Starting phenix.real_space_refine on Thu Feb 22 08:00:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbc_31878/02_2024/7vbc_31878.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbc_31878/02_2024/7vbc_31878.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbc_31878/02_2024/7vbc_31878.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbc_31878/02_2024/7vbc_31878.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbc_31878/02_2024/7vbc_31878.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vbc_31878/02_2024/7vbc_31878.pdb" } resolution = 3.01 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= -0.001 sd= 0.112 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 188 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 39 5.49 5 Mg 1 5.21 5 S 226 5.16 5 C 21078 2.51 5 N 5832 2.21 5 O 6233 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 23": "OE1" <-> "OE2" Residue "A GLU 24": "OE1" <-> "OE2" Residue "A ARG 37": "NH1" <-> "NH2" Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 62": "OE1" <-> "OE2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A GLU 272": "OE1" <-> "OE2" Residue "A GLU 348": "OE1" <-> "OE2" Residue "A GLU 571": "OE1" <-> "OE2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A GLU 651": "OE1" <-> "OE2" Residue "A GLU 698": "OE1" <-> "OE2" Residue "A ARG 722": "NH1" <-> "NH2" Residue "A PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 793": "NH1" <-> "NH2" Residue "A GLU 800": "OE1" <-> "OE2" Residue "A GLU 818": "OE1" <-> "OE2" Residue "A GLU 835": "OE1" <-> "OE2" Residue "A GLU 867": "OE1" <-> "OE2" Residue "A GLU 920": "OE1" <-> "OE2" Residue "A GLU 942": "OE1" <-> "OE2" Residue "A GLU 997": "OE1" <-> "OE2" Residue "A GLU 1021": "OE1" <-> "OE2" Residue "A PHE 1031": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1055": "OE1" <-> "OE2" Residue "A ARG 1085": "NH1" <-> "NH2" Residue "A GLU 1098": "OE1" <-> "OE2" Residue "A GLU 1106": "OE1" <-> "OE2" Residue "A ARG 1110": "NH1" <-> "NH2" Residue "A ARG 1122": "NH1" <-> "NH2" Residue "A GLU 1130": "OE1" <-> "OE2" Residue "A ARG 1133": "NH1" <-> "NH2" Residue "A GLU 1164": "OE1" <-> "OE2" Residue "A GLU 1183": "OE1" <-> "OE2" Residue "A GLU 1292": "OE1" <-> "OE2" Residue "A GLU 1330": "OE1" <-> "OE2" Residue "A ARG 1340": "NH1" <-> "NH2" Residue "A GLU 1352": "OE1" <-> "OE2" Residue "A ARG 1500": "NH1" <-> "NH2" Residue "A GLU 1521": "OE1" <-> "OE2" Residue "A GLU 1575": "OE1" <-> "OE2" Residue "A GLU 1622": "OE1" <-> "OE2" Residue "A GLU 1624": "OE1" <-> "OE2" Residue "A GLU 1675": "OE1" <-> "OE2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B GLU 29": "OE1" <-> "OE2" Residue "B GLU 37": "OE1" <-> "OE2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B GLU 218": "OE1" <-> "OE2" Residue "B PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 291": "OE1" <-> "OE2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B GLU 306": "OE1" <-> "OE2" Residue "B GLU 321": "OE1" <-> "OE2" Residue "B GLU 341": "OE1" <-> "OE2" Residue "B GLU 360": "OE1" <-> "OE2" Residue "B GLU 363": "OE1" <-> "OE2" Residue "B GLU 390": "OE1" <-> "OE2" Residue "B GLU 586": "OE1" <-> "OE2" Residue "B ARG 588": "NH1" <-> "NH2" Residue "B GLU 594": "OE1" <-> "OE2" Residue "B GLU 638": "OE1" <-> "OE2" Residue "B GLU 650": "OE1" <-> "OE2" Residue "B TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 754": "OE1" <-> "OE2" Residue "B GLU 835": "OE1" <-> "OE2" Residue "B GLU 845": "OE1" <-> "OE2" Residue "B GLU 955": "OE1" <-> "OE2" Residue "B GLU 964": "OE1" <-> "OE2" Residue "B GLU 987": "OE1" <-> "OE2" Residue "B GLU 989": "OE1" <-> "OE2" Residue "B PHE 993": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1029": "NH1" <-> "NH2" Residue "B TYR 1096": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 8": "OE1" <-> "OE2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "C GLU 104": "OE1" <-> "OE2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C GLU 263": "OE1" <-> "OE2" Residue "C GLU 291": "OE1" <-> "OE2" Residue "C ARG 298": "NH1" <-> "NH2" Residue "E ARG 55": "NH1" <-> "NH2" Residue "E GLU 128": "OE1" <-> "OE2" Residue "E GLU 141": "OE1" <-> "OE2" Residue "E GLU 147": "OE1" <-> "OE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H GLU 107": "OE1" <-> "OE2" Residue "L GLU 25": "OE1" <-> "OE2" Residue "N GLU 33": "OE1" <-> "OE2" Residue "N GLU 41": "OE1" <-> "OE2" Residue "N GLU 54": "OE1" <-> "OE2" Residue "N GLU 91": "OE1" <-> "OE2" Residue "N GLU 100": "OE1" <-> "OE2" Residue "N GLU 119": "OE1" <-> "OE2" Residue "N ARG 148": "NH1" <-> "NH2" Residue "G GLU 84": "OE1" <-> "OE2" Residue "G GLU 101": "OE1" <-> "OE2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "M GLU 45": "OE1" <-> "OE2" Residue "M GLU 63": "OE1" <-> "OE2" Residue "M GLU 100": "OE1" <-> "OE2" Residue "M GLU 105": "OE1" <-> "OE2" Residue "I GLU 51": "OE1" <-> "OE2" Residue "I ARG 