedral : 8.237 167.420 8522 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.24 % Favored : 93.68 % Rotamer: Outliers : 0.75 % Allowed : 8.34 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.48 (0.10), residues: 7817 helix: 1.10 (0.08), residues: 3948 sheet: -1.46 (0.23), residues: 500 loop : -1.92 (0.10), residues: 3369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP h 497 HIS 0.005 0.001 HIS A 393 PHE 0.024 0.001 PHE B 179 TYR 0.018 0.001 TYR D 179 ARG 0.006 0.000 ARG d 539 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 6557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 480 time to evaluate : 5.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 32 residues processed: 503 average time/residue: 0.5404 time to fit residues: 478.2734 Evaluate side-chains 463 residues out of total 6557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 431 time to evaluate : 5.100 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.4424 time to fit residues: 33.5872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 393 optimal weight: 6.9990 chunk 219 optimal weight: 9.9990 chunk 589 optimal weight: 10.0000 chunk 482 optimal weight: 8.9990 chunk 195 optimal weight: 20.0000 chunk 709 optimal weight: 6.9990 chunk 766 optimal weight: 0.8980 chunk 631 optimal weight: 5.9990 chunk 703 optimal weight: 0.0370 chunk 241 optimal weight: 10.0000 chunk 569 optimal weight: 4.9990 overall best weight: 3.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 497 ASN ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 482 ASN e 191 ASN g 389 ASN ** g 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 384 GLN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 484 HIS E 303 GLN ** E 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 480 ASN ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 390 HIS Q 523 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 61207 Z= 0.269 Angle : 0.626 8.084 82664 Z= 0.307 Chirality : 0.043 0.172 9914 Planarity : 0.004 0.073 10525 Dihedral : 8.054 153.244 8522 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.93 % Favored : 92.99 % Rotamer: Outliers : 0.93 % Allowed : 12.92 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.62 (0.10), residues: 7817 helix: 0.97 (0.08), residues: 3959 sheet: -1.69 (0.22), residues: 547 loop : -1.94 (0.10), residues: 3311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP q 506 HIS 0.004 0.001 HIS a 113 PHE 0.025 0.001 PHE b 155 TYR 0.018 0.001 TYR H 419 ARG 0.004 0.000 ARG g 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 6557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 455 time to evaluate : 5.136 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: 61 outliers final: 25 residues processed: 502 average time/residue: 0.5439 time to fit residues: 482.2226 Evaluate side-chains 445 residues out of total 6557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 420 time to evaluate : 5.118 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.4460 time to fit residues: 28.2219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 701 optimal weight: 30.0000 chunk 533 optimal weight: 20.0000 chunk 368 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 338 optimal weight: 0.5980 chunk 476 optimal weight: 0.7980 chunk 712 optimal weight: 5.9990 chunk 753 optimal weight: 20.0000 chunk 372 optimal weight: 30.0000 chunk 674 optimal weight: 0.8980 chunk 203 optimal weight: 0.7980 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 110 GLN ** a 435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 147 HIS e 191 ASN g 389 ASN ** g 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 502 GLN D 98 GLN ** E 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 480 ASN H 30 GLN ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 523 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 61207 Z= 0.175 Angle : 0.591 12.971 82664 Z= 0.286 Chirality : 0.042 0.268 9914 Planarity : 0.004 0.078 10525 Dihedral : 7.761 144.449 8522 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.97 % Favored : 93.95 % Rotamer: Outliers : 1.37 % Allowed : 14.47 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.57 (0.10), residues: 7817 helix: 0.99 (0.08), residues: 3965 sheet: -1.62 (0.23), residues: 512 loop : -1.91 (0.10), residues: 3340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP h 497 HIS 0.003 0.001 HIS b 148 PHE 0.022 0.001 PHE b 155 TYR 0.016 0.001 TYR z 353 ARG 0.004 0.000 ARG G 398 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 6557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 475 time to evaluate : 5.134 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: 90 outliers final: 29 residues processed: 547 average time/residue: 0.5445 time to fit residues: 525.0021 Evaluate side-chains 463 residues out of total 6557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 434 time to evaluate : 5.091 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.4345 time to fit residues: 30.9351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 627 optimal weight: 0.0170 chunk 427 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 561 optimal weight: 30.0000 chunk 311 optimal weight: 9.9990 chunk 643 optimal weight: 0.9990 chunk 521 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 384 optimal weight: 0.7980 chunk 676 optimal weight: 0.2980 chunk 190 optimal weight: 2.9990 overall best weight: 0.