Starting phenix.real_space_refine on Sat Apr 6 12:22:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ras_19023/04_2024/8ras_19023_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ras_19023/04_2024/8ras_19023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ras_19023/04_2024/8ras_19023.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ras_19023/04_2024/8ras_19023.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ras_19023/04_2024/8ras_19023_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ras_19023/04_2024/8ras_19023_updated.pdb" } resolution = 2.62 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= 0.140 sd= 0.155 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 2 7.16 5 Zn 1 6.06 5 P 80 5.49 5 Mg 1 5.21 5 S 268 5.16 5 C 36108 2.51 5 N 9924 2.21 5 O 10931 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 23": "OD1" <-> "OD2" Residue "B GLU 194": "OE1" <-> "OE2" Residue "C GLU 33": "OE1" <-> "OE2" Residue "C ASP 425": "OD1" <-> "OD2" Residue "C GLU 506": "OE1" <-> "OE2" Residue "C TYR 809": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1020": "OE1" <-> "OE2" Residue "D TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 294": "OE1" <-> "OE2" Residue "D GLU 364": "OE1" <-> "OE2" Residue "D ASP 599": "OD1" <-> "OD2" Residue "D TYR 637": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 666": "OE1" <-> "OE2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E GLU 114": "OE1" <-> "OE2" Residue "E ASP 155": "OD1" <-> "OD2" Residue "E ASP 253": "OD1" <-> "OD2" Residue "E GLU 318": "OE1" <-> "OE2" Residue "E TYR 1049": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 1150": "OE1" <-> "OE2" Residue "E GLU 1166": "OE1" <-> "OE2" Residue "E PHE 1363": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 192": "OE1" <-> "OE2" Residue "F ASP 276": "OD1" <-> "OD2" Residue "F ASP 299": "OD1" <-> "OD2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 605": "OE1" <-> "OE2" Residue "G GLU 491": "OE1" <-> "OE2" Residue "G PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 548": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 691": "OE1" <-> "OE2" Residue "G GLU 763": "OE1" <-> "OE2" Residue "G ASP 776": "OD1" <-> "OD2" Residue "H ASP 358": "OD1" <-> "OD2" Residue "H GLU 394": "OE1" <-> "OE2" Residue "H GLU 471": "OE1" <-> "OE2" Residue "H TYR 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 542": "OE1" <-> "OE2" Residue "H ASP 605": "OD1" <-> "OD2" Residue "I ASP 93": "OD1" <-> "OD2" Residue "I PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 189": "OE1" <-> "OE2" Residue "J GLU 265": "OE1" <-> "OE2" Residue "J GLU 293": "OE1" <-> "OE2" Residue "J GLU 334": "OE1" <-> "OE2" Residue "K ASP 88": "OD1" <-> "OD2" Residue "K ASP 89": "OD1" <-> "OD2" Residue "K PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 280": "OE1" <-> "OE2" Residue "K TYR 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 327": "OE1" <-> "OE2" Residue "L PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 192": "OD1" <-> "OD2" Residue "L GLU 437": "OE1" <-> "OE2" Residue "L ASP 475": "OD1" <-> "OD2" Residue "M ASP 139": "OD1" <-> "OD2" Residue "M GLU 242": "OE1" <-> "OE2" Residue "N PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 184": "OD1" <-> "OD2" Residue "O GLU 139": "OE1" <-> "OE2" Residue "P GLU 86": "OE1" <-> "OE2" Residue "P ASP 102": "OD1" <-> "OD2" Residue "P GLU 126": "OE1" <-> "OE2" Residue "P GLU 139": "OE1" <-> "OE2" Residue "P ASP 160": "OD1" <-> "OD2" Residue "P ASP 164": "OD1" <-> "OD2" Residue "P ASP 184": "OD1" <-> "OD2" Residue "Q GLU 578": "OE1" <-> "OE2" Residue "Q ASP 604": "OD1" <-> "OD2" Residue "Q ASP 657": "OD1" <-> "OD2" Residue "Q TYR 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 695": "OD1" <-> "OD2" Residue "Q TYR 746": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 135": "OD1" <-> "OD2" Residue "S GLU 230": "OE1" <-> "OE2" Residue "S ASP 272": "OD1" <-> "OD2" Residue "S GLU 418": "OE1" <-> "OE2" Residue "S GLU 422": "OE1" <-> "OE2" Residue "T GLU 59": "OE1" <-> "OE2" Residue "T TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 57315 Number of models: 1 Model: "" Number of chains: 45 Chain: "A" Number of atoms: 2449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2449 Classifications: {'peptide': 301} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 286} Chain breaks: 2 Chain: "B" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1722 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 205} Chain breaks: 1 Chain: "C" Number of atoms: 5772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5772 Classifications: {'peptide': 726} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 34, 'TRANS': 691} Chain breaks: 7 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 4787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4787 Classifications: {'peptide': 585} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 553} Chain breaks: 6 Chain: "E" Number of atoms: 7308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 912, 7308 Classifications: {'peptide': 912} Link IDs: {'PTRANS': 33, 'TRANS': 878} Chain breaks: 18 Chain: "F" Number of atoms: 4593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 568, 4593 Classifications: {'peptide': 568} Link IDs: {'PTRANS': 22, 'TRANS': 545} Chain breaks: 4 Chain: "G" Number of atoms: 3040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3040 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 8, 'TRANS': 376} Chain breaks: 2 Chain: "H" Number of atoms: 3701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3701 Classifications: {'peptide': 440} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 405} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1771 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "J" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1970 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 14, 'TRANS': 219} Chain breaks: 1 Chain: "K" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3022 Classifications: {'peptide': 374} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 350} Chain: "L" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3348 Classifications: {'peptide': 408} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 381} Chain breaks: 2 Chain: "M" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1714 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 15, 'TRANS': 188} Chain: "N" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 Chain: "O" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 923 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 107} Chain: "P" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 865 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "Q" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1740 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 209} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 944 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain breaks: 2 Chain: "S" Number of atoms: 3056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3056 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Chain: "T" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 881 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 638 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Chain breaks: 1 Chain: "Y" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 813 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "Z" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 215 Classifications: {'RNA': 10} Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 4} Link IDs: {'rna2p': 1, 'rna3p': 8} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "C" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 54 Classifications: {'water': 54} Link IDs: {None: 53} Chain: "D" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 24 Classifications: {'water': 24} Link IDs: {None: 23} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "I" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "K" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "L" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "M" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "N" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16437 SG CYS E 220 97.283 113.428 109.446 1.00 66.65 S ATOM 16906 SG CYS E 293 94.634 112.057 111.778 1.00 55.31 S ATOM 16964 SG CYS E 300 95.151 110.521 108.259 1.00 54.48 S ATOM 16989 SG CYS E 303 97.725 109.883 110.759 1.00 70.32 S Time building chain proxies: 22.00, per 1000 atoms: 0.38 Number of scatterers: 57315 At special positions: 0 Unit cell: (149, 210, 267, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 Fe 2 26.01 S 268 16.00 P 80 15.00 Mg 1 11.99 O 10931 8.00 N 9924 7.00 C 36108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.37 Conformation dependent library (CDL) restraints added in 6.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E8001 " pdb="ZN ZN E8001 " - pdb=" SG CYS E 300 " pdb="ZN ZN E8001 " - pdb=" SG CYS E 220 " pdb="ZN ZN E8001 " - pdb=" SG CYS E 303 " pdb="ZN ZN E8001 " - pdb=" SG CYS E 293 " Number of angles added : 6 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12804 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 284 helices and 55 sheets defined 40.5% alpha, 11.5% beta 37 base pairs and 56 stacking pairs defined. Time for finding SS restraints: 17.82 Creating SS restraints... Processing helix chain 'A' and resid 41 through 55 Processing helix chain 'A' and resid 84 through 93 removed outlier: 3.513A pdb=" N GLU A 93 " --> pdb=" O MET A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 211 through 230 Proline residue: A 228 - end of helix Processing helix chain 'A' and resid 249 through 261 removed outlier: 4.201A pdb=" N PHE A 253 " --> pdb=" O PRO A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 281 through 289 Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 303 through 308 Processing helix chain 'A' and resid 314 through 326 Processing helix chain 'B' and resid 41 through 55 Processing helix chain 'B' and resid 84 through 93 removed outlier: 3.568A pdb=" N GLU B 93 " --> pdb=" O MET B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 120 No H-bonds generated for 'chain 'B' and resid 118 through 120' Processing helix chain 'B' and resid 211 through 230 Proline residue: B 228 - end of helix Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'C' and resid 66 through 71 removed outlier: 3.623A pdb=" N VAL C 70 " --> pdb=" O GLU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 311 No H-bonds generated for 'chain 'C' and resid 309 through 311' Processing helix chain 'C' and resid 317 through 329 Processing helix chain 'C' and resid 362 through 371 Processing helix chain 'C' and resid 383 through 391 removed outlier: 3.785A pdb=" N ILE C 387 " --> pdb=" O PRO C 383 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N GLY C 390 " --> pdb=" O GLN C 386 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG C 391 " --> pdb=" O ILE C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 417 No H-bonds generated for 'chain 'C' and resid 415 through 417' Processing helix chain 'C' and resid 473 through 476 No H-bonds generated for 'chain 'C' and resid 473 through 476' Processing helix chain 'C' and resid 494 through 496 No H-bonds generated for 'chain 'C' and resid 494 through 496' Processing helix chain 'C' and resid 512 through 514 No H-bonds generated for 'chain 'C' and resid 512 through 514' Processing helix chain 'C' and resid 530 through 532 No H-bonds generated for 'chain 'C' and resid 530 through 532' Processing helix chain 'C' and resid 536 through 538 No H-bonds generated for 'chain 'C' and resid 536 through 538' Processing helix chain 'C' and resid 541 through 553 removed outlier: 3.752A pdb=" N MET C 546 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG C 552 " --> pdb=" O SER C 548 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLN C 553 " --> pdb=" O ASN C 549 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 577 Processing helix chain 'C' and resid 677 through 681 removed outlier: 3.876A pdb=" N TYR C 681 " --> pdb=" O CYS C 678 " (cutoff:3.500A) Processing helix chain 'C' and resid 856 through 862 Proline residue: C 860 - end of helix Processing helix chain 'C' and resid 865 through 880 removed outlier: 3.503A pdb=" N GLU C 870 " --> pdb=" O GLN C 867 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N CYS C 871 " --> pdb=" O ILE C 868 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 872 " --> pdb=" O PHE C 869 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY C 877 " --> pdb=" O GLY C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 890 through 892 No H-bonds generated for 'chain 'C' and resid 890 through 892' Processing helix chain 'C' and resid 897 through 912 Processing helix chain 'C' and resid 989 through 998 Processing helix chain 'C' and resid 1001 through 1008 Processing helix chain 'C' and resid 1015 through 1027 removed outlier: 3.552A pdb=" N GLN C1019 " --> pdb=" O ILE C1015 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE C1026 " --> pdb=" O LEU C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1039 through 1051 Processing helix chain 'D' and resid 17 through 24 Processing helix chain 'D' and resid 58 through 61 No H-bonds generated for 'chain 'D' and resid 58 through 61' Processing helix chain 'D' and resid 99 through 101 No H-bonds generated for 'chain 'D' and resid 99 through 101' Processing helix chain 'D' and resid 116 through 119 No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 125 through 130 Processing helix chain 'D' and resid 134 through 142 Processing helix chain 'D' and resid 169 through 178 removed outlier: 3.821A pdb=" N TYR D 173 " --> pdb=" O GLN D 169 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ILE D 175 " --> pdb=" O TRP D 171 " (cutoff:3.500A) Proline residue: D 176 - end of helix Processing helix chain 'D' and resid 182 through 190 removed outlier: 4.407A pdb=" N ASN D 189 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARG D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 204 removed outlier: 3.538A pdb=" N ILE D 199 " --> pdb=" O GLY D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 224 Processing helix chain 'D' and resid 236 through 256 removed outlier: 3.968A pdb=" N LYS D 241 " --> pdb=" O ILE D 237 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N PHE D 254 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE D 255 " --> pdb=" O ALA D 251 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG D 256 " --> pdb=" O LYS D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 264 Processing helix chain 'D' and resid 274 through 276 No H-bonds generated for 'chain 'D' and resid 274 through 276' Processing helix chain 'D' and resid 292 through 309 removed outlier: 3.561A pdb=" N THR D 305 " --> pdb=" O TYR D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 336 Processing helix chain 'D' and resid 356 through 360 Processing helix chain 'D' and resid 366 through 369 No H-bonds generated for 'chain 'D' and resid 366 through 369' Processing helix chain 'D' and resid 399 through 405 Processing helix chain 'D' and resid 407 through 416 Processing helix chain 'D' and resid 423 through 431 Processing helix chain 'D' and resid 435 through 445 removed outlier: 4.005A pdb=" N GLU D 439 " --> pdb=" O PRO D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 462 No H-bonds generated for 'chain 'D' and resid 460 through 462' Processing helix chain 'D' and resid 480 through 486 removed outlier: 3.551A pdb=" N CYS D 483 " --> pdb=" O PRO D 480 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LYS D 484 " --> pdb=" O LEU D 481 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY D 485 " --> pdb=" O VAL D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 512 Processing helix chain 'D' and resid 515 through 517 No H-bonds generated for 'chain 'D' and resid 515 through 517' Processing helix chain 'D' and resid 534 through 543 Processing helix chain 'D' and resid 549 through 551 No H-bonds generated for 'chain 'D' and resid 549 through 551' Processing helix chain 'D' and resid 584 through 592 Processing helix chain 'D' and resid 656 through 675 Processing helix chain 'E' and resid 16 through 30 Processing helix chain 'E' and resid 32 through 53 removed outlier: 3.507A pdb=" N HIS E 37 " --> pdb=" O ALA E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 87 Processing helix chain 'E' and resid 93 through 122 removed outlier: 4.338A pdb=" N ASN E 116 " --> pdb=" O ARG E 112 " (cutoff:3.500A) Proline residue: E 117 - end of helix Processing helix chain 'E' and resid 127 through 133 Processing helix chain 'E' and resid 140 through 147 removed outlier: 3.512A pdb=" N LEU E 146 " --> pdb=" O GLN E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 210 removed outlier: 3.894A pdb=" N TYR E 183 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLY E 184 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA E 185 " --> pdb=" O SER E 181 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER E 197 " --> pdb=" O ALA E 193 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N TYR E 201 " --> pdb=" O SER E 197 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL E 210 " --> pdb=" O LEU E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 246 No H-bonds generated for 'chain 'E' and resid 243 through 246' Processing helix chain 'E' and