86": "NH1" <-> "NH2" Residue "I GLU 93": "OE1" <-> "OE2" Residue "I ARG 100": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 33414 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 11775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1477, 11775 Classifications: {'peptide': 1477} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 71, 'TRANS': 1405} Chain breaks: 8 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 8912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1123, 8912 Classifications: {'peptide': 1123} Link IDs: {'PTRANS': 63, 'TRANS': 1059} Chain breaks: 1 Chain: "C" Number of atoms: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2697 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 17, 'TRANS': 319} Chain: "E" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1641 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 10, 'TRANS': 188} Chain breaks: 1 Chain: "F" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 610 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 5, 'TRANS': 70} Chain: "H" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1176 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain: "J" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 507 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "K" Number of atoms: 863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 863 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "L" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 379 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "N" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1105 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 24, 'TRANS': 126} Chain: "G" Number of atoms: 1229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1229 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain breaks: 1 Chain: "M" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 867 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "I" Number of atoms: 822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 822 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Chain breaks: 1 Chain: "R" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 128 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 3} Link IDs: {'rna3p': 5} Chain: "T" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 415 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "U" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 282 Classifications: {'DNA': 14} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 13} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 455 SG CYS A 64 60.733 54.068 57.791 1.00 70.96 S ATOM 529 SG CYS A 74 63.053 55.707 59.323 1.00 63.65 S ATOM 767 SG CYS A 104 61.764 106.330 46.911 1.00 76.34 S ATOM 1517 SG CYS A 205 64.778 108.738 46.331 1.00 87.17 S ATOM 20240 SG CYS B1070 74.206 64.067 47.501 1.00 51.70 S ATOM 20262 SG CYS B1073 74.291 67.017 45.977 1.00 54.67 S ATOM 20396 SG CYS B1098 71.031 63.729 46.863 1.00 72.84 S ATOM 20417 SG CYS B1101 72.960 64.544 44.248 1.00 83.89 S ATOM 26866 SG CYS J 7 77.793 46.388 127.804 1.00 34.15 S ATOM 26890 SG CYS J 10 81.523 44.624 129.269 1.00 21.98 S ATOM 27154 SG CYS J 44 80.852 47.764 129.666 1.00 21.89 S ATOM 27160 SG CYS J 45 78.846 45.572 131.825 1.00 24.31 S ATOM 28230 SG CYS L 19 36.383 46.381 111.478 1.00 40.38 S ATOM 28366 SG CYS L 36 34.024 44.317 109.993 1.00 44.67 S ATOM 28392 SG CYS L 39 32.941 46.773 111.820 1.00 47.99 S Residues with excluded nonbonded symmetry interactions: 161 residue: pdb=" N GLY N 127 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY N 127 " occ=0.00 residue: pdb=" N GLY N 144 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY N 144 " occ=0.00 residue: pdb=" N GLY N 153 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY N 153 " occ=0.00 residue: pdb=" N GLY N 154 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY N 154 " occ=0.00 residue: pdb=" N SER G 46 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER G 46 " occ=0.00 residue: pdb=" N CYS G 47 " occ=0.00 ... (4 atoms not shown) pdb=" SG CYS G 47 " occ=0.00 residue: pdb=" N LEU G 48 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU G 48 " occ=0.00 residue: pdb=" N VAL G 49 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 VAL G 49 " occ=0.00 residue: pdb=" N ALA G 50 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA G 50 " occ=0.00 residue: pdb=" N GLY G 51 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY G 51 " occ=0.00 residue: pdb=" N PRO G 52 " occ=0.00 ... (5 atoms not shown) pdb=" CD PRO G 52 " occ=0.00 residue: pdb=" N HIS G 53 " occ=0.00 ... (8 atoms not shown) pdb=" NE2 HIS G 53 " occ=0.00 ... (remaining 149 not shown) Time building chain proxies: 18.20, per 1000 atoms: 0.54 Number of scatterers: 33414 At special positions: 0 Unit cell: (155.992, 161.262, 176.018, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 226 16.00 P 39 15.00 Mg 1 11.99 O 6233 8.00 N 5832 7.00 C 21078 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: 13.45 Conformation dependent library (CDL) restraints added in 6.