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 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** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 191 ASN ** g 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 GLN ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 523 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 61207 Z= 0.144 Angle : 0.585 9.633 82664 Z= 0.282 Chirality : 0.041 0.298 9914 Planarity : 0.003 0.075 10525 Dihedral : 7.501 143.793 8522 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.90 % Favored : 94.03 % Rotamer: Outliers : 0.96 % Allowed : 16.14 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.10), residues: 7817 helix: 1.05 (0.09), residues: 3949 sheet: -1.58 (0.23), residues: 522 loop : -1.86 (0.10), residues: 3346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP h 497 HIS 0.004 0.000 HIS z 161 PHE 0.020 0.001 PHE b 155 TYR 0.026 0.001 TYR q 304 ARG 0.003 0.000 ARG d 539 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 6557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 490 time to evaluate : 5.176 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: 63 outliers final: 12 residues processed: 543 average time/residue: 0.5399 time to fit residues: 514.5873 Evaluate side-chains 463 residues out of total 6557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 451 time to evaluate : 5.057 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4268 time to fit residues: 16.8058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 253 optimal weight: 0.8980 chunk 678 optimal weight: 10.0000 chunk 149 optimal weight: 8.9990 chunk 442 optimal weight: 0.0070 chunk 186 optimal weight: 5.9990 chunk 754 optimal weight: 9.9990 chunk 626 optimal weight: 0.9990 chunk 349 optimal weight: 4.9990 chunk 62 optimal weight: 6.9990 chunk 249 optimal weight: 8.9990 chunk 396 optimal weight: 1.9990 overall best weight: 1.7804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 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** ** b 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 391 HIS ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 384 GLN ** q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 306 ASN Q 523 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 61207 Z= 0.177 Angle : 0.600 11.059 82664 Z= 0.288 Chirality : 0.042 0.357 9914 Planarity : 0.003 0.078 10525 Dihedral : 7.374 146.650 8522 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.19 % Favored : 93.73 % Rotamer: Outliers : 0.93 % Allowed : 17.52 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.45 (0.10), residues: 7817 helix: 1.09 (0.09), residues: 3944 sheet: -1.48 (0.23), residues: 509 loop : -1.85 (0.10), residues: 3364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP h 497 HIS 0.005 0.001 HIS b 175 PHE 0.019 0.001 PHE b 155 TYR 0.015 0.001 TYR D 439 ARG 0.007 0.000 ARG g 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 6557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 447 time to evaluate : 5.085 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: 61 outliers final: 24 residues processed: 485 average time/residue: 0.5657 time to fit residues: 483.2435 Evaluate side-chains 453 residues out of total 6557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 429 time to evaluate : 5.112 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.4614 time to fit residues: 27.9059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 727 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 429 optimal weight: 3.9990 chunk 551 optimal weight: 5.9990 chunk 427 optimal weight: 3.9990 chunk 635 optimal weight: 0.2980 chunk 421 optimal weight: 7.9990 chunk 751 optimal weight: 7.9990 chunk 470 optimal weight: 20.0000 chunk 458 optimal weight: 6.9990 chunk 347 optimal weight: 4.9990 overall best weight: 3.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 61 ASN ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 191 ASN e 481 GLN ** g 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 GLN E 298 ASN ** E 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 480 ASN ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 523 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 61207 Z= 0.243 Angle : 0.630 11.339 82664 Z= 0.304 Chirality : 0.043 0.331 9914 Planarity : 0.004 0.075 10525 Dihedral : 7.366 149.714 8522 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.55 % Favored : 93.37 % Rotamer: Outliers : 0.95 % Allowed : 17.89 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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 (0.10), residues: 7817 helix: 1.07 (0.09), residues: 3958 sheet: -1.42 (0.23), residues: 505 loop : -1.87 (0.10), residues: 3354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP b 130 HIS 0.005 0.001 HIS b 175 PHE 0.021 0.001 PHE b 155 TYR 0.017 0.001 TYR D 439 ARG 0.005 0.000 ARG G 388 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 6557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 438 time to evaluate : 5.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 27 residues processed: 489 average time/residue: 0.5352 time to fit residues: 461.2271 Evaluate side-chains 446 residues out of total 6557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 419 time to evaluate : 5.116 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.4494 time to fit residues: 29.7892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 465 optimal weight: 9.9990 chunk 300 optimal weight: 8.9990 chunk 449 optimal weight: 0.8980 chunk 226 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 chunk 477 optimal weight: 5.9990 chunk 512 optimal weight: 4.9990 chunk 371 optimal weight: 9.9990 chunk 70 optimal weight: 9.9990 chunk 590 optimal weight: 20.0000 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 366 ASN ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 130 GLN H 134 ASN H 241 ASN ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 523 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 61207 Z= 0.288 Angle : 0.669 10.251 82664 Z= 0.324 Chirality : 0.043 0.314 9914 Planarity : 0.004 0.076 10525 Dihedral : 7.415 149.164 8522 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.73 % Favored : 93.19 % Rotamer: Outliers : 0.82 % Allowed : 18.53 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: -0.56 (0.10), residues: 7817 helix: 0.97 (0.08), residues: 3968 sheet: -1.39 (0.23), residues: 503 loop : -1.89 (0.10), residues: 3346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP b 130 HIS 0.008 0.001 HIS G 469 PHE 0.019 0.001 PHE Q 363 TYR 0.018 0.001 TYR H 419 ARG 0.008 0.000 ARG D 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 6557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 438 time to evaluate : 5.