resid 271 through 279 Processing helix chain 'E' and resid 290 through 292 No H-bonds generated for 'chain 'E' and resid 290 through 292' Processing helix chain 'E' and resid 301 through 304 No H-bonds generated for 'chain 'E' and resid 301 through 304' Processing helix chain 'E' and resid 320 through 330 Processing helix chain 'E' and resid 366 through 368 No H-bonds generated for 'chain 'E' and resid 366 through 368' Processing helix chain 'E' and resid 567 through 569 No H-bonds generated for 'chain 'E' and resid 567 through 569' Processing helix chain 'E' and resid 1002 through 1005 No H-bonds generated for 'chain 'E' and resid 1002 through 1005' Processing helix chain 'E' and resid 1009 through 1014 removed outlier: 4.742A pdb=" N LYS E1013 " --> pdb=" O ASP E1010 " (cutoff:3.500A) Processing helix chain 'E' and resid 1146 through 1153 Processing helix chain 'E' and resid 1163 through 1179 removed outlier: 3.671A pdb=" N ARG E1174 " --> pdb=" O LYS E1170 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N CYS E1175 " --> pdb=" O GLY E1171 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR E1177 " --> pdb=" O ASN E1173 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ARG E1178 " --> pdb=" O ARG E1174 " (cutoff:3.500A) Processing helix chain 'E' and resid 1184 through 1212 removed outlier: 3.787A pdb=" N GLN E1212 " --> pdb=" O VAL E1208 " (cutoff:3.500A) Processing helix chain 'E' and resid 1218 through 1228 removed outlier: 3.808A pdb=" N GLN E1227 " --> pdb=" O ILE E1223 " (cutoff:3.500A) Processing helix chain 'E' and resid 1251 through 1260 Processing helix chain 'E' and resid 1274 through 1279 removed outlier: 3.553A pdb=" N SER E1278 " --> pdb=" O ILE E1274 " (cutoff:3.500A) Processing helix chain 'E' and resid 1284 through 1288 Processing helix chain 'E' and resid 1293 through 1302 Processing helix chain 'E' and resid 1312 through 1318 Processing helix chain 'E' and resid 1325 through 1327 No H-bonds generated for 'chain 'E' and resid 1325 through 1327' Processing helix chain 'F' and resid 65 through 83 Processing helix chain 'F' and resid 87 through 100 Processing helix chain 'F' and resid 106 through 118 Processing helix chain 'F' and resid 122 through 135 Processing helix chain 'F' and resid 141 through 154 Processing helix chain 'F' and resid 157 through 169 Processing helix chain 'F' and resid 175 through 187 Processing helix chain 'F' and resid 191 through 203 Processing helix chain 'F' and resid 210 through 222 Processing helix chain 'F' and resid 226 through 239 Processing helix chain 'F' and resid 245 through 257 removed outlier: 4.054A pdb=" N VAL F 254 " --> pdb=" O CYS F 250 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N THR F 257 " --> pdb=" O SER F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 272 Processing helix chain 'F' and resid 276 through 278 No H-bonds generated for 'chain 'F' and resid 276 through 278' Processing helix chain 'F' and resid 282 through 293 Processing helix chain 'F' and resid 301 through 313 Processing helix chain 'F' and resid 322 through 334 Processing helix chain 'F' and resid 338 through 350 removed outlier: 4.091A pdb=" N ASN F 350 " --> pdb=" O ARG F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 362 removed outlier: 5.911A pdb=" N ALA F 361 " --> pdb=" O LEU F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 377 Processing helix chain 'F' and resid 381 through 393 Processing helix chain 'F' and resid 412 through 414 No H-bonds generated for 'chain 'F' and resid 412 through 414' Processing helix chain 'F' and resid 432 through 438 Processing helix chain 'F' and resid 460 through 462 No H-bonds generated for 'chain 'F' and resid 460 through 462' Processing helix chain 'F' and resid 475 through 495 removed outlier: 3.609A pdb=" N GLN F 495 " --> pdb=" O LEU F 491 " (cutoff:3.500A) Processing helix chain 'F' and resid 542 through 548 Processing helix chain 'F' and resid 559 through 566 Processing helix chain 'F' and resid 608 through 615 Processing helix chain 'F' and resid 745 through 754 Processing helix chain 'F' and resid 760 through 762 No H-bonds generated for 'chain 'F' and resid 760 through 762' Processing helix chain 'F' and resid 766 through 769 No H-bonds generated for 'chain 'F' and resid 766 through 769' Processing helix chain 'F' and resid 773 through 778 removed outlier: 3.809A pdb=" N LYS F 776 " --> pdb=" O THR F 773 " (cutoff:3.500A) Processing helix chain 'F' and resid 788 through 805 Processing helix chain 'F' and resid 811 through 816 Processing helix chain 'F' and resid 836 through 840 removed outlier: 3.750A pdb=" N LEU F 840 " --> pdb=" O THR F 836 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 836 through 840' Processing helix chain 'G' and resid 421 through 432 Processing helix chain 'G' and resid 436 through 447 Processing helix chain 'G' and resid 455 through 467 Processing helix chain 'G' and resid 471 through 483 removed outlier: 3.881A pdb=" N HIS G 482 " --> pdb=" O PHE G 478 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLU G 483 " --> pdb=" O ASN G 479 " (cutoff:3.500A) Processing helix chain 'G' and resid 490 through 502 Processing helix chain 'G' and resid 506 through 519 Processing helix chain 'G' and resid 525 through 537 Processing helix chain 'G' and resid 541 through 554 Processing helix chain 'G' and resid 560 through 572 Processing helix chain 'G' and resid 576 through 589 removed outlier: 3.790A pdb=" N ALA G 588 " --> pdb=" O GLU G 584 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N SER G 589 " --> pdb=" O GLU G 585 " (cutoff:3.500A) Processing helix chain 'G' and resid 595 through 607 Processing helix chain 'G' and resid 611 through 623 removed outlier: 3.896A pdb=" N GLU G 620 " --> pdb=" O GLU G 616 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N SER G 623 " --> pdb=" O GLU G 619 " (cutoff:3.500A) Processing helix chain 'G' and resid 629 through 637 Processing helix chain 'G' and resid 647 through 657 Processing helix chain 'G' and resid 662 through 679 removed outlier: 3.939A pdb=" N ARG G 667 " --> pdb=" O GLY G 663 " (cutoff:3.500A) Processing helix chain 'G' and resid 682 through 695 removed outlier: 3.623A pdb=" N LYS G 694 " --> pdb=" O ASN G 690 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ARG G 695 " --> pdb=" O GLU G 691 " (cutoff:3.500A) Processing helix chain 'G' and resid 718 through 734 Processing helix chain 'G' and resid 754 through 757 Processing helix chain 'G' and resid 765 through 778 Processing helix chain 'G' and resid 796 through 801 removed outlier: 3.510A pdb=" N GLN G 801 " --> pdb=" O SER G 797 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 79 Processing helix chain 'H' and resid 90 through 98 Processing helix chain 'H' and resid 110 through 119 Processing helix chain 'H' and resid 121 through 130 Processing helix chain 'H' and resid 135 through 142 Processing helix chain 'H' and resid 180 through 194 removed outlier: 4.405A pdb=" N ALA H 189 " --> pdb=" O PHE H 185 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N HIS H 190 " --> pdb=" O ILE H 186 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LYS H 191 " --> pdb=" O ARG H 187 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU H 192 " --> pdb=" O GLU H 188 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N MET H 193 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N ALA H 194 " --> pdb=" O HIS H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 199 through 201 No H-bonds generated for 'chain 'H' and resid 199 through 201' Processing helix chain 'H' and resid 210 through 212 No H-bonds generated for 'chain 'H' and resid 210 through 212' Processing helix chain 'H' and resid 214 through 216 No H-bonds generated for 'chain 'H' and resid 214 through 216' Processing helix chain 'H' and resid 220 through 247 removed outlier: 5.647A pdb=" N ASP H 238 " --> pdb=" O GLU H 234 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ARG H 239 " --> pdb=" O ALA H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 261 No H-bonds generated for 'chain 'H' and resid 259 through 261' Processing helix chain 'H' and resid 269 through 271 No H-bonds generated for 'chain 'H' and resid 269 through 271' Processing helix chain 'H' and resid 307 through 315 removed outlier: 3.808A pdb=" N ILE H 313 " --> pdb=" O TRP H 310 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ARG H 314 " --> pdb=" O PHE H 311 " (cutoff:3.500A) Processing helix chain 'H' and resid 350 through 352 No H-bonds generated for 'chain 'H' and resid 350 through 352' Processing helix chain 'H' and resid 371 through 377 Processing helix chain 'H' and resid 402 through 423 removed outlier: 3.761A pdb=" N ASP H 405 " --> pdb=" O PRO H 402 " (cutoff:3.500A) Processing helix chain 'H' and resid 474 through 483 Processing helix chain 'H' and resid 504 through 537 Processing helix chain 'I' and resid 68 through 74 Processing helix chain 'I' and resid 78 through 90 Processing helix chain 'I' and resid 101 through 109 Processing helix chain 'I' and resid 118 through 133 Processing helix chain 'I' and resid 144 through 153 removed outlier: 4.014A pdb=" N GLU I 148 " --> pdb=" O GLY I 145 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ASP I 153 " --> pdb=" O ILE I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 169 Processing helix chain 'I' and resid 199 through 202 Processing helix chain 'I' and resid 214 through 217 No H-bonds generated for 'chain 'I' and resid 214 through 217' Processing helix chain 'I' and resid 225 through 235 Processing helix chain 'I' and resid 239 through 251 removed outlier: 3.917A pdb=" N SER I 244 " --> pdb=" O ASN I 240 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA I 251 " --> pdb=" O ALA I 247 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 209 No H-bonds generated for 'chain 'J' and resid 206 through 209' Processing helix chain 'J' and resid 235 through 237 No H-bonds generated for 'chain 'J' and resid 235 through 237' Processing helix chain 'J' and resid 255 through 266 Processing helix chain 'J' and resid 278 through 306 removed outlier: 6.066A pdb=" N HIS J 289 " --> pdb=" O ARG J 285 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N LEU J 290 " --> pdb=" O ALA J 286 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N PHE J 291 " --> pdb=" O ARG J 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 308 through 315 removed outlier: 4.434A pdb=" N GLU J 314 " --> pdb=" O ALA J 310 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N TRP J 315 " --> pdb=" O PHE J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 325 through 335 Processing helix chain 'J' and resid 339 through 349 removed outlier: 3.951A pdb=" N HIS J 349 " --> pdb=" O GLU J 345 " (cutoff:3.500A) Processing helix chain 'J' and resid 352 through 361 removed outlier: 4.628A pdb=" N GLY J 360 " --> pdb=" O ARG J 356 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR J 361 " --> pdb=" O ILE J 357 " (cutoff:3.500A) Processing helix chain 'J' and resid 369 through 372 No H-bonds generated for 'chain 'J' and resid 369 through 372' Processing helix chain 'J' and resid 376 through 382 removed outlier: 3.956A pdb=" N GLN J 381 " --> pdb=" O ASP J 377 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ILE J 382 " --> pdb=" O GLN J 378 " (cutoff:3.500A) Processing helix chain 'J' and resid 391 through 393 No H-bonds generated for 'chain 'J' and resid 391 through 393' Processing helix chain 'J' and resid 416 through 422 Processing helix chain 'K' and resid 119 through 127 removed outlier: 4.314A pdb=" N LYS K 123 " --> pdb=" O SER K 120 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP K 127 " --> pdb=" O MET K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 133 No H-bonds generated for 'chain 'K' and resid 131 through 133' Processing helix chain 'K' and resid 140 through 149 Processing helix chain 'K' and resid 164 through 175 Processing helix chain 'K' and resid 201 through 203 No H-bonds generated for 'chain 'K' and resid 201 through 203' Processing helix chain 'K' and resid 214 through 216 No H-bonds generated for 'chain 'K' and resid 214 through 216' Processing helix chain 'K' and resid 220 through 222 No H-bonds generated for 'chain 'K' and resid 220 through 222' Processing helix chain 'K' and resid 225 through 230 Processing helix chain 'K' and resid 240 through 242 No H-bonds generated for 'chain 'K' and resid 240 through 242' Processing helix chain 'K' and resid 244 through 260 Processing helix chain 'K' and resid 272 through 275 Processing helix chain 'K' and resid 278 through 290 removed outlier: 4.934A pdb=" N LYS K 287 " --> pdb=" O LYS K 283 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N SER K 288 " --> pdb=" O LEU K 284 " (cutoff:3.500A) Processing helix chain 'K' and resid 299 through 306 Processing helix chain 'K' and resid 308 through 316 Processing helix chain 'K' and resid 326 through 329 Processing helix chain 'K' and resid 340 through 346 Proline residue: K 345 - end of helix Processing helix chain 'K' and resid 381 through 383 No H-bonds generated for 'chain 'K' and resid 381 through 383' Processing helix chain 'K' and resid 392 through 406 removed outlier: 3.660A pdb=" N THR K 406 " --> pdb=" O ARG K 402 " (cutoff:3.500A) Processing helix chain 'K' and resid 408 through 411 removed outlier: 3.549A pdb=" N PHE K 411 " --> pdb=" O PRO K 408 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 408 through 411' Processing helix chain 'K' and resid 414 through 433 removed outlier: 3.875A pdb=" N PHE K 423 " --> pdb=" O ARG K 419 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA K 424 " --> pdb=" O GLN K 420 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN K 432 " --> pdb=" O GLY K 428 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N TRP K 433 " --> pdb=" O ILE K 429 " (cutoff:3.500A) Processing helix chain 'K' and resid 444 through 454 Processing helix chain 'K' and resid 457 through 459 No H-bonds generated for 'chain 'K' and resid 457 through 459' Processing helix chain 'L' and resid 77 through 86 removed outlier: 3.774A pdb=" N GLY L 83 " --> pdb=" O PHE L 79 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ARG L 86 " --> pdb=" O ILE L 82 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 126 No H-bonds generated for 'chain 'L' and resid 124 through 126' Processing helix chain 'L' and resid 148 through 155 removed outlier: 3.523A pdb=" N SER L 155 " --> pdb=" O ASP L 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 175 Processing helix chain 'L' and resid 180 through 187 removed outlier: 3.607A pdb=" N TYR L 184 " --> pdb=" O TRP L 181 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY L 185 " --> pdb=" O ARG L 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 199 No H-bonds generated for 'chain 'L' and resid 197 through 199' Processing helix chain 'L' and resid 202 through 207 removed outlier: 3.705A pdb=" N GLU L 207 " --> pdb=" O GLU L 203 " (cutoff:3.500A) Processing helix chain 'L' and resid 211 through 231 Processing helix chain 'L' and resid 238 through 241 No H-bonds generated for 'chain 'L' and resid 238 through 241' Processing helix chain 'L' and resid 247 through 260 Processing helix chain 'L' and resid 330 through 336 Processing helix chain 'L' and resid 359 through 366 Processing helix chain 'L' and resid 390 through 398 Processing helix chain 'L' and resid 411 through 431 Processing helix chain 'L' and resid 436 through 444 Processing helix chain 'L' and resid 451 through 481 Processing helix chain 'M' and resid 138 through 140 No H-bonds generated for 'chain 'M' and resid 138 through 140' Processing helix chain 'M' and resid 233 through 235 No H-bonds generated for 'chain 'M' and resid 233 through 235' Processing helix chain 'M' and resid 277 through 279 No H-bonds generated for 'chain 'M' and resid 277 through 279' Processing helix chain 'M' and resid 296 through 298 No H-bonds generated for 'chain 'M' and resid 296 through 298' Processing helix chain 'M' and resid 302 through 324 removed outlier: 4.306A pdb=" N LYS M 324 " --> pdb=" O LYS M 320 " (cutoff:3.500A) Processing helix chain 'M' and resid 328 through 330 No H-bonds generated for 'chain 'M' and resid 328 through 330' Processing helix chain 'N' and resid 66 through 75 Processing helix chain 'N' and resid 77 through 87 Processing helix chain 'N' and resid 99 through 109 removed outlier: 3.611A pdb=" N ASN N 107 " --> pdb=" O LEU N 103 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ARG N 108 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY N 109 " --> pdb=" O SER N 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 115 through 130 Processing helix chain 'N' and resid 142 through 151 Processing helix chain 'N' and resid 154 through 167 Processing helix chain 'N' and resid 211 through 214 Processing helix chain 'N' and resid 226 through 228 No H-bonds generated for 'chain 'N' and resid 226 through 228' Processing helix chain 'N' and resid 237 through 247 Processing helix chain 'N' and resid 251 through 269 Processing helix chain 'O' and resid 84 through 92 Processing helix chain 'O' and resid 110 through 124 Processing helix chain 'O' and resid 140 through 145 Processing helix chain 'O' and resid 174 through 184 Processing helix chain 'P' and resid 84 through 92 Processing helix chain 'P' and resid 109 through 124 Processing helix chain 'P' and resid 140 through 