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" ND1 HIS A 77 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 64 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb=" ZN A2002 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 205 " pdb="ZN ZN A2002 " - pdb=" SG CYS A 104 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1073 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1098 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1101 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1070 " pdb=" ZN J1001 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 10 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 45 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 44 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 7 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 39 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 36 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 19 " Number of angles added : 12 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7670 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 38 sheets defined 33.1% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.92 Creating SS restraints... Processing helix chain 'A' and resid 92 through 102 Processing helix chain 'A' and resid 113 through 128 Processing helix chain 'A' and resid 132 through 144 removed outlier: 4.667A pdb=" N TYR A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 172 removed outlier: 4.260A pdb=" N TYR A 164 " --> pdb=" O GLU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 180 removed outlier: 3.957A pdb=" N ALA A 179 " --> pdb=" O SER A 176 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS A 180 " --> pdb=" O GLN A 177 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 176 through 180' Processing helix chain 'A' and resid 184 through 199 removed outlier: 3.540A pdb=" N LYS A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 280 removed outlier: 3.700A pdb=" N LYS A 270 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N PHE A 275 " --> pdb=" O ASN A 271 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N TYR A 278 " --> pdb=" O PHE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 296 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 322 through 348 Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.503A pdb=" N ILE A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 removed outlier: 3.908A pdb=" N ASP A 407 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 476 through 487 Processing helix chain 'A' and resid 513 through 520 removed outlier: 3.642A pdb=" N LYS A 520 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 559 No H-bonds generated for 'chain 'A' and resid 557 through 559' Processing helix chain 'A' and resid 581 through 586 removed outlier: 3.830A pdb=" N TYR A 585 " --> pdb=" O ASN A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 611 removed outlier: 3.784A pdb=" N GLU A 607 " --> pdb=" O LEU A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 633 No H-bonds generated for 'chain 'A' and resid 631 through 633' Processing helix chain 'A' and resid 634 through 642 removed outlier: 3.567A pdb=" N GLY A 638 " --> pdb=" O HIS A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 654 Processing helix chain 'A' and resid 657 through 662 Processing helix chain 'A' and resid 684 through 696 removed outlier: 3.810A pdb=" N ASN A 694 " --> pdb=" O THR A 690 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 733 removed outlier: 3.654A pdb=" N MET A 732 " --> pdb=" O PRO A 729 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N CYS A 733 " --> pdb=" O ASP A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 770 Processing helix chain 'A' and resid 770 through 792 removed outlier: 3.674A pdb=" N SER A 774 " --> pdb=" O GLY A 770 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LEU A 789 " --> pdb=" O PHE A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 820 removed outlier: 3.608A pdb=" N THR A 820 " --> pdb=" O ILE A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 831 removed outlier: 3.772A pdb=" N ALA A 826 " --> pdb=" O CYS A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 851 Processing helix chain 'A' and resid 857 through 866 removed outlier: 3.847A pdb=" N ILE A 861 " --> pdb=" O ASP A 857 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 881 removed outlier: 3.588A pdb=" N ALA A 879 " --> pdb=" O GLU A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 905 through 910 Processing helix chain 'A' and resid 944 through 948 Processing helix chain 'A' and resid 960 through 996 removed outlier: 3.655A pdb=" N LEU A 975 " --> pdb=" O GLY