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 54 outliers final: 23 residues processed: 479 average time/residue: 0.5338 time to fit residues: 450.7592 Evaluate side-chains 444 residues out of total 6557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 421 time to evaluate : 5.059 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.4253 time to fit residues: 25.8344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 683 optimal weight: 0.2980 chunk 720 optimal weight: 2.9990 chunk 657 optimal weight: 7.9990 chunk 700 optimal weight: 4.9990 chunk 421 optimal weight: 30.0000 chunk 305 optimal weight: 4.9990 chunk 550 optimal weight: 10.0000 chunk 214 optimal weight: 7.9990 chunk 633 optimal weight: 0.8980 chunk 662 optimal weight: 3.9990 chunk 698 optimal weight: 2.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 132 GLN ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 110 GLN a 366 ASN b 391 HIS ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 406 HIS ** g 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 ASN D 189 ASN D 406 HIS ** E 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 480 ASN ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 61207 Z= 0.204 Angle : 0.643 15.472 82664 Z= 0.308 Chirality : 0.042 0.301 9914 Planarity : 0.004 0.076 10525 Dihedral : 7.269 150.388 8522 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.20 % Favored : 93.72 % Rotamer: Outliers : 0.29 % Allowed : 19.14 % Favored : 80.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.10), residues: 7817 helix: 1.00 (0.09), residues: 3960 sheet: -1.37 (0.23), residues: 497 loop : -1.88 (0.10), residues: 3360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP b 130 HIS 0.004 0.001 HIS b 175 PHE 0.018 0.001 PHE b 155 TYR 0.018 0.001 TYR q 304 ARG 0.004 0.000 ARG d 153 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 6557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 438 time to evaluate : 5.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 12 residues processed: 452 average time/residue: 0.5681 time to fit residues: 453.9878 Evaluate side-chains 428 residues out of total 6557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 416 time to evaluate : 5.144 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4464 time to fit residues: 17.3118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 460 optimal weight: 0.9990 chunk 740 optimal weight: 0.9980 chunk 452 optimal weight: 0.8980 chunk 351 optimal weight: 0.9980 chunk 514 optimal weight: 4.9990 chunk 777 optimal weight: 2.9990 chunk 715 optimal weight: 40.0000 chunk 618 optimal weight: 30.0000 chunk 64 optimal weight: 0.1980 chunk 477 optimal weight: 0.9990 chunk 379 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 481 GLN ** g 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 245 ASN ** q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 ASN E 311 ASN ** E 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 480 ASN ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 61207 Z= 0.157 Angle : 0.638 14.252 82664 Z= 0.303 Chirality : 0.042 0.292 9914 Planarity : 0.003 0.075 10525 Dihedral : 7.046 152.803 8522 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.04 % Favored : 93.89 % Rotamer: Outliers : 0.14 % Allowed : 19.60 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.10), residues: 7817 helix: 1.07 (0.09), residues: 3947 sheet: -1.43 (0.22), residues: 537 loop : -1.83 (0.10), residues: 3333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP h 497 HIS 0.005 0.001 HIS b 175 PHE 0.018 0.001 PHE b 155 TYR 0.041 0.001 TYR H 419 ARG 0.004 0.000 ARG G 388 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15634 Ramachandran restraints generated. 7817 Oldfield, 0 Emsley, 7817 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 6557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 449 time to evaluate : 5.130 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: 9 outliers final: 5 residues processed: 457 average time/residue: 0.5654 time to fit residues: 452.8234 Evaluate side-chains 431 residues out of total 6557 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 426 time to evaluate : 5.082 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 5 average time/residue: 0.5748 time to fit residues: 12.1794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 491 optimal weight: 4.9990 chunk 659 optimal weight: 7.9990 chunk 189 optimal weight: 0.6980 chunk 570 optimal weight: 50.0000 chunk 91 optimal weight: 6.9990 chunk 171 optimal weight: 30.0000 chunk 619 optimal weight: 20.0000 chunk 259 optimal weight: 0.0470 chunk 636 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 overall best weight: 2.2882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** z 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 170 ASN b 391 HIS ** b 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 406 HIS g 220 ASN ** g 399 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 174 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 337 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 172 ASN ** E 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 480 ASN ** H 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.139814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.087754 restraints weight = 157447.782| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 5.94 r_work: 0.3219 rms_B_bonded: 5.45 restraints_weight: 2.0000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 61207 Z= 0.205 Angle : 0.654 13.186 82664 Z= 0.311 Chirality : 0.042 0.287 9914 Planarity : 0.003 0.073 10525 Dihedral : 7.031 154.922 8522 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.38 % Favored : 93.54 % Rotamer: Outliers : 0.23 % Allowed : 19.77 % Favored : 80.01 % 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: -0.43 (0.10), residues: 7817 helix: 1.09 (0.09), residues: 3943 sheet: -1.45 (0.22), residues: 537 loop : -1.82 (0.10), residues: 3337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP b 130 HIS 0.005 0.001 HIS E 182 PHE 0.020 0.001 PHE B 335 TYR 0.029 0.001 TYR H 419 ARG 0.004 0.000 ARG a 145 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12113.15 seconds wall clock time: 215 minutes 34.55 seconds (12934.55 seconds total)