145 Processing helix chain 'P' and resid 174 through 183 Processing helix chain 'Q' and resid 352 through 360 Processing helix chain 'Q' and resid 541 through 547 removed outlier: 3.956A pdb=" N ASN Q 545 " --> pdb=" O HIS Q 541 " (cutoff:3.500A) Processing helix chain 'Q' and resid 596 through 609 removed outlier: 3.614A pdb=" N ARG Q 607 " --> pdb=" O LEU Q 603 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLU Q 608 " --> pdb=" O ASP Q 604 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU Q 609 " --> pdb=" O SER Q 605 " (cutoff:3.500A) Processing helix chain 'Q' and resid 626 through 639 removed outlier: 4.058A pdb=" N ARG Q 629 " --> pdb=" O ARG Q 626 " (cutoff:3.500A) Proline residue: Q 630 - end of helix Processing helix chain 'Q' and resid 655 through 665 removed outlier: 3.581A pdb=" N LEU Q 663 " --> pdb=" O LEU Q 659 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLY Q 665 " --> pdb=" O ASP Q 661 " (cutoff:3.500A) Processing helix chain 'Q' and resid 670 through 678 Processing helix chain 'Q' and resid 697 through 706 Processing helix chain 'Q' and resid 736 through 745 Processing helix chain 'Q' and resid 747 through 752 removed outlier: 3.682A pdb=" N HIS Q 751 " --> pdb=" O VAL Q 747 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 78 Processing helix chain 'R' and resid 81 through 92 removed outlier: 4.215A pdb=" N SER R 92 " --> pdb=" O ARG R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 113 Processing helix chain 'R' and resid 115 through 117 No H-bonds generated for 'chain 'R' and resid 115 through 117' Processing helix chain 'R' and resid 124 through 136 removed outlier: 3.702A pdb=" N LEU R 136 " --> pdb=" O ARG R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 142 through 144 No H-bonds generated for 'chain 'R' and resid 142 through 144' Processing helix chain 'S' and resid 194 through 196 No H-bonds generated for 'chain 'S' and resid 194 through 196' Processing helix chain 'S' and resid 226 through 231 Processing helix chain 'S' and resid 250 through 260 Processing helix chain 'S' and resid 274 through 285 Processing helix chain 'S' and resid 323 through 325 No H-bonds generated for 'chain 'S' and resid 323 through 325' Processing helix chain 'S' and resid 329 through 331 No H-bonds generated for 'chain 'S' and resid 329 through 331' Processing helix chain 'S' and resid 334 through 339 Processing helix chain 'S' and resid 347 through 350 Processing helix chain 'S' and resid 353 through 368 Processing helix chain 'S' and resid 381 through 384 Processing helix chain 'S' and resid 387 through 400 removed outlier: 5.154A pdb=" N GLU S 396 " --> pdb=" O SER S 392 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL S 397 " --> pdb=" O LEU S 393 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU S 400 " --> pdb=" O GLU S 396 " (cutoff:3.500A) Processing helix chain 'S' and resid 408 through 414 Processing helix chain 'S' and resid 430 through 432 No H-bonds generated for 'chain 'S' and resid 430 through 432' Processing helix chain 'S' and resid 488 through 504 Processing helix chain 'S' and resid 506 through 508 No H-bonds generated for 'chain 'S' and resid 506 through 508' Processing helix chain 'S' and resid 512 through 537 Processing helix chain 'S' and resid 569 through 572 No H-bonds generated for 'chain 'S' and resid 569 through 572' Processing helix chain 'T' and resid 41 through 45 Processing helix chain 'T' and resid 55 through 60 Processing helix chain 'T' and resid 63 through 65 No H-bonds generated for 'chain 'T' and resid 63 through 65' Processing sheet with id= A, first strand: chain 'A' and resid 14 through 22 removed outlier: 6.387A pdb=" N ARG A 31 " --> pdb=" O VAL A 18 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N SER A 20 " --> pdb=" O TYR A 29 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N TYR A 29 " --> pdb=" O SER A 20 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 104 through 111 removed outlier: 3.705A pdb=" N ARG A 64 " --> pdb=" O LYS A 150 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N GLU A 152 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ILE A 62 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN A 154 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N THR A 60 " --> pdb=" O ASN A 154 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 114 through 117 removed outlier: 3.534A pdb=" N ALA A 137 " --> pdb=" O ILE A 116 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 14 through 22 removed outlier: 6.352A pdb=" N ARG B 31 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N SER B 20 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TYR B 29 " --> pdb=" O SER B 20 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 169 through 171 removed outlier: 6.530A pdb=" N LYS B 150 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA B 65 " --> pdb=" O GLY B 148 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N GLY B 148 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N PHE B 67 " --> pdb=" O CYS B 146 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N CYS B 146 " --> pdb=" O PHE B 67 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 110 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 114 through 117 Processing sheet with id= G, first strand: chain 'C' and resid 77 through 80 removed outlier: 3.791A pdb=" N GLY C 102 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 113 through 115 Processing sheet with id= I, first strand: chain 'C' and resid 125 through 128 removed outlier: 3.503A pdb=" N LEU C 127 " --> pdb=" O ARG C 313 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 392 through 394 Processing sheet with id= K, first strand: chain 'C' and resid 451 through 455 removed outlier: 3.530A pdb=" N SER C 452 " --> pdb=" O LEU C 471 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 498 through 503 Processing sheet with id= M, first strand: chain 'C' and resid 604 through 609 removed outlier: 3.751A pdb=" N TYR C 591 " --> pdb=" O ILE C 598 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N SER C 600 " --> pdb=" O ILE C 589 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N ILE C 589 " --> pdb=" O SER C 600 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 852 through 854 removed outlier: 7.552A pdb=" N ILE C 675 " --> pdb=" O SER C 833 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE C 835 " --> pdb=" O ILE C 675 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 687 through 693 removed outlier: 3.575A pdb=" N ASP C 789 " --> pdb=" O TYR C 809 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N SER C 811 " --> pdb=" O VAL C 787 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N VAL C 787 " --> pdb=" O SER C 811 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 1057 through 1060 removed outlier: 4.828A pdb=" N HIS C1057 " --> pdb=" O LYS C1070 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 612 through 615 removed outlier: 5.880A pdb=" N MET C 622 " --> pdb=" O TYR C 613 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 105 through 108 Processing sheet with id= S, first strand: chain 'D' and resid 146 through 148 Processing sheet with id= T, first strand: chain 'D' and resid 475 through 479 removed outlier: 7.504A pdb=" N ILE D 476 " --> pdb=" O ARG D 381 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL D 383 " --> pdb=" O ILE D 476 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU D 478 " --> pdb=" O VAL D 383 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL D 385 " --> pdb=" O LEU D 478 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 579 through 581 removed outlier: 4.078A pdb=" N ILE D 650 " --> pdb=" O TRP D 606 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 226 through 228 Processing sheet with id= W, first strand: chain 'E' and resid 360 through 363 removed outlier: 3.734A pdb=" N LEU E 387 " --> pdb=" O ILE E 402 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 370 through 373 removed outlier: 6.863A pdb=" N VAL E 354 " --> pdb=" O ILE E 422 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 448 through 451 Processing sheet with id= Z, first strand: chain 'E' and resid 467 through 469 Processing sheet with id= AA, first strand: chain 'E' and resid 571 through 573 removed outlier: 3.795A pdb=" N LYS E 571 " --> pdb=" O LEU E 578 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY E 875 " --> pdb=" O ARG E 856 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG E 856 " --> pdb=" O GLY E 875 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 809 through 811 Processing sheet with id= AC, first strand: chain 'E' and resid 924 through 926 Processing sheet with id= AD, first strand: chain 'E' and resid 946 through 949 removed outlier: 6.252A pdb=" N ARG E1102 " --> pdb=" O VAL E1091 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N VAL E1091 " --> pdb=" O ARG E1102 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'E' and resid 1039 through 1042 removed outlier: 3.718A pdb=" N ASN E1047 " --> pdb=" O ASN E1042 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'E' and resid 1248 through 1250 removed outlier: 4.768A pdb=" N LYS E1231 " --> pdb=" O VAL E1270 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'E' and resid 255 through 257 removed outlier: 6.432A pdb=" N ILE E 257 " --> pdb=" O CYS E 261 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N CYS E 261 " --> pdb=" O ILE E 257 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'E' and resid 438 through 443 removed outlier: 3.769A pdb=" N VAL E1130 " --> pdb=" O ILE E 442 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'G' and resid 702 through 704 removed outlier: 6.801A pdb=" N LEU G 745 " --> pdb=" O TRP G 709 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N VAL G 711 " --> pdb=" O LEU G 745 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL G 747 " --> pdb=" O VAL G 711 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'H' and resid 301 through 304 removed outlier: 6.374A pdb=" N ASP H 294 " --> pdb=" O VAL H 282 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N VAL H 282 " --> pdb=" O ASP H 294 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N GLU H 326 " --> pdb=" O PHE H 344 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N PHE H 344 " --> pdb=" O GLU H 326 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'I' and resid 187 through 194 removed outlier: 3.717A pdb=" N ARG I 187 " --> pdb=" O LYS I 182 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU I 181 " --> pdb=" O PRO I 206 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'K' and resid 153 through 157 removed outlier: 6.399A pdb=" N ILE K 233 " --> pdb=" O CYS K 94 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N PHE K 96 " --> pdb=" O ILE K 233 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N HIS K 235 " --> pdb=" O PHE K 96 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU K 263 " --> pdb=" O PHE K 234 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N PHE K 236 " --> pdb=" O LEU K 263 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N PHE K 265 " --> pdb=" O PHE K 236 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ILE K 294 " --> pdb=" O PHE K 266 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU K 353 " --> pdb=" O ILE K 295 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N VAL K 297 " --> pdb=" O LEU K 353 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL K 355 " --> pdb=" O VAL K 297 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'K' and resid 158 through 161 Processing sheet with id= AN, first strand: chain 'K' and resid 195 through 199 removed outlier: 6.012A pdb=" N LYS K 197 " --> pdb=" O THR K 209 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N THR K 209 " --> pdb=" O LYS K 197 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LYS K 199 " --> pdb=" O ALA K 207 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ALA K 207 " --> pdb=" O LYS K 199 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'L' and resid 93 through 97 Processing sheet with id= AP, first strand: chain 'L' and resid 128 through 131 Processing sheet with id= AQ, first strand: chain 'L' and resid 293 through 298 removed outlier: 6.223A pdb=" N SER L 308 " --> pdb=" O VAL L 118 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VAL L 118 " --> pdb=" O SER L 308 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'M' and resid 141 through 145 removed outlier: 6.709A pdb=" N GLU M 168 " --> pdb=" O ARG M 154 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'M' and resid 259 through 262 removed outlier: 6.669A pdb=" N TYR M 200 " --> pdb=" O SER M 225 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL M 227 " --> pdb=" O SER M 198 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N SER M 198 " --> pdb=" O VAL M 227 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU M 229 " --> pdb=" O ALA M 196 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N ALA M 196 " --> pdb=" O LEU M 229 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'M' and resid 265 through 267 removed outlier: 6.741A pdb=" N PHE M 291 " --> pdb=" O LEU M 266 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'N' and resid 200 through 206 removed outlier: 5.902A pdb=" N TYR N 178 " --> pdb=" O PRO N 218 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'O' and resid 129 through 135 removed outlier: 7.796A pdb=" N VAL O 132 " --> pdb=" O PRO O 98 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ILE O 100 " --> pdb=" O VAL O 132 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL O 134 " --> pdb=" O ILE O 100 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP O 102 " --> pdb=" O VAL O 134 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR O 153 " --> pdb=" O PHE O 103 " (cutoff:3.500A) Processing sheet with id= AW, first strand: chain 'P' and resid 129 through 135 removed outlier: 7.680A pdb=" N VAL P 132 " --> pdb=" O PRO P 98 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE P 100 " --> pdb=" O VAL P 132 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL P 134 " --> pdb=" O ILE P 100 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ASP P 102 " --> pdb=" O VAL P 134 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'Q' and resid 586 through 591 removed outlier: 7.436A pdb=" N ASP Q 712 " --> pdb=" O GLY Q 587 " (cutoff:3.500A) removed outlier: 9.048A pdb=" N ILE Q 589 " --> pdb=" O ASP Q 712 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL Q 714 " --> pdb=" O ILE Q 589 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N ASP Q 591 " --> pdb=" O VAL Q 714 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL Q 716 " --> pdb=" O ASP Q 591 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL Q 642 " --> pdb=" O THR Q 616 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N ILE Q 618 " --> pdb=" O VAL Q 642 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N MET Q 644 " --> pdb=" O ILE Q 618 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain 'Q' and resid 724 through 727 Processing sheet with id= AZ, first strand: chain 'S' and resid 263 through 267 removed outlier: 6.678A pdb=" N MET S 342 " --> pdb=" O CYS S 204 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE S 206 " --> pdb=" O MET S 342 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TYR S 344 " --> pdb=" O PHE S 206 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL S 372 " --> pdb=" O PHE S 343 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N PHE S 345 " --> pdb=" O VAL S 372 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE S 374 " --> pdb=" O PHE S 345 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL S 403 " --> pdb=" O TYR S 375 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE S 451 " --> pdb=" O ILE S 404 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N VAL S 406 " --> pdb=" O ILE S 451 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N PHE S 453 " --> pdb=" O VAL S 406 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'S' and resid 268 through 271 Processing sheet with id= BB, first strand: chain 'T' and resid 68 through 71 removed outlier: 3.879A pdb=" N GLU T 90 " --> pdb=" O SER T 129 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ARG T 131 " --> pdb=" O ILE T 88 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ILE T 88 " --> pdb=" O ARG T 131 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N CYS T 133 " --> pdb=" O VAL T 86 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N VAL T 86 " --> pdb=" O CYS T 133 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LYS T 135 " --> pdb=" O GLN T 84 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N GLN T 84 " --> pdb=" O LYS T 135 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain 'T' and resid 75 through 80 removed outlier: 3.727A pdb=" N TRP T 78 " --> pdb=" O ALA T 120 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA T 120 " --> pdb=" O TRP T 78 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL T 93 " --> pdb=" O PHE T 106 " (cutoff:3.500A) 1996 hydrogen bonds defined for protein. 