A 971 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TYR A 987 " --> pdb=" O SER A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1030 removed outlier: 3.614A pdb=" N LYS A1028 " --> pdb=" O ASP A1025 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN A1030 " --> pdb=" O PRO A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1036 through 1043 Processing helix chain 'A' and resid 1043 through 1051 Processing helix chain 'A' and resid 1052 through 1059 removed outlier: 3.705A pdb=" N VAL A1056 " --> pdb=" O HIS A1052 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A1057 " --> pdb=" O LEU A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1079 Processing helix chain 'A' and resid 1087 through 1092 Processing helix chain 'A' and resid 1095 through 1103 removed outlier: 4.500A pdb=" N ALA A1102 " --> pdb=" O GLU A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1126 removed outlier: 4.043A pdb=" N GLN A1118 " --> pdb=" O SER A1114 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLU A1119 " --> pdb=" O PRO A1115 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N MET A1120 " --> pdb=" O GLY A1116 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU A1126 " --> pdb=" O ARG A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1136 through 1140 removed outlier: 3.765A pdb=" N ALA A1140 " --> pdb=" O LYS A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1150 removed outlier: 3.531A pdb=" N VAL A1149 " --> pdb=" O PRO A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1179 removed outlier: 3.800A pdb=" N THR A1165 " --> pdb=" O GLU A1161 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A1176 " --> pdb=" O GLN A1172 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLN A1177 " --> pdb=" O GLU A1173 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A1179 " --> pdb=" O ALA A1175 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1202 removed outlier: 3.948A pdb=" N THR A1194 " --> pdb=" O ASP A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1210 through 1226 removed outlier: 3.758A pdb=" N LEU A1214 " --> pdb=" O ALA A1210 " (cutoff:3.500A) Proline residue: A1222 - end of helix Processing helix chain 'A' and resid 1244 through 1252 Processing helix chain 'A' and resid 1271 through 1286 removed outlier: 3.926A pdb=" N LYS A1279 " --> pdb=" O LEU A1275 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N SER A1280 " --> pdb=" O LYS A1276 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR A1286 " --> pdb=" O LYS A1282 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1293 No H-bonds generated for 'chain 'A' and resid 1291 through 1293' Processing helix chain 'A' and resid 1323 through 1331 removed outlier: 4.030A pdb=" N TYR A1326 " --> pdb=" O PRO A1323 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A1327 " --> pdb=" O HIS A1324 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N GLN A1328 " --> pdb=" O ALA A1325 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLN A1329 " --> pdb=" O TYR A1326 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU A1330 " --> pdb=" O TYR A1327 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS A1331 " --> pdb=" O GLN A1328 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1323 through 1331' Processing helix chain 'A' and resid 1334 through 1345 Processing helix chain 'A' and resid 1345 through 1359 removed outlier: 4.115A pdb=" N MET A1351 " --> pdb=" O PHE A1347 " (cutoff:3.500A) Processing helix chain 'A' and resid 1497 through 1509 removed outlier: 3.639A pdb=" N ARG A1501 " --> pdb=" O ALA A1497 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1547 Processing helix chain 'A' and resid 1585 through 1592 removed outlier: 4.968A pdb=" N LYS A1590 " --> pdb=" O GLU A1587 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA A1592 " --> pdb=" O PHE A1589 " (cutoff:3.500A) Processing helix chain 'A' and resid 1607 through 1612 Processing helix chain 'A' and resid 1613 through 1631 removed outlier: 4.247A pdb=" N ARG A1619 " --> pdb=" O GLU A1615 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A1620 " --> pdb=" O ALA A1616 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A1631 " --> pdb=" O ASP A1627 " (cutoff:3.500A) Processing helix chain 'A' and resid 1637 through 1649 removed outlier: 3.758A pdb=" N LEU A1641 " --> pdb=" O ASP A1637 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A1643 " --> pdb=" O ARG A1639 " (cutoff:3.500A) Processing helix chain 'A' and resid 1676 through 1687 Processing helix chain 'A' and resid 1695 through 1702 removed outlier: 3.656A pdb=" N VAL A1702 " --> pdb=" O ALA A1698 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 51 removed outlier: 3.582A pdb=" N SER B 45 " --> pdb=" O ALA B 41 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE B 46 " --> pdb=" O HIS B 42 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS B 51 " --> pdb=" O ASN B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 61 removed outlier: 4.003A pdb=" N GLY B 55 " --> pdb=" O HIS B 51 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 159 removed outlier: 3.664A pdb=" N GLU B 158 " --> pdb=" O GLN B 154 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 154 through 159' Processing helix chain 'B' and resid 195 through 202 removed outlier: 3.677A pdb=" N LYS B 199 " --> pdb=" O PRO B 196 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR B 200 " --> pdb=" O LYS B 197 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY B 202 " --> pdb=" O LYS B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 257 Processing helix chain 'B' and resid 260 through 269 removed outlier: 3.524A pdb=" N ILE B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 289 removed outlier: 3.830A pdb=" N ARG B 279 " --> pdb=" O ASP B 275 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL B 289 " --> pdb=" O MET B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 309 Processing helix chain 'B' and resid 319 through 332 removed outlier: 3.554A pdb=" N ILE B 332 " --> pdb=" O PHE B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 358 Processing helix chain 'B' and resid 368 through 372 Processing helix chain 'B' and resid 376 through 404 removed outlier: 3.636A pdb=" N GLU B 387 " --> pdb=" O MET B 383 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ALA B 404 " --> pdb=" O PHE B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 412 removed outlier: 3.560A pdb=" N MET B 411 " --> pdb=" O THR B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 423 removed outlier: 3.667A pdb=" N THR B 421 " --> pdb=" O MET B 417 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N MET B 422 " --> pdb=" O ARG B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 436 removed outlier: 4.092A pdb=" N PHE B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU B 431 " --> pdb=" O THR B 427 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU B 433 " --> pdb=" O PRO B 429 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE B 434 " --> pdb=" O PHE B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 466 removed outlier: 3.652A pdb=" N TYR B 465 " --> pdb=" O ASN B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 480 removed outlier: 3.662A pdb=" N ALA B 479 " --> pdb=" O ALA B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 538 removed outlier: 3.652A pdb=" N CYS B 535 " --> pdb=" O PRO B 531 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASN B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 585 Processing helix chain 'B' and resid 637 through 642 removed outlier: 3.610A pdb=" N ILE B 640 " --> pdb=" O MET B 637 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE B 641 " --> pdb=" O GLU B 638 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N MET B 642 " --> pdb=" O GLN B 639 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 637 through 642' Processing helix chain 'B' and resid 676 through 680 removed outlier: 3.559A pdb=" N ASN B 680 " --> pdb=" O SER B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 692 removed outlier: 3.504A pdb=" N ASN B 685 " --> pdb=" O GLN B 681 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN B 690 " --> pdb=" O MET B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 730 Processing helix chain 'B' and resid 761 through 766 Processing helix chain 'B' and resid 800 through 804 removed outlier: 3.838A pdb=" N LEU B 804 " --> pdb=" O PRO B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 924 removed outlier: 3.662A pdb=" N ARG B 923 " --> pdb=" O GLY B 919 " (cutoff:3.500A) Processing helix chain 'B' and resid 925 through 942 removed outlier: 4.199A pdb=" N LEU B 929 " --> pdb=" O THR B 925 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N MET B 933 " --> pdb=" O LEU B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 968 Processing helix chain 'B' and resid 1038 through 1048 removed outlier: 3.761A pdb=" N ARG B1042 " --> pdb=" O GLY B1038 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ASP B1043 " --> pdb=" O GLU B1039 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA B1044 " --> pdb=" O MET B1040 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS B1048 " --> pdb=" O ALA B1044 " (cutoff:3.500A) Processing helix chain 'B' and resid 1050 through 1062 Processing helix chain 'B' and resid 1113 through 1125 Processing helix chain 'C' and resid 41 through 49 Processing helix chain 'C' and resid 69 through 83 Processing helix chain 'C' and resid 102 through 112 Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 169 through 171 No H-bonds generated for 'chain 'C' and resid 169 through 171' Processing helix chain 'C' and resid 222 through 226 Processing helix chain 'C' and resid 248 through 256 removed outlier: 