5610 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 97 hydrogen bonds 194 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 56 stacking parallelities Total time for adding SS restraints: 19.64 Time building geometry restraints manager: 19.09 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: 18400 1.34 - 1.46: 10543 1.46 - 1.58: 28952 1.58 - 1.70: 157 1.70 - 1.82: 444 Bond restraints: 58496 Sorted by residual: bond pdb=" C2 SAH L8001 " pdb=" N3 SAH L8001 " ideal model delta sigma weight residual 1.322 1.380 -0.058 2.00e-02 2.50e+03 8.37e+00 bond pdb=" C8 SAH L8001 " pdb=" N7 SAH L8001 " ideal model delta sigma weight residual 1.299 1.351 -0.052 2.00e-02 2.50e+03 6.88e+00 bond pdb=" C2 SAH L8001 " pdb=" N1 SAH L8001 " ideal model delta sigma weight residual 1.330 1.379 -0.049 2.00e-02 2.50e+03 6.09e+00 bond pdb=" C6 SAH L8001 " pdb=" N1 SAH L8001 " ideal model delta sigma weight residual 1.338 1.377 -0.039 2.00e-02 2.50e+03 3.75e+00 bond pdb=" CG ARG H 519 " pdb=" CD ARG H 519 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.10e+00 ... (remaining 58491 not shown) Histogram of bond angle deviations from ideal: 90.72 - 99.41: 8 99.41 - 108.09: 3251 108.09 - 116.77: 37497 116.77 - 125.45: 37396 125.45 - 134.13: 1267 Bond angle restraints: 79419 Sorted by residual: angle pdb=" CA GLU F 365 " pdb=" CB GLU F 365 " pdb=" CG GLU F 365 " ideal model delta sigma weight residual 114.10 123.74 -9.64 2.00e+00 2.50e-01 2.32e+01 angle pdb=" C CYS G 599 " pdb=" N MET G 600 " pdb=" CA MET G 600 " ideal model delta sigma weight residual 121.58 113.10 8.48 1.95e+00 2.63e-01 1.89e+01 angle pdb=" CG SAH L8001 " pdb=" SD SAH L8001 " pdb=" C5' SAH L8001 " ideal model delta sigma weight residual 101.77 90.72 11.05 3.00e+00 1.11e-01 1.36e+01 angle pdb=" N GLU F 365 " pdb=" CA GLU F 365 " pdb=" CB GLU F 365 " ideal model delta sigma weight residual 114.27 108.63 5.64 1.64e+00 3.72e-01 1.18e+01 angle pdb=" CB LYS Q 675 " pdb=" CG LYS Q 675 " pdb=" CD LYS Q 675 " ideal model delta sigma weight residual 111.30 119.01 -7.71 2.30e+00 1.89e-01 1.12e+01 ... (remaining 79414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.48: 32453 27.48 - 54.96: 2332 54.96 - 82.45: 267 82.45 - 109.93: 30 109.93 - 137.41: 1 Dihedral angle restraints: 35083 sinusoidal: 15256 harmonic: 19827 Sorted by residual: dihedral pdb=" CA ILE E1182 " pdb=" C ILE E1182 " pdb=" N PRO E1183 " pdb=" CA PRO E1183 " ideal model delta harmonic sigma weight residual 180.00 -141.18 -38.82 0 5.00e+00 4.00e-02 6.03e+01 dihedral pdb=" CA LEU S 314 " pdb=" C LEU S 314 " pdb=" N LYS S 315 " pdb=" CA LYS S 315 " ideal model delta harmonic sigma weight residual 180.00 157.12 22.88 0 5.00e+00 4.00e-02 2.09e+01 dihedral pdb=" CA ASP L 246 " pdb=" C ASP L 246 " pdb=" N ALA L 247 " pdb=" CA ALA L 247 " ideal model delta harmonic sigma weight residual -180.00 -157.85 -22.15 0 5.00e+00 4.00e-02 1.96e+01 ... (remaining 35080 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 6402 0.041 - 0.082: 1561 0.082 - 0.123: 611 0.123 - 0.164: 34 0.164 - 0.205: 4 Chirality restraints: 8612 Sorted by residual: chirality pdb=" CA PRO E1183 " pdb=" N PRO E1183 " pdb=" C PRO E1183 " pdb=" CB PRO E1183 " both_signs ideal model delta sigma weight residual False 2.72 2.51 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CG LEU G 497 " pdb=" CB LEU G 497 " pdb=" CD1 LEU G 497 " pdb=" CD2 LEU G 497 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" CA MET G 600 " pdb=" N MET G 600 " pdb=" C MET G 600 " pdb=" CB MET G 600 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.88e-01 ... (remaining 8609 not shown) Planarity restraints: 9969 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 625 " 0.074 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO C 626 " -0.191 5.00e-02 4.00e+02 pdb=" CA PRO C 626 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO C 626 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 365 " 0.016 2.00e-02 2.50e+03 3.24e-02 1.05e+01 pdb=" C GLU F 365 " -0.056 2.00e-02 2.50e+03 pdb=" O GLU F 365 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP F 366 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 652 " -0.017 2.00e-02 2.50e+03 1.50e-02 4.49e+00 pdb=" CG TYR G 652 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TYR G 652 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR G 652 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR G 652 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR G 652 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR G 652 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR G 652 " -0.002 2.00e-02 2.50e+03 ... (remaining 9966 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 590 2.56 - 3.15: 44247 3.15 - 3.73: 94086 3.73 - 4.32: 135794 4.32 - 4.90: 218293 Nonbonded interactions: 493010 Sorted by model distance: nonbonded pdb=" OD1 ASP D 491 " pdb="MG MG D 701 " model vdw 1.980 2.170 nonbonded pdb=" OD1 ASP D 489 " pdb="MG MG D 701 " model vdw 1.996 2.170 nonbonded pdb=" OD1 ASP D 493 " pdb="MG MG D 701 " model vdw 2.049 2.170 nonbonded pdb=" OD2 ASP I 211 " pdb="FE FE I8001 " model vdw 2.070 2.260 nonbonded pdb=" OD2 ASP N 223 " pdb="FE FE N8001 " model vdw 2.097 2.260 ... (remaining 493005 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 'O' and resid 78 through 185) selection = chain 'P' } 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=1.00 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: 7.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 44.410 Check model and map are aligned: 0.650 Set scattering table: 0.390 Process input model: 130.460 Find NCS groups from input model: 1.520 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 197.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 0.073 58496 Z= 0.171 Angle : 0.514 11.046 79419 Z= 0.265 Chirality : 0.041 0.205 8612 Planarity : 0.004 0.111 9969 Dihedral : 17.476 137.411 22279 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.05 % Favored : 96.89 % Rotamer: Outliers : 0.93 % Allowed : 19.19 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: 0.61 (0.10), residues: 6685 helix: 1.08 (0.10), residues: 2752 sheet: 0.24 (0.17), residues: 868 loop : -0.05 (0.11), residues: 3065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP H 517 HIS 0.005 0.001 HIS F 344 PHE 0.017 0.001 PHE I 172 TYR 0.037 0.001 TYR G 652 ARG 0.015 0.000 ARG C 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 997 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 941 time to evaluate : 4.899 Fit side-chains revert: symmetry clash REVERT: A 74 TYR cc_start: 0.7691 (m-80) cc_final: 0.7428 (m-80) REVERT: A 141 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8296 (pt0) REVERT: A 143 ILE cc_start: 0.7894 (mp) cc_final: 0.7471 (tp) REVERT: A 289 LYS cc_start: 0.7724 (ptpp) cc_final: 0.7518 (ptpp) REVERT: B 86 GLU cc_start: 0.8498 (mm-30) cc_final: 0.7815 (tm-30) REVERT: B 150 LYS cc_start: 0.8315 (ttpt) cc_final: 0.7831 (tppp) REVERT: C 506 GLU cc_start: 0.7292 (pm20) cc_final: 0.7073 (pm20) REVERT: C 612 MET cc_start: 0.7316 (mtm) cc_final: 0.6999 (mtm) REVERT: C 614 GLN cc_start: 0.7756 (mm-40) cc_final: 0.7535 (mm110) REVERT: C 729 MET cc_start: 0.6612 (mtm) cc_final: 0.6188 (mtp) REVERT: C 940 GLN cc_start: 0.8777 (mm110) cc_final: 0.8473 (mm110) REVERT: C 977 ARG cc_start: 0.8193 (ttt180) cc_final: 0.7859 (ttt90) REVERT: C 1020 GLU cc_start: 0.7578 (mm-30) cc_final: 0.7297 (mp0) REVERT: C 1035 GLU cc_start: 0.7809 (tt0) cc_final: 0.7592 (mt-10) REVERT: D 349 HIS cc_start: 0.7612 (m170) cc_final: 0.7381 (m170) REVERT: E 405 LYS cc_start: 0.8056 (mmmt) cc_final: 0.7698 (mmtm) REVERT: E 572 ARG cc_start: 0.7071 (ttm170) cc_final: 0.6705 (ttm170) REVERT: E 804 GLU cc_start: 0.7235 (mt-10) cc_final: 0.6734 (pt0) REVERT: E 841 LEU cc_start: 0.7258 (tt) cc_final: 0.6950 (pt) REVERT: E 1151 GLN cc_start: 0.8477 (tt0) cc_final: 0.8248 (pt0) REVERT: E 1182 ILE cc_start: 0.7555 (pp) cc_final: 0.7113 (pt) REVERT: F 407 ARG cc_start: 0.7544 (tpt170) cc_final: 0.7289 (tpm-80) REVERT: G 643 ASP cc_start: 0.7504 (m-30) cc_final: 0.7223 (m-30) REVERT: G 658 ASN cc_start: 0.6974 (t0) cc_final: 0.6745 (t0) REVERT: G 694 LYS cc_start: 0.6366 (pttt) cc_final: 0.5594 (tppt) REVERT: H 525 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8037 (tp30) REVERT: H 535 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7749 (mp10) REVERT: I 141 MET cc_start: 0.6708 (mmm) cc_final: 0.6476 (tpp) REVERT: I 143 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7421 (tp) REVERT: I 146 VAL cc_start: 0.8152 (t) cc_final: 0.7939 (m) REVERT: J 274 LYS cc_start: 0.8570 (mmmm) cc_final: 0.8369 (tptp) REVERT: J 416 MET cc_start: 0.9062 (tpt) cc_final: 0.8822 (tpt) REVERT: K 314 ARG cc_start: 0.7828 (ttp80) cc_final: 0.7605 (ttp80) REVERT: K 410 MET cc_start: 0.7997 (mtp) cc_final: 0.7786 (mtp) REVERT: L 192 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7960 (p0) REVERT: L 463 ARG cc_start: 0.8399 (ttt180) cc_final: 0.8159 (ttt-90) REVERT: M 169 MET cc_start: 0.8262 (mtp) cc_final: 0.7890 (mtm) REVERT: M 176 THR cc_start: 0.8750 (m) cc_final: 0.8462 (p) REVERT: N 64 MET cc_start: 0.6449 (ttt) cc_final: 0.6232 (mtp) REVERT: O 94 GLU cc_start: 0.7952 (tp30) cc_final: 0.7573 (tp30) REVERT: Q 632 MET cc_start: 0.4842 (mpt) cc_final: 0.4339 (mtm) REVERT: R 113 LYS cc_start: 0.8259 (mttp) cc_final: 0.8059 (ttmm) outliers start: 56 outliers final: 29 residues processed: 987 average time/residue: 1.5339 time to fit residues: 1882.7709 Evaluate side-chains 795 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 762 time to evaluate : 4.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain C residue 659 VAL Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 515 SER Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain G residue 480 THR Chi-restraints excluded: chain G residue 579 CYS Chi-restraints excluded: chain G residue 708 VAL Chi-restraints excluded: chain G residue 711 VAL Chi-restraints excluded: chain H residue 516 HIS Chi-restraints excluded: chain H residue 525 GLU Chi-restraints excluded: chain H residue 535 GLN Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain J residue 335 THR Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain N residue 63 HIS Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain Q residue 579 LEU Chi-restraints excluded: chain Q residue 595 THR Chi-restraints excluded: chain Q residue 633 THR Chi-restraints excluded: chain Q residue 669 THR Chi-restraints excluded: chain S residue 273 ASP Chi-restraints excluded: chain S residue 334 VAL Chi-restraints excluded: chain T residue 133 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 682 random chunks: chunk 575 optimal weight: 0.2980 chunk 516 optimal weight: 4.9990 chunk 286 optimal weight: 9.9990 chunk 176 optimal weight: 10.0000 chunk 348 optimal weight: 6.9990 chunk 276 optimal weight: 8.9990 chunk 534 optimal weight: 10.0000 chunk 206 optimal weight: 5.9990 chunk 325 optimal weight: 4.9990 chunk 397 optimal weight: 40.0000 chunk 619 optimal weight: 4.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 ASN A 193 ASN A 276 GLN A 303 GLN B 14 GLN B 76 ASN B 196 GLN C 17 GLN C 58 GLN C 116 ASN C 124 ASN C 128 GLN C 414 HIS C 516 HIS C 542 ASN C 623 HIS C 624 GLN C 812 GLN C 867 GLN C 883 HIS C 974 GLN C 982 GLN C1014 HIS C1057 HIS C1068 ASN D 128 ASN D 464 GLN D 518 ASN D 674 GLN E 49 GLN E 90 ASN E 378 HIS E1020 HIS E1038 ASN E1053 GLN E1151 GLN E1291 GLN F 84 ASN F 270 ASN F 363 ASN F 788 GLN ** G 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 628 ASN G 630 HIS ** G 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 ASN I 149 GLN I 171 GLN I 223 ASN J 329 GLN J 415 ASN K 110 HIS K 112 ASN K 328 GLN K 414 GLN L 220 GLN L 233 HIS M 142 HIS M 190 GLN N 107 ASN ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 183 ASN P 88 GLN Q 745 GLN R 71 GLN S 195 HIS S 284 ASN S 371 ASN S 395 GLN S 562 ASN T 81 GLN T 84 GLN Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 58496 Z= 0.387 Angle : 0.611 10.533 79419 Z= 0.320 Chirality : 0.046 0.254 8612 Planarity : 0.005 0.075 9969 Dihedral : 11.611 136.654 8481 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.72 % Favored : 96.22 % Rotamer: Outliers : 4.15 % Allowed : 18.16 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: 0.34 (0.10), residues: 6685 helix: 0.87 (0.10), residues: 2775 sheet: 0.14 (0.17), residues: 832 loop : -0.23 (0.11), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP G 678 HIS 0.014 0.001 HIS F 487 PHE 0.028 0.002 PHE B 226 TYR 0.032 0.002 TYR G 652 ARG 0.010 0.001 ARG S 231 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1034 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 784 time to evaluate : 4.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLN cc_start: 0.7626 (OUTLIER) cc_final: 0.7327 (tt0) REVERT: A 196 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8444 (mt0) REVERT: B 119 ARG cc_start: 0.7902 (ttm110) cc_final: 0.7680 (ttp80) REVERT: C 313 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7305 (ptp90) REVERT: C 471 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8611 (mp) REVERT: C 506 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7418 (pm20) REVERT: C 596 LYS cc_start: 0.7759 (OUTLIER) cc_final: 0.7385 (pttt) REVERT: C 977 ARG cc_start: 0.8356 (ttt180) cc_final: 0.7896 (ttt90) REVERT: C 1020 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7194 (mp0) REVERT: C 1063 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8214 (mmpt) REVERT: D 98 ARG cc_start: 0.6570 (OUTLIER) cc_final: 0.4453 (pmt170) REVERT: D 147 PHE cc_start: 0.7571 (t80) cc_final: 0.7241 (t80) REVERT: D 442 GLN cc_start: 0.8537 (OUTLIER) cc_final: 0.8321 (pp30) REVERT: D 666 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8121 (tm-30) REVERT: E 574 ARG cc_start: 0.7100 (ttm110) cc_final: 0.6484 (ttp-170) REVERT: E 804 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6731 (pt0) REVERT: E 841 LEU cc_start: 0.7107 (tt) cc_final: 0.6858 (pt) REVERT: E 1005 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7349 (mtpm) REVERT: E 1150 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8754 (tt0) REVERT: F 85 ARG cc_start: 0.8115 (mpp80) cc_final: 0.7910 (mpp80) REVERT: F 203 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8152 (mpt-90) REVERT: F 407 ARG cc_start: 0.7706 (tpt170) cc_final: 0.7358 (tpm-80) REVERT: F 488 ARG cc_start: 0.6483 (OUTLIER) cc_final: 0.4753 (mmp-170) REVERT: G 596 MET cc_start: 0.5615 (mpm) cc_final: 0.5268 (mtm) REVERT: G 658 ASN cc_start: 0.7287 (t0) cc_final: 0.7043 (t0) REVERT: H 279 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8055 (tp30) REVERT: I 95 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7222 (ttm-80) REVERT: I 143 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7456 (tp) REVERT: I 153 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.6725 (m-30) REVERT: J 261 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8780 (mtmp) REVERT: J 274 LYS cc_start: 0.8585 (mmmm) cc_final: 0.8364 (tptp) REVERT: J 317 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8526 (ptpp) REVERT: L 432 TYR cc_start: 0.7866 (m-10) cc_final: 0.7395 (m-10) REVERT: L 463 ARG cc_start: 0.8371 (ttt180) cc_final: 0.8143 (ttt-90) REVERT: M 176 THR cc_start: 0.8754 (m) cc_final: 0.8313 (p) REVERT: M 191 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7198 (tttt) REVERT: O 94 GLU cc_start: 0.7939 (tp30) cc_final: 0.7585 (tp30) REVERT: O 160 ASP cc_start: 0.7711 (t0) cc_final: 0.7377 (t0) REVERT: P 90 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7657 (mm) REVERT: R 57 MET cc_start: 0.8961 (ttm) cc_final: 0.8744 (mtp) REVERT: S 229 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.8444 (tt0) REVERT: T 135 LYS cc_start: 0.7593 (mmmt) cc_final: 0.7120 (mmmm) outliers start: 250 outliers final: 83 residues processed: 945 average time/residue: 1.4430 time to fit residues: 1714.8117 Evaluate side-chains 828 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 722 time to evaluate : 4.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain C residue 74 LEU Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 505 GLN Chi-restraints excluded: chain C residue 506 GLU Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 923 TYR Chi-restraints excluded: chain C residue 939 GLU Chi-restraints excluded: chain C residue 956 VAL Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain C residue 1063 LYS Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 442 GLN Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain D residue 645 LYS Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 425 ILE Chi-restraints excluded: chain E residue 928 PHE Chi-restraints excluded: chain E residue 945 ASN Chi-restraints excluded: chain E residue 1005 LYS Chi-restraints excluded: chain E residue 1150 GLU Chi-restraints excluded: chain E residue 1164 ASN Chi-restraints excluded: chain E residue 1177 THR Chi-restraints excluded: chain E residue 1201 LEU Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 203 ARG Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 416 TRP Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 804 GLU Chi-restraints excluded: chain F residue 836 THR Chi-restraints excluded: chain G residue 517 VAL Chi-restraints excluded: chain G residue 527 THR Chi-restraints excluded: chain G residue 533 GLU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 551 MET Chi-restraints excluded: chain G residue 579 CYS Chi-restraints excluded: chain G residue 732 LEU Chi-restraints excluded: chain G residue 822 THR Chi-restraints excluded: chain H residue 279 GLU Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain H residue 516 HIS Chi-restraints excluded: chain H residue 525 GLU Chi-restraints excluded: chain H residue 527 LEU Chi-restraints excluded: chain I residue 95 ARG Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 197 ILE Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain J residue 261 LYS Chi-restraints excluded: chain J residue 317 LYS Chi-restraints excluded: chain J residue 335 THR Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain K residue 210 VAL Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain K residue 390 THR Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain M residue 136 ILE Chi-restraints excluded: chain M residue 191 LYS Chi-restraints excluded: chain N residue 63 HIS Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain P residue 89 ASP Chi-restraints excluded: chain P residue 90 LEU Chi-restraints excluded: chain P residue 120 MET Chi-restraints excluded: chain P residue 141 GLU Chi-restraints excluded: chain Q residue 595 THR Chi-restraints excluded: chain Q residue 618 ILE Chi-restraints excluded: chain Q residue 633 THR Chi-restraints excluded: chain Q residue 643 THR Chi-restraints excluded: chain Q residue 713 MET Chi-restraints excluded: chain Q residue 715 VAL Chi-restraints excluded: chain Q residue 723 SER Chi-restraints excluded: chain Q residue 757 THR Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain R residue 114 ASN Chi-restraints excluded: chain R residue 121 THR Chi-restraints excluded: chain S residue 229 GLN Chi-restraints excluded: chain S residue 272 ASP Chi-restraints excluded: chain S residue 273 ASP Chi-restraints excluded: chain S residue 389 GLU Chi-restraints excluded: chain S residue 575 SER Chi-restraints excluded: chain T residue 122 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 682 random chunks: chunk 344 optimal weight: 7.9990 chunk 192 optimal weight: 1.9990 chunk 515 optimal weight: 6.9990 chunk 421 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 620 optimal weight: 0.6980 chunk 670 optimal weight: 8.9990 chunk 552 optimal weight: 20.0000 chunk 615 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 chunk 497 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 GLN C 124 ASN ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN C 551 GLN C 982 GLN C1068 ASN E 87 HIS ** G 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 409 GLN ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 149 GLN I 171 GLN I 223 ASN M 161 ASN ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 88 GLN ** T 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 58496 Z= 0.276 Angle : 0.541 13.159 79419 Z= 0.282 Chirality : 0.043 0.175 8612 Planarity : 0.004 0.059 9969 Dihedral : 11.560 142.805 8462 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.26 % Favored : 96.68 % Rotamer: Outliers : 3.97 % Allowed : 18.82 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: 0.46 (0.10), residues: 6685 helix: 1.02 (0.10), residues: 2777 sheet: 0.19 (0.17), residues: 842 loop : -0.22 (0.11), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 127 HIS 0.010 0.001 HIS F 487 PHE 0.021 0.001 PHE B 226 TYR 0.024 0.001 TYR G 652 ARG 0.009 0.000 ARG H 519 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1005 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 766 time to evaluate : 4.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7259 (tt0) REVERT: B 119 ARG cc_start: 0.7970 (ttm110) cc_final: 0.7744 (ttp80) REVERT: C 313 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7324 (ptp90) REVERT: C 478 TYR cc_start: 0.8076 (m-80) cc_final: 0.7820 (m-80) REVERT: C 596 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7393 (pttt) REVERT: C 1020 GLU cc_start: 0.7627 (mm-30) cc_final: 0.7326 (mp0) REVERT: C 1063 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8233 (mmpt) REVERT: D 14 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8345 (tt) REVERT: D 147 PHE cc_start: 0.7575 (t80) cc_final: 0.7227 (t80) REVERT: D 442 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8349 (pp30) REVERT: D 595 ARG cc_start: 0.8342 (mtt-85) cc_final: 0.8031 (mtt-85) REVERT: D 663 ARG cc_start: 0.8419 (OUTLIER) cc_final: 0.7604 (mmm160) REVERT: D 666 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.8069 (tm-30) REVERT: E 804 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6908 (pt0) REVERT: E 841 LEU cc_start: 0.6999 (tt) cc_final: 0.6794 (pt) REVERT: E 1150 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8641 (tt0) REVERT: F 203 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8139 (mpt-90) REVERT: F 206 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8891 (mtm) REVERT: F 407 ARG cc_start: 0.7760 (tpt170) cc_final: 0.7437 (tpm-80) REVERT: F 418 GLU cc_start: 0.5686 (OUTLIER) cc_final: 0.5437 (pt0) REVERT: F 488 ARG cc_start: 0.6489 (OUTLIER) cc_final: 0.4708 (mmp-170) REVERT: G 621 MET cc_start: 0.6025 (tpt) cc_final: 0.5648 (tmt) REVERT: G 658 ASN cc_start: 0.7310 (t0) cc_final: 0.7015 (t0) REVERT: H 542 GLU cc_start: 0.7571 (OUTLIER) cc_final: 0.7093 (mt-10) REVERT: I 143 ILE cc_start: 0.7812 (OUTLIER) cc_final: 0.7521 (tp) REVERT: I 153 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.6748 (m-30) REVERT: I 227 LYS cc_start: 0.7138 (OUTLIER) cc_final: 0.6576 (ptmt) REVERT: I 243 MET cc_start: 0.8104 (tpp) cc_final: 0.7688 (mmt) REVERT: J 274 LYS cc_start: 0.8526 (mmmm) cc_final: 0.8269 (mmmt) REVERT: J 329 GLN cc_start: 0.8918 (tp-100) cc_final: 0.8671 (tp40) REVERT: K 312 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7170 (tm-30) REVERT: L 444 ASP cc_start: 0.8286 (OUTLIER) cc_final: 0.8059 (m-30) REVERT: M 191 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7177 (tttt) REVERT: N 268 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.6727 (mtp180) REVERT: O 94 GLU cc_start: 0.7919 (tp30) cc_final: 0.7579 (tp30) REVERT: O 141 GLU cc_start: 0.8186 (mp0) cc_final: 0.7892 (pm20) REVERT: Q 632 MET cc_start: 0.5302 (mpt) cc_final: 0.4427 (mtm) REVERT: S 229 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8424 (tt0) outliers start: 239 outliers final: 77 residues processed: 914 average time/residue: 1.4887 time to fit residues: 1699.7712 Evaluate side-chains 828 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 729 time to evaluate : 4.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 CYS Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 505 GLN Chi-restraints excluded: chain C residue 506 GLU Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 923 TYR Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain C residue 1063 LYS Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 442 GLN Chi-restraints excluded: chain D residue 515 SER Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain D residue 645 LYS Chi-restraints excluded: chain D residue 663 ARG Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 808 ILE Chi-restraints excluded: chain E residue 945 ASN Chi-restraints excluded: chain E residue 995 LEU Chi-restraints excluded: chain E residue 1003 VAL Chi-restraints excluded: chain E residue 1056 ASN Chi-restraints excluded: chain E residue 1150 GLU Chi-restraints excluded: chain E residue 1164 ASN Chi-restraints excluded: chain E residue 1177 THR Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 203 ARG Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 836 THR Chi-restraints excluded: chain G residue 517 VAL Chi-restraints excluded: chain G residue 527 THR Chi-restraints excluded: chain G residue 533 GLU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 579 CYS Chi-restraints excluded: chain G residue 711 VAL Chi-restraints excluded: chain G residue 732 LEU Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 516 HIS Chi-restraints excluded: chain H residue 525 GLU Chi-restraints excluded: chain H residue 527 LEU Chi-restraints excluded: chain H residue 542 GLU Chi-restraints excluded: chain I residue 143 ILE Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 220 ASP Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain J residue 335 THR Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain K residue 257 SER Chi-restraints excluded: chain K residue 312 GLU Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 444 ASP Chi-restraints excluded: chain M residue 136 ILE Chi-restraints excluded: chain M residue 191 LYS Chi-restraints excluded: chain M residue 329 SER Chi-restraints excluded: chain N residue 63 HIS Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 238 ILE Chi-restraints excluded: chain N residue 268 ARG Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain P residue 120 MET Chi-restraints excluded: chain Q residue 595 THR Chi-restraints excluded: chain Q residue 605 SER Chi-restraints excluded: chain Q residue 643 THR Chi-restraints excluded: chain Q residue 713 MET Chi-restraints excluded: chain Q residue 715 VAL Chi-restraints excluded: chain Q residue 757 THR Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain R residue 114 ASN Chi-restraints excluded: chain R residue 121 THR Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain S residue 229 GLN Chi-restraints excluded: chain S residue 272 ASP Chi-restraints excluded: chain S residue 273 ASP Chi-restraints excluded: chain S residue 297 SER Chi-restraints excluded: chain T residue 85 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 682 random chunks: chunk 613 optimal weight: 30.0000 chunk 466 optimal weight: 0.7980 chunk 322 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 296 optimal weight: 1.9990 chunk 416 optimal weight: 0.9990 chunk 622 optimal weight: 3.9990 chunk 659 optimal weight: 4.9990 chunk 325 optimal weight: 1.9990 chunk 590 optimal weight: 6.9990 chunk 177 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 ASN ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN C1068 ASN E1151 GLN E1206 GLN E1291 GLN F 158 GLN ** G 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 640 ASN ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 149 GLN I 166 ASN ** I 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 223 ASN ** I 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 88 GLN S 510 ASN ** T 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 58496 Z= 0.211 Angle : 0.518 15.517 79419 Z= 0.269 Chirality : 0.042 0.191 8612 Planarity : 0.004 0.051 9969 Dihedral : 11.475 144.773 8459 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.50 % Favored : 96.44 % Rotamer: Outliers : 3.59 % Allowed : 19.70 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: 0.57 (0.10), residues: 6685 helix: 1.14 (0.10), residues: 2785 sheet: 0.18 (0.17), residues: 867 loop : -0.18 (0.11), residues: 3033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP T 69 HIS 0.008 0.001 HIS F 487 PHE 0.018 0.001 PHE B 226 TYR 0.019 0.001 TYR C1010 ARG 0.008 0.000 ARG H 519 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 975 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 759 time to evaluate : 4.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7236 (tt0) REVERT: B 119 ARG cc_start: 0.7972 (ttm110) cc_final: 0.7760 (ttp80) REVERT: C 313 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7313 (ptp90) REVERT: C 478 TYR cc_start: 0.8041 (m-80) cc_final: 0.7771 (m-80) REVERT: C 596 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7388 (pttt) REVERT: C 1020 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7322 (mp0) REVERT: C 1063 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8250 (mmpt) REVERT: D 98 ARG cc_start: 0.6618 (OUTLIER) cc_final: 0.4392 (pmt170) REVERT: D 188 ARG cc_start: 0.7184 (tpt-90) cc_final: 0.6747 (ttt90) REVERT: D 349 HIS cc_start: 0.7667 (m170) cc_final: 0.7442 (m-70) REVERT: D 442 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8359 (pp30) REVERT: D 595 ARG cc_start: 0.8353 (mtt-85) cc_final: 0.8009 (mtt-85) REVERT: D 663 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7580 (mmm160) REVERT: D 666 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8032 (tm-30) REVERT: E 84 LYS cc_start: 0.8593 (mmmt) cc_final: 0.8377 (tptm) REVERT: E 804 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6912 (pt0) REVERT: F 167 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.8402 (ttt) REVERT: F 203 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8050 (mpt-90) REVERT: F 206 MET cc_start: 0.9117 (OUTLIER) cc_final: 0.8863 (mtm) REVERT: F 407 ARG cc_start: 0.7740 (tpt170) cc_final: 0.7502 (tpm-80) REVERT: F 418 GLU cc_start: 0.5701 (OUTLIER) cc_final: 0.5412 (pt0) REVERT: G 596 MET cc_start: 0.5632 (mpm) cc_final: 0.5336 (mtm) REVERT: G 621 MET cc_start: 0.6003 (tpt) cc_final: 0.5724 (tmt) REVERT: G 658 ASN cc_start: 0.7366 (t0) cc_final: 0.7079 (t0) REVERT: H 200 GLU cc_start: 0.6588 (mp0) cc_final: 0.6367 (mp0) REVERT: H 474 LEU cc_start: 0.4464 (OUTLIER) cc_final: 0.4264 (pt) REVERT: H 542 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7066 (mt-10) REVERT: I 153 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.6782 (m-30) REVERT: I 227 LYS cc_start: 0.7129 (OUTLIER) cc_final: 0.6574 (ptmt) REVERT: I 243 MET cc_start: 0.7997 (tpp) cc_final: 0.7652 (mmt) REVERT: J 274 LYS cc_start: 0.8497 (mmmm) cc_final: 0.8274 (mmmt) REVERT: K 312 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7129 (tm-30) REVERT: M 191 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7127 (tttt) REVERT: N 110 ASN cc_start: 0.8032 (OUTLIER) cc_final: 0.7618 (p0) REVERT: N 268 ARG cc_start: 0.7066 (OUTLIER) cc_final: 0.6677 (mtp-110) REVERT: O 94 GLU cc_start: 0.7912 (tp30) cc_final: 0.7589 (tp30) REVERT: O 141 GLU cc_start: 0.8191 (mp0) cc_final: 0.7890 (pm20) REVERT: S 229 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8406 (tt0) REVERT: T 89 GLU cc_start: 0.7246 (pm20) cc_final: 0.6678 (pm20) outliers start: 216 outliers final: 82 residues processed: 897 average time/residue: 1.5213 time to fit residues: 1700.0746 Evaluate side-chains 829 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 726 time to evaluate : 4.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 505 GLN Chi-restraints excluded: chain C residue 506 GLU Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 923 TYR Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain C residue 1063 LYS Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 442 GLN Chi-restraints excluded: chain D residue 515 SER Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain D residue 645 LYS Chi-restraints excluded: chain D residue 663 ARG Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain D residue 673 SER Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 358 TYR Chi-restraints excluded: chain E residue 576 ARG Chi-restraints excluded: chain E residue 901 MET Chi-restraints excluded: chain E residue 945 ASN Chi-restraints excluded: chain E residue 995 LEU Chi-restraints excluded: chain E residue 997 THR Chi-restraints excluded: chain E residue 1056 ASN Chi-restraints excluded: chain E residue 1177 THR Chi-restraints excluded: chain E residue 1361 ILE Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 203 ARG Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 416 TRP Chi-restraints excluded: chain F residue 418 GLU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 836 THR Chi-restraints excluded: chain G residue 463 GLU Chi-restraints excluded: chain G residue 527 THR Chi-restraints excluded: chain G residue 533 GLU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 579 CYS Chi-restraints excluded: chain G residue 711 VAL Chi-restraints excluded: chain G residue 732 LEU Chi-restraints excluded: chain G residue 822 THR Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 474 LEU Chi-restraints excluded: chain H residue 516 HIS Chi-restraints excluded: chain H residue 527 LEU Chi-restraints excluded: chain H residue 542 GLU Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 220 ASP Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain J residue 335 THR Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain K residue 312 GLU Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 392 SER Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain M residue 136 ILE Chi-restraints excluded: chain M residue 191 LYS Chi-restraints excluded: chain M residue 329 SER Chi-restraints excluded: chain N residue 63 HIS Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 110 ASN Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 268 ARG Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain P residue 120 MET Chi-restraints excluded: chain Q residue 595 THR Chi-restraints excluded: chain Q residue 633 THR Chi-restraints excluded: chain Q residue 643 THR Chi-restraints excluded: chain Q residue 757 THR Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain R residue 114 ASN Chi-restraints excluded: chain R residue 121 THR Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain S residue 229 GLN Chi-restraints excluded: chain S residue 272 ASP Chi-restraints excluded: chain S residue 273 ASP Chi-restraints excluded: chain S residue 297 SER Chi-restraints excluded: chain S residue 334 VAL Chi-restraints excluded: chain S residue 488 SER Chi-restraints excluded: chain T residue 41 LEU Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 122 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 682 random chunks: chunk 549 optimal weight: 6.9990 chunk 374 optimal weight: 4.9990 chunk 9 optimal weight: 4.9990 chunk 490 optimal weight: 0.7980 chunk 271 optimal weight: 6.9990 chunk 562 optimal weight: 20.0000 chunk 455 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 336 optimal weight: 10.0000 chunk 591 optimal weight: 9.9990 chunk 166 optimal weight: 0.9980 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 GLN C 124 ASN ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN C1068 ASN E 48 GLN E1151 GLN E1365 HIS ** G 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 215 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 223 ASN ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 88 GLN ** T 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 58496 Z= 0.301 Angle : 0.567 15.434 79419 Z= 0.292 Chirality : 0.044 0.176 8612 Planarity : 0.004 0.055 9969 Dihedral : 11.493 143.389 8451 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.59 % Favored : 96.35 % Rotamer: Outliers : 3.80 % Allowed : 20.03 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.10), residues: 6685 helix: 1.05 (0.10), residues: 2786 sheet: 0.16 (0.17), residues: 856 loop : -0.23 (0.11), residues: 3043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP T 69 HIS 0.011 0.001 HIS F 487 PHE 0.025 0.001 PHE B 226 TYR 0.023 0.001 TYR Q 673 ARG 0.010 0.000 ARG C 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1002 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 773 time to evaluate : 5.