3.953A pdb=" N GLU C 252 " --> pdb=" O GLU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 281 Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 317 through 341 Processing helix chain 'E' and resid 5 through 24 Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 36 through 44 Processing helix chain 'E' and resid 83 through 98 removed outlier: 3.717A pdb=" N TYR E 90 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG E 93 " --> pdb=" O VAL E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.937A pdb=" N LYS E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N GLN E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 4.289A pdb=" N ILE E 126 " --> pdb=" O PRO E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 164 removed outlier: 3.845A pdb=" N THR E 157 " --> pdb=" O LYS E 153 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU E 158 " --> pdb=" O GLU E 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 30 through 38 Processing helix chain 'J' and resid 42 through 51 removed outlier: 3.755A pdb=" N MET J 48 " --> pdb=" O CYS J 44 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) Processing helix chain 'J' and resid 55 through 60 Processing helix chain 'K' and resid 48 through 60 Processing helix chain 'K' and resid 93 through 128 removed outlier: 3.659A pdb=" N ASN K 101 " --> pdb=" O GLN K 97 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG K 128 " --> pdb=" O GLN K 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 36 Processing helix chain 'N' and resid 52 through 57 Processing helix chain 'N' and resid 99 through 102 Processing helix chain 'G' and resid 60 through 64 removed outlier: 3.785A pdb=" N LEU G 64 " --> pdb=" O PRO G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 74 removed outlier: 3.800A pdb=" N ARG G 72 " --> pdb=" O ARG G 68 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLN G 74 " --> pdb=" O GLY G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 156 through 160 removed outlier: 3.738A pdb=" N GLU G 159 " --> pdb=" O PRO G 156 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLN G 160 " --> pdb=" O LYS G 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 156 through 160' Processing helix chain 'M' and resid 35 through 39 Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.517A pdb=" N ASN M 82 " --> pdb=" O LEU M 79 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1690 through 1691 removed outlier: 4.803A pdb=" N GLY A 14 " --> pdb=" O ASP B1133 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP B1133 " --> pdb=" O GLY A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 79 through 88 removed outlier: 10.825A pdb=" N LEU A 83 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 11.151A pdb=" N VAL A 303 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 9.783A pdb=" N LEU A 85 " --> pdb=" O PHE A 301 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N PHE A 301 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 216 through 217 removed outlier: 3.671A pdb=" N THR A 224 " --> pdb=" O ARG A 216 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 436 through 437 removed outlier: 3.837A pdb=" N VAL A 437 " --> pdb=" O ILE B1035 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE B1035 " --> pdb=" O VAL A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 561 through 564 Processing sheet with id=AA6, first strand: chain 'A' and resid 445 through 447 removed outlier: 6.040A pdb=" N CYS A 446 " --> pdb=" O LEU A 577 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ILE A 456 " --> pdb=" O ARG A 567 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 467 through 471 removed outlier: 4.137A pdb=" N MET A 496 " --> pdb=" O CYS A 539 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N HIS A 541 " --> pdb=" O ALA A 494 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ALA A 494 " --> pdb=" O HIS A 541 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 705 through 708 Processing sheet with id=AA9, first strand: chain 'A' and resid 917 through 918 Processing sheet with id=AB1, first strand: chain 'A' and resid 1000 through 1001 removed outlier: 6.862A pdb=" N VAL A1007 " --> pdb=" O VAL A1015 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1562 through 1565 removed outlier: 3.685A pdb=" N VAL A1577 " --> pdb=" O ASN A1565 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL A1266 " --> pdb=" O LEU A1578 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1288 through 1289 removed outlier: 3.716A pdb=" N VAL A1288 " --> pdb=" O TYR A1554 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR A1554 " --> pdb=" O VAL A1288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1298 through 1300 Processing sheet with id=AB5, first strand: chain 'A' and resid 1713 through 1714 Processing sheet with id=AB6, first strand: chain 'B' and resid 64 through 68 removed outlier: 3.530A pdb=" N PHE B 75 " --> pdb=" O PHE B 64 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N ASP B 117 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ALA B 80 " --> pdb=" O THR B 115 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N THR B 115 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE B 82 " --> pdb=" O LYS B 113 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LYS B 113 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA B 116 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N PHE B 133 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 118 " --> pdb=" O LYS B 131 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LYS B 131 " --> pdb=" O ILE B 118 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N TRP B 120 " --> pdb=" O ILE B 129 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE B 129 " --> pdb=" O TRP B 120 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL B 122 " --> pdb=" O LYS B 127 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LYS B 127 " --> pdb=" O VAL B 122 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 373 through 375 removed outlier: 3.507A pdb=" N LEU B 182 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N MET B 181 " --> pdb=" O CYS B 471 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 190 through 193 removed outlier: 5.363A pdb=" N TYR B 208 " --> pdb=" O TYR B 228 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN B 223 " --> pdb=" O ILE B 239 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE B 239 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 519 through 520 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 632 through 635 current: chain 'B' and resid 658 through 660 Processing sheet with id=AC1, first strand: chain 'B' and resid 553 through 554 Processing sheet with id=AC2, first strand: chain 'B' and resid 594 through 598 Processing sheet with id=AC3, first strand: chain 'B' and resid 695 through 696 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 695 through 696 current: chain 'B' and resid 913 through 915 removed outlier: 7.462A pdb=" N MET B 757 " --> pdb=" O SER B 894 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU B 896 " --> pdb=" O MET B 757 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL B 759 " --> pdb=" O LEU B 896 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LYS B 882 " --> pdb=" O LEU B1002 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 712 through 714 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 771 through 780 current: chain 'B' and resid 847 through 855 removed outlier: 7.965A pdb=" N CYS B 847 " --> pdb=" O PRO B 874 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N VAL B 849 " --> pdb=" O ARG B 872 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N ARG B 872 " --> pdb=" O VAL B 849 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN B 851 " --> pdb=" O THR B 870 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N CYS B 866 " --> pdb=" O CYS B 855 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 866 through 874 current: chain 'L' and resid 25 through 26 Processing sheet with id=AC5, first strand: chain 'B' and resid 828 through 830 removed outlier: 3.516A pdb=" N TYR B 828 " --> pdb=" O PHE B 837 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU B 835 " --> pdb=" O ASN B 830 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1018 through 1019 removed outlier: 3.565A pdb=" N GLN B1024 " --> pdb=" O ASP B1019 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1065 through 1069 removed outlier: 3.552A pdb=" N ASP B1108 " --> pdb=" O VAL B1069 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 1079 through 1080 Processing sheet with id=AC9, first strand: chain 'C' and resid 13 through 14 removed outlier: 4.699A pdb=" N LEU C 236 " --> pdb=" O VAL C 302 " (cutoff:3.500A) removed outlier: 9.134A pdb=" N ASP C 304 " --> pdb=" O ARG C 234 " (cutoff:3.500A) removed outlier: 10.256A pdb=" N ARG C 234 " --> pdb=" O ASP C 304 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 173 through 176 removed outlier: 4.561A pdb=" N GLN C 139 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLU C 207 " --> pdb=" O ASN C 96 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ASN C 96 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ASP C 209 " --> pdb=" O VAL C 94 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N VAL C 94 " --> pdb=" O ASP C 209 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU C 211 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL C 92 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N HIS C 213 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 167 through 168 removed outlier: 3.519A pdb=" N ALA C 200 " --> pdb=" O VAL C 168 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 263 through 265 