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7265 (tt0) REVERT: A 196 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8443 (mt0) REVERT: B 146 CYS cc_start: 0.7848 (t) cc_final: 0.7047 (m) REVERT: C 313 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7335 (ptp90) REVERT: C 407 ASN cc_start: 0.7527 (t0) cc_final: 0.7292 (t0) REVERT: C 471 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8620 (mp) REVERT: C 478 TYR cc_start: 0.7995 (m-80) cc_final: 0.7727 (m-80) REVERT: C 495 GLU cc_start: 0.8501 (mp0) cc_final: 0.7955 (mp0) REVERT: C 596 LYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7399 (pttt) REVERT: C 1020 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7370 (mp0) REVERT: C 1063 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8281 (mmpt) REVERT: D 14 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8449 (tt) REVERT: D 98 ARG cc_start: 0.6594 (OUTLIER) cc_final: 0.4439 (pmt170) REVERT: D 188 ARG cc_start: 0.7162 (tpt-90) cc_final: 0.6688 (ttt90) REVERT: D 349 HIS cc_start: 0.7670 (m170) cc_final: 0.7451 (m-70) REVERT: D 442 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8372 (pp30) REVERT: D 595 ARG cc_start: 0.8342 (mtt-85) cc_final: 0.7963 (mtt-85) REVERT: D 663 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7581 (mmm160) REVERT: D 666 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8061 (tm-30) REVERT: E 84 LYS cc_start: 0.8581 (mmmt) cc_final: 0.8331 (tptm) REVERT: E 862 VAL cc_start: 0.6817 (OUTLIER) cc_final: 0.6573 (m) REVERT: E 1085 TYR cc_start: 0.8057 (m-80) cc_final: 0.7845 (m-80) REVERT: F 167 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8425 (ttt) REVERT: F 203 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.7979 (mpt-90) REVERT: F 206 MET cc_start: 0.9152 (OUTLIER) cc_final: 0.8792 (mtm) REVERT: F 488 ARG cc_start: 0.6514 (OUTLIER) cc_final: 0.4755 (mmp-170) REVERT: G 621 MET cc_start: 0.6014 (tpt) cc_final: 0.5789 (tmt) REVERT: H 200 GLU cc_start: 0.6583 (mp0) cc_final: 0.6339 (mp0) REVERT: H 542 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7113 (mt-10) REVERT: I 153 ASP cc_start: 0.7655 (OUTLIER) cc_final: 0.6809 (m-30) REVERT: I 223 ASN cc_start: 0.6954 (OUTLIER) cc_final: 0.6514 (p0) REVERT: I 243 MET cc_start: 0.7897 (tpp) cc_final: 0.7630 (mmt) REVERT: J 274 LYS cc_start: 0.8512 (mmmm) cc_final: 0.8289 (mmmt) REVERT: K 312 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7145 (tm-30) REVERT: M 191 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7132 (tttt) REVERT: N 71 TYR cc_start: 0.5937 (OUTLIER) cc_final: 0.5279 (t80) REVERT: N 110 ASN cc_start: 0.8062 (OUTLIER) cc_final: 0.7629 (p0) REVERT: N 268 ARG cc_start: 0.7072 (OUTLIER) cc_final: 0.6738 (mtp180) REVERT: O 94 GLU cc_start: 0.7904 (tp30) cc_final: 0.7586 (tp30) REVERT: O 141 GLU cc_start: 0.8192 (mp0) cc_final: 0.7900 (pm20) REVERT: S 229 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8420 (tt0) REVERT: S 356 MET cc_start: 0.8006 (ttt) cc_final: 0.7609 (ttt) REVERT: T 52 LYS cc_start: 0.7895 (mtmm) cc_final: 0.7495 (mtmm) outliers start: 229 outliers final: 101 residues processed: 914 average time/residue: 1.5101 time to fit residues: 1725.0477 Evaluate side-chains 869 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 743 time to evaluate : 4.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 505 GLN Chi-restraints excluded: chain C residue 506 GLU Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 729 MET Chi-restraints excluded: chain C residue 923 TYR Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain C residue 1063 LYS Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 442 GLN Chi-restraints excluded: chain D residue 515 SER Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain D residue 645 LYS Chi-restraints excluded: chain D residue 663 ARG Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 576 ARG Chi-restraints excluded: chain E residue 808 ILE Chi-restraints excluded: chain E residue 862 VAL Chi-restraints excluded: chain E residue 864 THR Chi-restraints excluded: chain E residue 901 MET Chi-restraints excluded: chain E residue 928 PHE Chi-restraints excluded: chain E residue 945 ASN Chi-restraints excluded: chain E residue 995 LEU Chi-restraints excluded: chain E residue 997 THR Chi-restraints excluded: chain E residue 1003 VAL Chi-restraints excluded: chain E residue 1056 ASN Chi-restraints excluded: chain E residue 1164 ASN Chi-restraints excluded: chain E residue 1177 THR Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 203 ARG Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 762 ASP Chi-restraints excluded: chain F residue 836 THR Chi-restraints excluded: chain G residue 517 VAL Chi-restraints excluded: chain G residue 527 THR Chi-restraints excluded: chain G residue 533 GLU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 579 CYS Chi-restraints excluded: chain G residue 586 MET Chi-restraints excluded: chain G residue 711 VAL Chi-restraints excluded: chain G residue 732 LEU Chi-restraints excluded: chain G residue 822 THR Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 378 CYS Chi-restraints excluded: chain H residue 516 HIS Chi-restraints excluded: chain H residue 527 LEU Chi-restraints excluded: chain H residue 542 GLU Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 223 ASN Chi-restraints excluded: chain J residue 335 THR Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain K residue 257 SER Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain K residue 312 GLU Chi-restraints excluded: chain K residue 390 THR Chi-restraints excluded: chain K residue 392 SER Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain M residue 136 ILE Chi-restraints excluded: chain M residue 191 LYS Chi-restraints excluded: chain M residue 329 SER Chi-restraints excluded: chain N residue 63 HIS Chi-restraints excluded: chain N residue 71 TYR Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 110 ASN Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 268 ARG Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain P residue 120 MET Chi-restraints excluded: chain Q residue 579 LEU Chi-restraints excluded: chain Q residue 595 THR Chi-restraints excluded: chain Q residue 605 SER Chi-restraints excluded: chain Q residue 633 THR Chi-restraints excluded: chain Q residue 643 THR Chi-restraints excluded: chain Q residue 699 VAL Chi-restraints excluded: chain Q residue 713 MET Chi-restraints excluded: chain Q residue 715 VAL Chi-restraints excluded: chain Q residue 757 THR Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain R residue 114 ASN Chi-restraints excluded: chain R residue 121 THR Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain S residue 229 GLN Chi-restraints excluded: chain S residue 272 ASP Chi-restraints excluded: chain S residue 273 ASP Chi-restraints excluded: chain S residue 297 SER Chi-restraints excluded: chain S residue 334 VAL Chi-restraints excluded: chain S residue 488 SER Chi-restraints excluded: chain T residue 67 SER Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 122 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 682 random chunks: chunk 221 optimal weight: 9.9990 chunk 593 optimal weight: 30.0000 chunk 130 optimal weight: 0.4980 chunk 387 optimal weight: 9.9990 chunk 162 optimal weight: 0.8980 chunk 659 optimal weight: 0.7980 chunk 547 optimal weight: 10.0000 chunk 305 optimal weight: 10.0000 chunk 54 optimal weight: 20.0000 chunk 218 optimal weight: 4.9990 chunk 346 optimal weight: 10.0000 overall best weight: 3.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 ASN ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN C1068 ASN E1151 GLN E1291 GLN F 158 GLN ** G 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 GLN I 223 ASN M 161 ASN ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 88 GLN ** T 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 58496 Z= 0.317 Angle : 0.573 16.037 79419 Z= 0.295 Chirality : 0.044 0.210 8612 Planarity : 0.004 0.055 9969 Dihedral : 11.516 143.257 8451 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.71 % Favored : 96.23 % Rotamer: Outliers : 3.70 % Allowed : 20.48 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: 6685 helix: 1.01 (0.10), residues: 2789 sheet: 0.15 (0.17), residues: 856 loop : -0.26 (0.11), residues: 3040 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP T 69 HIS 0.010 0.001 HIS F 487 PHE 0.025 0.002 PHE B 226 TYR 0.023 0.002 TYR G 652 ARG 0.008 0.000 ARG G 580 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 746 time to evaluate : 5.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLN cc_start: 0.7700 (OUTLIER) cc_final: 0.7296 (tt0) REVERT: A 141 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8403 (pt0) REVERT: A 196 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8448 (mt0) REVERT: B 51 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.7414 (ttp80) REVERT: B 146 CYS cc_start: 0.7820 (t) cc_final: 0.7024 (m) REVERT: C 313 ARG cc_start: 0.8385 (OUTLIER) cc_final: 0.7341 (ptp90) REVERT: C 407 ASN cc_start: 0.7564 (t0) cc_final: 0.7302 (t0) REVERT: C 471 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8582 (mp) REVERT: C 478 TYR cc_start: 0.7926 (m-80) cc_final: 0.7648 (m-80) REVERT: C 495 GLU cc_start: 0.8505 (mp0) cc_final: 0.7973 (mp0) REVERT: C 596 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7376 (pttt) REVERT: C 1020 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7397 (mp0) REVERT: C 1063 LYS cc_start: 0.8926 (OUTLIER) cc_final: 0.8275 (mmpt) REVERT: D 14 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8413 (tt) REVERT: D 98 ARG cc_start: 0.6596 (OUTLIER) cc_final: 0.4414 (pmt170) REVERT: D 188 ARG cc_start: 0.7167 (tpt-90) cc_final: 0.6700 (ttt90) REVERT: D 349 HIS cc_start: 0.7667 (m170) cc_final: 0.7428 (m-70) REVERT: D 442 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8392 (pp30) REVERT: D 595 ARG cc_start: 0.8362 (mtt-85) cc_final: 0.7956 (mtt-85) REVERT: D 663 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7578 (mmm160) REVERT: D 666 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8056 (tm-30) REVERT: E 84 LYS cc_start: 0.8587 (mmmt) cc_final: 0.8337 (tptm) REVERT: E 224 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7461 (mmt90) REVERT: E 1150 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8619 (tt0) REVERT: F 203 ARG cc_start: 0.8892 (OUTLIER) cc_final: 0.7985 (mpt-90) REVERT: F 206 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8843 (mtm) REVERT: F 297 SER cc_start: 0.8948 (p) cc_final: 0.8588 (t) REVERT: F 426 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.7006 (mt) REVERT: F 488 ARG cc_start: 0.6508 (OUTLIER) cc_final: 0.4758 (mmp-170) REVERT: G 601 MET cc_start: 0.7216 (OUTLIER) cc_final: 0.6105 (mmt) REVERT: H 542 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7153 (mt-10) REVERT: I 153 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.6861 (m-30) REVERT: I 208 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7884 (tp) REVERT: I 223 ASN cc_start: 0.6644 (OUTLIER) cc_final: 0.6305 (p0) REVERT: J 274 LYS cc_start: 0.8512 (mmmm) cc_final: 0.8295 (mmmt) REVERT: K 312 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7122 (tm-30) REVERT: L 444 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7996 (m-30) REVERT: M 191 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7165 (tttt) REVERT: N 71 TYR cc_start: 0.6215 (OUTLIER) cc_final: 0.5556 (t80) REVERT: N 103 LEU cc_start: 0.6448 (OUTLIER) cc_final: 0.5890 (tm) REVERT: N 110 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7633 (p0) REVERT: N 268 ARG cc_start: 0.7075 (OUTLIER) cc_final: 0.6741 (mtp180) REVERT: O 94 GLU cc_start: 0.7886 (tp30) cc_final: 0.7580 (tp30) REVERT: O 141 GLU cc_start: 0.8186 (mp0) cc_final: 0.7912 (pm20) REVERT: R 122 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.7891 (tttt) REVERT: S 229 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8426 (tt0) REVERT: S 356 MET cc_start: 0.7995 (ttt) cc_final: 0.7673 (ttt) REVERT: S 360 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8741 (mm) REVERT: S 385 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.7149 (pm20) REVERT: T 52 LYS cc_start: 0.7905 (mtmm) cc_final: 0.7509 (mtmm) outliers start: 223 outliers final: 109 residues processed: 888 average time/residue: 1.5305 time to fit residues: 1693.6435 Evaluate side-chains 872 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 729 time to evaluate : 4.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 505 GLN Chi-restraints excluded: chain C residue 506 GLU Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 630 ARG Chi-restraints excluded: chain C residue 729 MET Chi-restraints excluded: chain C residue 923 TYR Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain C residue 1063 LYS Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 334 THR Chi-restraints excluded: chain D residue 442 GLN Chi-restraints excluded: chain D residue 515 SER Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain D residue 645 LYS Chi-restraints excluded: chain D residue 663 ARG Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 293 CYS Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 576 ARG Chi-restraints excluded: chain E residue 808 ILE Chi-restraints excluded: chain E residue 864 THR Chi-restraints excluded: chain E residue 901 MET Chi-restraints excluded: chain E residue 945 ASN Chi-restraints excluded: chain E residue 995 LEU Chi-restraints excluded: chain E residue 997 THR Chi-restraints excluded: chain E residue 1150 GLU Chi-restraints excluded: chain E residue 1164 ASN Chi-restraints excluded: chain E residue 1177 THR Chi-restraints excluded: chain F residue 98 ILE Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 203 ARG Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 762 ASP Chi-restraints excluded: chain F residue 836 THR Chi-restraints excluded: chain G residue 463 GLU Chi-restraints excluded: chain G residue 517 VAL Chi-restraints excluded: chain G residue 527 THR Chi-restraints excluded: chain G residue 533 GLU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 579 CYS Chi-restraints excluded: chain G residue 586 MET Chi-restraints excluded: chain G residue 601 MET Chi-restraints excluded: chain G residue 711 VAL Chi-restraints excluded: chain G residue 732 LEU Chi-restraints excluded: chain G residue 822 THR Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 219 LEU Chi-restraints excluded: chain H residue 321 MET Chi-restraints excluded: chain H residue 378 CYS Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain H residue 516 HIS Chi-restraints excluded: chain H residue 521 LEU Chi-restraints excluded: chain H residue 527 LEU Chi-restraints excluded: chain H residue 542 GLU Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 198 ASN Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain I residue 223 ASN Chi-restraints excluded: chain J residue 335 THR Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain K residue 257 SER Chi-restraints excluded: chain K residue 259 LYS Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain K residue 312 GLU Chi-restraints excluded: chain K residue 390 THR Chi-restraints excluded: chain K residue 392 SER Chi-restraints excluded: chain L residue 104 ILE Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 444 ASP Chi-restraints excluded: chain M residue 136 ILE Chi-restraints excluded: chain M residue 191 LYS Chi-restraints excluded: chain M residue 329 SER Chi-restraints excluded: chain N residue 63 HIS Chi-restraints excluded: chain N residue 71 TYR Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 110 ASN Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 238 ILE Chi-restraints excluded: chain N residue 268 ARG Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain P residue 120 MET Chi-restraints excluded: chain Q residue 354 THR Chi-restraints excluded: chain Q residue 595 THR Chi-restraints excluded: chain Q residue 633 THR Chi-restraints excluded: chain Q residue 643 THR Chi-restraints excluded: chain Q residue 699 VAL Chi-restraints excluded: chain Q residue 713 MET Chi-restraints excluded: chain Q residue 715 VAL Chi-restraints excluded: chain Q residue 757 THR Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain R residue 114 ASN Chi-restraints excluded: chain R residue 121 THR Chi-restraints excluded: chain R residue 122 LYS Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain S residue 229 GLN Chi-restraints excluded: chain S residue 272 ASP Chi-restraints excluded: chain S residue 273 ASP Chi-restraints excluded: chain S residue 297 SER Chi-restraints excluded: chain S residue 334 VAL Chi-restraints excluded: chain S residue 360 LEU Chi-restraints excluded: chain S residue 385 GLN Chi-restraints excluded: chain S residue 488 SER Chi-restraints excluded: chain T residue 41 LEU Chi-restraints excluded: chain T residue 67 SER Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 122 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 682 random chunks: chunk 636 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 375 optimal weight: 7.9990 chunk 481 optimal weight: 4.9990 chunk 373 optimal weight: 10.0000 chunk 555 optimal weight: 20.0000 chunk 368 optimal weight: 4.9990 chunk 657 optimal weight: 6.9990 chunk 411 optimal weight: 30.0000 chunk 400 optimal weight: 5.9990 chunk 303 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 116 ASN C 124 ASN ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN C1068 ASN ** G 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 88 GLN T 81 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 58496 Z= 0.346 Angle : 0.594 16.795 79419 Z= 0.306 Chirality : 0.045 0.204 8612 Planarity : 0.005 0.050 9969 Dihedral : 11.551 142.636 8451 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.72 % Favored : 96.22 % Rotamer: Outliers : 3.80 % Allowed : 20.80 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: 0.35 (0.10), residues: 6685 helix: 0.94 (0.10), residues: 2790 sheet: 0.10 (0.17), residues: 869 loop : -0.29 (0.11), residues: 3026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP T 69 HIS 0.011 0.001 HIS F 487 PHE 0.027 0.002 PHE B 226 TYR 0.024 0.002 TYR G 652 ARG 0.010 0.000 ARG N 149 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 972 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 743 time to evaluate : 5.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7342 (tt0) REVERT: A 141 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8420 (pt0) REVERT: A 196 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8460 (mt0) REVERT: A 301 ASN cc_start: 0.7495 (OUTLIER) cc_final: 0.7077 (p0) REVERT: B 51 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.7413 (ttp80) REVERT: B 146 CYS cc_start: 0.7817 (t) cc_final: 0.7021 (m) REVERT: C 313 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7371 (ptp90) REVERT: C 407 ASN cc_start: 0.7587 (t0) cc_final: 0.7318 (t0) REVERT: C 471 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8595 (mp) REVERT: C 495 GLU cc_start: 0.8499 (mp0) cc_final: 0.7910 (mp0) REVERT: C 596 LYS cc_start: 0.7864 (OUTLIER) cc_final: 0.7370 (pttt) REVERT: C 1020 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7407 (mp0) REVERT: C 1063 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8280 (mmpt) REVERT: D 14 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8475 (tt) REVERT: D 98 ARG cc_start: 0.6603 (OUTLIER) cc_final: 0.4452 (pmt170) REVERT: D 188 ARG cc_start: 0.7185 (tpt-90) cc_final: 0.6798 (ttt90) REVERT: D 349 HIS cc_start: 0.7659 (m170) cc_final: 0.7418 (m-70) REVERT: D 442 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8394 (pp30) REVERT: D 595 ARG cc_start: 0.8371 (mtt-85) cc_final: 0.7940 (mtt-85) REVERT: D 663 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7574 (mmm160) REVERT: D 666 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8058 (tm-30) REVERT: E 84 LYS cc_start: 0.8601 (mmmt) cc_final: 0.8359 (tptm) REVERT: E 224 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7498 (mmt90) REVERT: E 405 LYS cc_start: 0.8153 (pmmt) cc_final: 0.7755 (mmtm) REVERT: E 466 ASN cc_start: 0.9001 (p0) cc_final: 0.8793 (p0) REVERT: E 862 VAL cc_start: 0.6810 (OUTLIER) cc_final: 0.6524 (m) REVERT: E 1150 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8629 (tt0) REVERT: F 118 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7498 (mt) REVERT: F 203 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.7963 (mpt-90) REVERT: F 206 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8826 (mtm) REVERT: F 297 SER cc_start: 0.8942 (p) cc_final: 0.8581 (t) REVERT: F 426 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.6988 (mt) REVERT: F 488 ARG cc_start: 0.6491 (OUTLIER) cc_final: 0.4750 (mmp-170) REVERT: G 601 MET cc_start: 0.7236 (OUTLIER) cc_final: 0.6058 (mmt) REVERT: H 542 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7160 (mt-10) REVERT: I 153 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.6895 (m-30) REVERT: I 183 ARG cc_start: 0.8649 (ttm-80) cc_final: 0.8448 (ttm-80) REVERT: I 208 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7907 (tp) REVERT: J 274 LYS cc_start: 0.8513 (mmmm) cc_final: 0.8298 (mmmt) REVERT: K 312 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7132 (tm-30) REVERT: L 438 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7099 (pp30) REVERT: L 444 ASP cc_start: 0.8244 (OUTLIER) cc_final: 0.7976 (m-30) REVERT: M 191 LYS cc_start: 0.7649 (OUTLIER) cc_final: 0.7164 (tttt) REVERT: N 71 TYR cc_start: 0.6308 (OUTLIER) cc_final: 0.5669 (t80) REVERT: N 103 LEU cc_start: 0.6451 (OUTLIER) cc_final: 0.5857 (tm) REVERT: N 255 SER cc_start: 0.6563 (OUTLIER) cc_final: 0.6158 (p) REVERT: N 268 ARG cc_start: 0.7067 (OUTLIER) cc_final: 0.6740 (mtp180) REVERT: O 94 GLU cc_start: 0.7871 (tp30) cc_final: 0.7571 (tp30) REVERT: O 141 GLU cc_start: 0.8200 (mp0) cc_final: 0.7939 (pm20) REVERT: R 122 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.7904 (tttt) REVERT: S 229 GLN cc_start: 0.8902 (OUTLIER) cc_final: 0.8433 (tt0) REVERT: S 356 MET cc_start: 0.7991 (ttt) cc_final: 0.7675 (ttt) REVERT: S 385 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.7173 (pm20) REVERT: T 52 LYS cc_start: 0.7957 (mtmm) cc_final: 0.7555 (mtmm) outliers start: 229 outliers final: 115 residues processed: 893 average time/residue: 1.5085 time to fit residues: 1686.5228 Evaluate side-chains 876 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 725 time to evaluate : 4.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 196 GLN Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 301 ASN Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 129 ILE Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 505 GLN Chi-restraints excluded: chain C residue 506 GLU Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 630 ARG Chi-restraints excluded: chain C residue 729 MET Chi-restraints excluded: chain C residue 923 TYR Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain C residue 1021 VAL Chi-restraints excluded: chain C residue 1063 LYS Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 14 LEU Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 442 GLN Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain D residue 515 SER Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain D residue 663 ARG Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain E residue 60 ASP Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 160 MET Chi-restraints excluded: chain E residue 224 ARG Chi-restraints excluded: chain E residue 293 CYS Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 576 ARG Chi-restraints excluded: chain E residue 808 ILE Chi-restraints excluded: chain E residue 862 VAL Chi-restraints excluded: chain E residue 864 THR Chi-restraints excluded: chain E residue 901 MET Chi-restraints excluded: chain E residue 928 PHE Chi-restraints excluded: chain E residue 945 ASN Chi-restraints excluded: chain E residue 990 TYR Chi-restraints excluded: chain E residue 995 LEU Chi-restraints excluded: chain E residue 997 THR Chi-restraints excluded: chain E residue 1087 LYS Chi-restraints excluded: chain E residue 1095 GLN Chi-restraints excluded: chain E residue 1150 GLU Chi-restraints excluded: chain E residue 1164 ASN Chi-restraints excluded: chain E residue 1177 THR Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 203 ARG Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 337 VAL Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 413 VAL Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 762 ASP Chi-restraints excluded: chain F residue 814 CYS Chi-restraints excluded: chain F residue 836 THR Chi-restraints excluded: chain G residue 517 VAL Chi-restraints excluded: chain G residue 527 THR Chi-restraints excluded: chain G residue 533 GLU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 579 CYS Chi-restraints excluded: chain G residue 586 MET Chi-restraints excluded: chain G residue 601 MET Chi-restraints excluded: chain G residue 711 VAL Chi-restraints excluded: chain G residue 732 LEU Chi-restraints excluded: chain G residue 822 THR Chi-restraints excluded: chain H residue 162 VAL Chi-restraints excluded: chain H residue 191 LYS Chi-restraints excluded: chain H residue 202 LEU Chi-restraints excluded: chain H residue 378 CYS Chi-restraints excluded: chain H residue 418 LEU Chi-restraints excluded: chain H residue 516 HIS Chi-restraints excluded: chain H residue 527 LEU Chi-restraints excluded: chain H residue 542 GLU Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain I residue 198 ASN Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain J residue 335 THR Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain K residue 257 SER Chi-restraints excluded: chain K residue 259 LYS Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain K residue 294 ILE Chi-restraints excluded: chain K residue 312 GLU Chi-restraints excluded: chain K residue 390 THR Chi-restraints excluded: chain K residue 392 SER Chi-restraints excluded: chain L residue 104 ILE Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain L residue 201 THR Chi-restraints excluded: chain L residue 303 ILE Chi-restraints excluded: chain L residue 438 GLN Chi-restraints excluded: chain L residue 444 ASP Chi-restraints excluded: chain M residue 136 ILE Chi-restraints excluded: chain M residue 191 LYS Chi-restraints excluded: chain M residue 329 SER Chi-restraints excluded: chain N residue 63 HIS Chi-restraints excluded: chain N residue 71 TYR Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 144 LEU Chi-restraints excluded: chain N residue 146 LEU Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 232 ASP Chi-restraints excluded: chain N residue 255 SER Chi-restraints excluded: chain N residue 268 ARG Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain P residue 120 MET Chi-restraints excluded: chain Q residue 354 THR Chi-restraints excluded: chain Q residue 595 THR Chi-restraints excluded: chain Q residue 633 THR Chi-restraints excluded: chain Q residue 699 VAL Chi-restraints excluded: chain Q residue 713 MET Chi-restraints excluded: chain Q residue 715 VAL Chi-restraints excluded: chain Q residue 757 THR Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain R residue 114 ASN Chi-restraints excluded: chain R residue 121 THR Chi-restraints excluded: chain R residue 122 LYS Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain S residue 229 GLN Chi-restraints excluded: chain S residue 272 ASP Chi-restraints excluded: chain S residue 273 ASP Chi-restraints excluded: chain S residue 297 SER Chi-restraints excluded: chain S residue 334 VAL Chi-restraints excluded: chain S residue 385 GLN Chi-restraints excluded: chain S residue 488 SER Chi-restraints excluded: chain T residue 67 SER Chi-restraints excluded: chain T residue 122 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 682 random chunks: chunk 406 optimal weight: 5.9990 chunk 262 optimal weight: 0.6980 chunk 392 optimal weight: 8.9990 chunk 198 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 417 optimal weight: 0.9980 chunk 447 optimal weight: 0.7980 chunk 324 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 516 optimal weight: 8.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 GLN C 124 ASN ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN C1068 ASN E1291 GLN F 158 GLN ** G 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 81 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 58496 Z= 0.163 Angle : 0.533 16.676 79419 Z= 0.274 Chirality : 0.042 0.206 8612 Planarity : 0.004 0.050 9969 Dihedral : 11.466 148.151 8451 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.10 % Favored : 96.84 % Rotamer: Outliers : 2.06 % Allowed : 22.44 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: 0.62 (0.10), residues: 6685 helix: 1.17 (0.10), residues: 2805 sheet: 0.23 (0.17), residues: 854 loop : -0.16 (0.11), residues: 3026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP T 69 HIS 0.006 0.001 HIS I 235 PHE 0.019 0.001 PHE D 157 TYR 0.029 0.001 TYR G 652 ARG 0.011 0.000 ARG C 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 754 time to evaluate : 5.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLN cc_start: 0.7693 (OUTLIER) cc_final: 0.7277 (tt0) REVERT: B 51 ARG cc_start: 0.9053 (OUTLIER) cc_final: 0.7347 (ttp80) REVERT: B 146 CYS cc_start: 0.7806 (t) cc_final: 0.7006 (m) REVERT: C 313 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.7302 (ptp90) REVERT: C 407 ASN cc_start: 0.7555 (t0) cc_final: 0.7285 (t0) REVERT: C 471 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8477 (mp) REVERT: C 493 ILE cc_start: 0.8332 (OUTLIER) cc_final: 0.7930 (pp) REVERT: C 495 GLU cc_start: 0.8428 (mp0) cc_final: 0.7803 (mp0) REVERT: C 596 LYS cc_start: 0.7916 (OUTLIER) cc_final: 0.7400 (pttt) REVERT: C 1020 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7383 (mp0) REVERT: C 1063 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8048 (mmpt) REVERT: D 188 ARG cc_start: 0.7246 (tpt-90) cc_final: 0.6860 (ttt90) REVERT: D 349 HIS cc_start: 0.7633 (m170) cc_final: 0.7393 (m-70) REVERT: D 442 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8371 (pp30) REVERT: D 595 ARG cc_start: 0.8371 (mtt-85) cc_final: 0.7968 (mtt-85) REVERT: D 666 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8012 (tm-30) REVERT: E 84 LYS cc_start: 0.8541 (mmmt) cc_final: 0.8322 (tptm) REVERT: E 405 LYS cc_start: 0.8156 (pmmt) cc_final: 0.7736 (mmtm) REVERT: E 1150 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8536 (tt0) REVERT: F 206 MET cc_start: 0.9097 (OUTLIER) cc_final: 0.8863 (mtm) REVERT: F 297 SER cc_start: 0.8918 (p) cc_final: 0.8573 (t) REVERT: F 426 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.7004 (mt) REVERT: F 429 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7899 (pt0) REVERT: F 488 ARG cc_start: 0.6417 (OUTLIER) cc_final: 0.4634 (mmp-170) REVERT: G 601 MET cc_start: 0.7252 (OUTLIER) cc_final: 0.6127 (mmt) REVERT: H 542 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7082 (mt-10) REVERT: L 444 ASP cc_start: 0.8227 (m-30) cc_final: 0.7955 (m-30) REVERT: N 71 TYR cc_start: 0.6107 (OUTLIER) cc_final: 0.5451 (t80) REVERT: N 103 LEU cc_start: 0.6208 (OUTLIER) cc_final: 0.5757 (tm) REVERT: N 268 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6682 (mtp-110) REVERT: O 94 GLU cc_start: 0.7851 (tp30) cc_final: 0.7551 (tp30) REVERT: O 141 GLU cc_start: 0.8199 (mp0) cc_final: 0.7930 (pm20) REVERT: Q 632 MET cc_start: 0.5123 (mpt) cc_final: 0.4304 (mtm) REVERT: S 229 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8401 (tt0) REVERT: T 89 GLU cc_start: 0.7080 (pm20) cc_final: 0.6243 (pm20) outliers start: 124 outliers final: 61 residues processed: 827 average time/residue: 1.5388 time to fit residues: 1590.6432 Evaluate side-chains 798 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 718 time to evaluate : 4.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain B residue 51 ARG Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 367 SER Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 505 GLN Chi-restraints excluded: chain C residue 506 GLU Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 923 TYR Chi-restraints excluded: chain C residue 1063 LYS Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 442 GLN Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain D residue 645 LYS Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 576 ARG Chi-restraints excluded: chain E residue 864 THR Chi-restraints excluded: chain E residue 945 ASN Chi-restraints excluded: chain E residue 990 TYR Chi-restraints excluded: chain E residue 995 LEU Chi-restraints excluded: chain E residue 997 THR Chi-restraints excluded: chain E residue 1056 ASN Chi-restraints excluded: chain E residue 1095 GLN Chi-restraints excluded: chain E residue 1150 GLU Chi-restraints excluded: chain E residue 1164 ASN Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 836 THR Chi-restraints excluded: chain G residue 517 VAL Chi-restraints excluded: chain G residue 533 GLU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 586 MET Chi-restraints excluded: chain G residue 601 MET Chi-restraints excluded: chain G residue 621 MET Chi-restraints excluded: chain H residue 516 HIS Chi-restraints excluded: chain H residue 521 LEU Chi-restraints excluded: chain H residue 527 LEU Chi-restraints excluded: chain H residue 542 GLU Chi-restraints excluded: chain J residue 335 THR Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 392 SER Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain M residue 329 SER Chi-restraints excluded: chain N residue 63 HIS Chi-restraints excluded: chain N residue 71 TYR Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 110 ASN Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 268 ARG Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain P residue 120 MET Chi-restraints excluded: chain Q residue 595 THR Chi-restraints excluded: chain Q residue 633 THR Chi-restraints excluded: chain Q residue 643 THR Chi-restraints excluded: chain Q residue 713 MET Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain R residue 121 THR Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain S residue 229 GLN Chi-restraints excluded: chain S residue 297 SER Chi-restraints excluded: chain S residue 334 VAL Chi-restraints excluded: chain T residue 88 ILE Chi-restraints excluded: chain T residue 122 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 682 random chunks: chunk 597 optimal weight: 40.0000 chunk 629 optimal weight: 4.9990 chunk 574 optimal weight: 0.7980 chunk 612 optimal weight: 9.9990 chunk 368 optimal weight: 0.9980 chunk 266 optimal weight: 1.9990 chunk 481 optimal weight: 0.9980 chunk 187 optimal weight: 1.9990 chunk 553 optimal weight: 20.0000 chunk 579 optimal weight: 1.9990 chunk 610 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 GLN C 124 ASN C 542 ASN C1068 ASN ** G 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 58496 Z= 0.182 Angle : 0.538 16.428 79419 Z= 0.276 Chirality : 0.042 0.208 8612 Planarity : 0.004 0.072 9969 Dihedral : 11.426 148.036 8445 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.44 % Favored : 96.51 % Rotamer: Outliers : 1.98 % Allowed : 22.79 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: 0.67 (0.10), residues: 6685 helix: 1.24 (0.10), residues: 2808 sheet: 0.17 (0.17), residues: 877 loop : -0.13 (0.12), residues: 3000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP H 517 HIS 0.008 0.001 HIS N 77 PHE 0.017 0.001 PHE D 157 TYR 0.034 0.001 TYR G 652 ARG 0.014 0.000 ARG C 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 856 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 737 time to evaluate : 5.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7235 (tt0) REVERT: B 146 CYS cc_start: 0.7802 (t) cc_final: 0.7014 (m) REVERT: C 313 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7309 (ptp90) REVERT: C 407 ASN cc_start: 0.7572 (t0) cc_final: 0.7290 (t0) REVERT: C 471 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8508 (mp) REVERT: C 495 GLU cc_start: 0.8453 (mp0) cc_final: 0.8023 (mp0) REVERT: C 596 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7399 (pttt) REVERT: C 1020 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7323 (mp0) REVERT: C 1063 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8201 (mmpt) REVERT: D 188 ARG cc_start: 0.7219 (tpt-90) cc_final: 0.6866 (ttt90) REVERT: D 349 HIS cc_start: 0.7628 (m170) cc_final: 0.7382 (m-70) REVERT: D 397 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9033 (mp) REVERT: D 442 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8358 (pp30) REVERT: D 595 ARG cc_start: 0.8355 (mtt-85) cc_final: 0.7926 (mtt-85) REVERT: D 666 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7994 (tm-30) REVERT: E 84 LYS cc_start: 0.8545 (mmmt) cc_final: 0.8329 (tptm) REVERT: E 874 ILE cc_start: 0.8037 (mt) cc_final: 0.7674 (mm) REVERT: E 1150 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8759 (tm-30) REVERT: F 203 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.7826 (mpt-90) REVERT: F 206 MET cc_start: 0.9100 (OUTLIER) cc_final: 0.8889 (mtm) REVERT: F 297 SER cc_start: 0.8902 (p) cc_final: 0.8572 (t) REVERT: F 426 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6998 (mt) REVERT: F 429 GLU cc_start: 0.8184 (mm-30) cc_final: 0.7900 (pt0) REVERT: F 488 ARG cc_start: 0.6447 (OUTLIER) cc_final: 0.4658 (mmp-170) REVERT: G 596 MET cc_start: 0.5564 (mpm) cc_final: 0.5272 (mmp) REVERT: G 601 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6050 (mmt) REVERT: H 542 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7059 (mt-10) REVERT: I 141 MET cc_start: 0.7088 (tpp) cc_final: 0.6645 (mmm) REVERT: I 153 ASP cc_start: 0.7720 (OUTLIER) cc_final: 0.6998 (m-30) REVERT: L 444 ASP cc_start: 0.8238 (m-30) cc_final: 0.7964 (m-30) REVERT: N 71 TYR cc_start: 0.6107 (OUTLIER) cc_final: 0.5466 (t80) REVERT: N 103 LEU cc_start: 0.6111 (OUTLIER) cc_final: 0.5655 (tm) REVERT: N 268 ARG cc_start: 0.7058 (OUTLIER) cc_final: 0.6711 (mtp180) REVERT: O 94 GLU cc_start: 0.7850 (tp30) cc_final: 0.7553 (tp30) REVERT: O 141 GLU cc_start: 0.8200 (mp0) cc_final: 0.7930 (pm20) REVERT: P 164 ASP cc_start: 0.7737 (m-30) cc_final: 0.7454 (m-30) REVERT: Q 632 MET cc_start: 0.5139 (mpt) cc_final: 0.4296 (mtm) REVERT: S 229 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8423 (tt0) REVERT: S 356 MET cc_start: 0.8040 (ttt) cc_final: 0.7555 (ttt) outliers start: 119 outliers final: 60 residues processed: 814 average time/residue: 1.5261 time to fit residues: 1554.2324 Evaluate side-chains 787 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 707 time to evaluate : 4.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain B residue 173 ASP Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 505 GLN Chi-restraints excluded: chain C residue 596 LYS Chi-restraints excluded: chain C residue 923 TYR Chi-restraints excluded: chain C residue 1063 LYS Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 442 GLN Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain D residue 645 LYS Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 576 ARG Chi-restraints excluded: chain E residue 864 THR Chi-restraints excluded: chain E residue 945 ASN Chi-restraints excluded: chain E residue 990 TYR Chi-restraints excluded: chain E residue 995 LEU Chi-restraints excluded: chain E residue 997 THR Chi-restraints excluded: chain E residue 1056 ASN Chi-restraints excluded: chain E residue 1087 LYS Chi-restraints excluded: chain E residue 1095 GLN Chi-restraints excluded: chain E residue 1150 GLU Chi-restraints excluded: chain E residue 1164 ASN Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 203 ARG Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 814 CYS Chi-restraints excluded: chain F residue 836 THR Chi-restraints excluded: chain G residue 517 VAL Chi-restraints excluded: chain G residue 533 GLU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 586 MET Chi-restraints excluded: chain G residue 601 MET Chi-restraints excluded: chain H residue 516 HIS Chi-restraints excluded: chain H residue 527 LEU Chi-restraints excluded: chain H residue 542 GLU Chi-restraints excluded: chain I residue 153 ASP Chi-restraints excluded: chain J residue 335 THR Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 383 THR Chi-restraints excluded: chain K residue 392 SER Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain M residue 136 ILE Chi-restraints excluded: chain M residue 329 SER Chi-restraints excluded: chain N residue 63 HIS Chi-restraints excluded: chain N residue 71 TYR Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 268 ARG Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain P residue 120 MET Chi-restraints excluded: chain Q residue 579 LEU Chi-restraints excluded: chain Q residue 595 THR Chi-restraints excluded: chain Q residue 633 THR Chi-restraints excluded: chain Q residue 643 THR Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain R residue 121 THR Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain S residue 229 GLN Chi-restraints excluded: chain S residue 297 SER Chi-restraints excluded: chain S residue 334 VAL Chi-restraints excluded: chain T residue 122 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 682 random chunks: chunk 402 optimal weight: 0.0020 chunk 647 optimal weight: 10.0000 chunk 395 optimal weight: 3.9990 chunk 307 optimal weight: 4.9990 chunk 450 optimal weight: 0.8980 chunk 679 optimal weight: 8.9990 chunk 625 optimal weight: 0.5980 chunk 541 optimal weight: 10.0000 chunk 56 optimal weight: 5.9990 chunk 417 optimal weight: 3.9990 chunk 331 optimal weight: 9.9990 overall best weight: 1.8992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 ASN C 542 ASN C1068 ASN F 158 GLN ** G 518 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 254 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 329 GLN K 328 GLN ** N 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 58496 Z= 0.214 Angle : 0.556 16.422 79419 Z= 0.284 Chirality : 0.043 0.232 8612 Planarity : 0.004 0.070 9969 Dihedral : 11.435 147.557 8445 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.37 % Favored : 96.57 % Rotamer: Outliers : 1.73 % Allowed : 23.11 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: 0.66 (0.10), residues: 6685 helix: 1.22 (0.10), residues: 2803 sheet: 0.20 (0.17), residues: 883 loop : -0.13 (0.12), residues: 2999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP H 517 HIS 0.009 0.001 HIS N 77 PHE 0.019 0.001 PHE B 226 TYR 0.033 0.001 TYR G 652 ARG 0.014 0.000 ARG C 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13370 Ramachandran restraints generated. 6685 Oldfield, 0 Emsley, 6685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 720 time to evaluate : 4.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7245 (tt0) REVERT: B 146 CYS cc_start: 0.7805 (t) cc_final: 0.7022 (m) REVERT: C 313 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7312 (ptp90) REVERT: C 407 ASN cc_start: 0.7610 (t0) cc_final: 0.7312 (t0) REVERT: C 471 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8537 (mp) REVERT: C 495 GLU cc_start: 0.8425 (mp0) cc_final: 0.7895 (mp0) REVERT: C 1020 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7346 (mp0) REVERT: C 1063 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8185 (mmpt) REVERT: D 188 ARG cc_start: 0.7216 (tpt-90) cc_final: 0.6862 (ttt90) REVERT: D 349 HIS cc_start: 0.7612 (m170) cc_final: 0.7366 (m-70) REVERT: D 397 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9023 (mp) REVERT: D 442 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8371 (pp30) REVERT: D 595 ARG cc_start: 0.8357 (mtt-85) cc_final: 0.7922 (mtt-85) REVERT: D 666 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7956 (tm-30) REVERT: D 670 GLN cc_start: 0.8702 (mm110) cc_final: 0.8425 (mm-40) REVERT: E 84 LYS cc_start: 0.8566 (mmmt) cc_final: 0.8335 (tptm) REVERT: E 405 LYS cc_start: 0.8170 (pmmt) cc_final: 0.7646 (ptmt) REVERT: E 874 ILE cc_start: 0.8041 (mt) cc_final: 0.7673 (mm) REVERT: E 1150 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8755 (tm-30) REVERT: F 203 ARG cc_start: 0.8891 (OUTLIER) cc_final: 0.7815 (mpt-90) REVERT: F 206 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8882 (mtm) REVERT: F 297 SER cc_start: 0.8900 (p) cc_final: 0.8570 (t) REVERT: F 426 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6996 (mt) REVERT: F 429 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7895 (pt0) REVERT: F 488 ARG cc_start: 0.6450 (OUTLIER) cc_final: 0.4666 (mmp-170) REVERT: G 596 MET cc_start: 0.5692 (mpm) cc_final: 0.5490 (mmp) REVERT: G 601 MET cc_start: 0.7218 (OUTLIER) cc_final: 0.6020 (mmt) REVERT: H 542 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7048 (mt-10) REVERT: I 141 MET cc_start: 0.7068 (tpp) cc_final: 0.6633 (mmm) REVERT: L 444 ASP cc_start: 0.8250 (m-30) cc_final: 0.7960 (m-30) REVERT: N 71 TYR cc_start: 0.6127 (OUTLIER) cc_final: 0.5491 (t80) REVERT: N 103 LEU cc_start: 0.6121 (OUTLIER) cc_final: 0.5658 (tm) REVERT: N 268 ARG cc_start: 0.7065 (OUTLIER) cc_final: 0.6723 (mtp180) REVERT: O 94 GLU cc_start: 0.7852 (tp30) cc_final: 0.7555 (tp30) REVERT: O 141 GLU cc_start: 0.8198 (mp0) cc_final: 0.7928 (pm20) REVERT: P 164 ASP cc_start: 0.7727 (m-30) cc_final: 0.7437 (m-30) REVERT: Q 632 MET cc_start: 0.5164 (mpt) cc_final: 0.4345 (mtm) REVERT: S 229 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.8426 (tt0) REVERT: S 356 MET cc_start: 0.8046 (ttt) cc_final: 0.7555 (ttt) REVERT: T 89 GLU cc_start: 0.6983 (pm20) cc_final: 0.6204 (pm20) outliers start: 104 outliers final: 65 residues processed: 780 average time/residue: 1.5623 time to fit residues: 1520.7459 Evaluate side-chains 797 residues out of total 6021 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 714 time to evaluate : 4.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ASP Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 111 GLN Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain C residue 313 ARG Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 469 LEU Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 505 GLN Chi-restraints excluded: chain C residue 506 GLU Chi-restraints excluded: chain C residue 729 MET Chi-restraints excluded: chain C residue 923 TYR Chi-restraints excluded: chain C residue 1063 LYS Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 397 LEU Chi-restraints excluded: chain D residue 442 GLN Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain D residue 645 LYS Chi-restraints excluded: chain D residue 666 GLU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 396 ILE Chi-restraints excluded: chain E residue 576 ARG Chi-restraints excluded: chain E residue 864 THR Chi-restraints excluded: chain E residue 990 TYR Chi-restraints excluded: chain E residue 995 LEU Chi-restraints excluded: chain E residue 997 THR Chi-restraints excluded: chain E residue 1056 ASN Chi-restraints excluded: chain E residue 1087 LYS Chi-restraints excluded: chain E residue 1095 GLN Chi-restraints excluded: chain E residue 1150 GLU Chi-restraints excluded: chain E residue 1164 ASN Chi-restraints excluded: chain F residue 167 MET Chi-restraints excluded: chain F residue 203 ARG Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 412 LEU Chi-restraints excluded: chain F residue 426 LEU Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 488 ARG Chi-restraints excluded: chain F residue 814 CYS Chi-restraints excluded: chain F residue 836 THR Chi-restraints excluded: chain G residue 517 VAL Chi-restraints excluded: chain G residue 533 GLU Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 586 MET Chi-restraints excluded: chain G residue 601 MET Chi-restraints excluded: chain H residue 516 HIS Chi-restraints excluded: chain H residue 527 LEU Chi-restraints excluded: chain H residue 542 GLU Chi-restraints excluded: chain J residue 335 THR Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain K residue 392 SER Chi-restraints excluded: chain L residue 192 ASP Chi-restraints excluded: chain M residue 136 ILE Chi-restraints excluded: chain M residue 329 SER Chi-restraints excluded: chain N residue 63 HIS Chi-restraints excluded: chain N residue 71 TYR Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 158 VAL Chi-restraints excluded: chain N residue 189 VAL Chi-restraints excluded: chain N residue 203 VAL Chi-restraints excluded: chain N residue 268 ARG Chi-restraints excluded: chain O residue 88 GLN Chi-restraints excluded: chain O residue 124 GLU Chi-restraints excluded: chain O residue 168 THR Chi-restraints excluded: chain P residue 120 MET Chi-restraints excluded: chain Q residue 579 LEU Chi-restraints excluded: chain Q residue 595 THR Chi-restraints excluded: chain Q residue 633 THR Chi-restraints excluded: chain Q residue 643 THR Chi-restraints excluded: chain Q residue 757 THR Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain R residue 121 THR Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain S residue 229 GLN Chi-restraints excluded: chain S residue 297 SER Chi-restraints excluded: chain S residue 334 VAL Chi-restraints excluded: chain T residue 122 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 682 random chunks: chunk 429 optimal weight: 20.0000 chunk 576 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 chunk 498 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 chunk 541 optimal weight: 9.9990 chunk 226 optimal weight: 4.9990 chunk 556 optimal weight: 20.0000 chunk 68 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 124 ASN ** C 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 542 ASN C1068 ASN ** G 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 126 ASN ** N 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.119519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.079484 restraints weight = 111582.626| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.90 r_work: 0.2988 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 58496 Z= 0.329 Angle : 0.605 16.610 79419 Z= 0.310 Chirality : 0.045 0.198 8612 Planarity : 0.005 0.066 9969 Dihedral : 11.508 143.727 8445 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.72 % Favored : 96.23 % Rotamer: Outliers : 2.11 % Allowed : 22.81 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.41 % Cis-general : 0.00 % Twisted Proline : 0.29 % 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: 6685 helix: 1.04 (0.10), residues: 2797 sheet: 0.08 (0.17), residues: 868 loop : -0.22 (0.11), residues: 3020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.002 TRP H 517 HIS 0.011 0.001 HIS F 487 PHE 0.028 0.002 PHE B 226 TYR 0.033 0.002 TYR G 652 ARG 0.014 0.000 ARG C 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25670.29 seconds wall clock time: 442 minutes 9.28 seconds (26529.28 seconds total)