Processing sheet with id=AD4, first strand: chain 'E' and resid 60 through 63 removed outlier: 6.169A pdb=" N ILE E 104 " --> pdb=" O PHE E 130 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 81 through 82 removed outlier: 3.523A pdb=" N VAL E 82 " --> pdb=" O GLY E 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.560A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 90 through 91 removed outlier: 5.453A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG H 98 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N LEU H 122 " --> pdb=" O ASP H 42 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU H 39 " --> pdb=" O CYS H 30 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU H 31 " --> pdb=" O VAL H 12 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N VAL H 12 " --> pdb=" O GLU H 31 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'K' and resid 27 through 31 Processing sheet with id=AD9, first strand: chain 'N' and resid 18 through 20 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 18 through 20 current: chain 'N' and resid 76 through 85 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 76 through 85 current: chain 'N' and resid 105 through 107 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 105 through 107 current: chain 'M' and resid 58 through 63 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 68 through 72 current: chain 'M' and resid 98 through 111 Processing sheet with id=AE1, first strand: chain 'G' and resid 48 through 59 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 48 through 59 current: chain 'G' and resid 112 through 123 No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'I' and resid 96 through 100 1018 hydrogen bonds defined for protein. 2814 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.53 Time building geometry restraints manager: 14.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 5476 1.29 - 1.43: 8859 1.43 - 1.57: 19432 1.57 - 1.70: 76 1.70 - 1.84: 349 Bond restraints: 34192 Sorted by residual: bond pdb=" C ARG M 66 " pdb=" N LEU M 67 " ideal model delta sigma weight residual 1.331 1.221 0.110 1.22e-02 6.72e+03 8.11e+01 bond pdb=" C PRO B 590 " pdb=" O PRO B 590 " ideal model delta sigma weight residual 1.246 1.176 0.070 8.50e-03 1.38e+04 6.80e+01 bond pdb=" C ALA M 61 " pdb=" N ALA M 62 " ideal model delta sigma weight residual 1.331 1.227 0.104 1.34e-02 5.57e+03 6.02e+01 bond pdb=" C ASN N 155 " pdb=" N PRO N 156 " ideal model delta sigma weight residual 1.329 1.419 -0.089 1.18e-02 7.18e+03 5.74e+01 bond pdb=" C GLU N 100 " pdb=" N ALA N 101 " ideal model delta sigma weight residual 1.334 1.240 0.093 1.24e-02 6.50e+03 5.67e+01 ... (remaining 34187 not shown) Histogram of bond angle deviations from ideal: 90.65 - 99.46: 38 99.46 - 108.28: 2810 108.28 - 117.09: 21475 117.09 - 125.90: 21499 125.90 - 134.72: 562 Bond angle restraints: 46384 Sorted by residual: angle pdb=" N VAL C 164 " pdb=" CA VAL C 164 " pdb=" C VAL C 164 " ideal model delta sigma weight residual 112.12 98.64 13.48 8.40e-01 1.42e+00 2.57e+02 angle pdb=" C CYS J 10 " pdb=" CA CYS J 10 " pdb=" CB CYS J 10 " ideal model delta sigma weight residual 110.90 90.65 20.25 1.58e+00 4.01e-01 1.64e+02 angle pdb=" C GLU A 875 " pdb=" N ILE A 876 " pdb=" CA ILE A 876 " ideal model delta sigma weight residual 121.34 102.85 18.49 1.62e+00 3.81e-01 1.30e+02 angle pdb=" N GLU A1507 " pdb=" CA GLU A1507 " pdb=" C GLU A1507 " ideal model delta sigma weight residual 111.07 99.36 11.71 1.07e+00 8.73e-01 1.20e+02 angle pdb=" N THR K 25 " pdb=" CA THR K 25 " pdb=" C THR K 25 " ideal model delta sigma weight residual 113.18 100.91 12.27 1.21e+00 6.83e-01 1.03e+02 ... (remaining 46379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.04: 18177 18.04 - 36.07: 1841 36.07 - 54.11: 535 54.11 - 72.15: 126 72.15 - 90.18: 37 Dihedral angle restraints: 20716 sinusoidal: 8824 harmonic: 11892 Sorted by residual: dihedral pdb=" N GLN A 553 " pdb=" C GLN A 553 " pdb=" CA GLN A 553 " pdb=" CB GLN A 553 " ideal model delta harmonic sigma weight residual 122.80 150.77 -27.97 0 2.50e+00 1.60e-01 1.25e+02 dihedral pdb=" C GLN A 553 " pdb=" N GLN A 553 " pdb=" CA GLN A 553 " pdb=" CB GLN A 553 " ideal model delta harmonic sigma weight residual -122.60 -150.32 27.72 0 2.50e+00 1.60e-01 1.23e+02 dihedral pdb=" C CYS J 10 " pdb=" N CYS J 10 " pdb=" CA CYS J 10 " pdb=" CB CYS J 10 " ideal model delta harmonic sigma weight residual -122.60 -101.38 -21.22 0 2.50e+00 1.60e-01 7.20e+01 ... (remaining 20713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.249: 4933 0.249 - 0.498: 188 0.498 - 0.746: 11 0.746 - 0.995: 0 0.995 - 1.244: 1 Chirality restraints: 5133 Sorted by residual: chirality pdb=" CA GLN A 553 " pdb=" N GLN A 553 " pdb=" C GLN A 553 " pdb=" CB GLN A 553 " both_signs ideal model delta sigma weight residual False 2.51 1.27 1.24 2.00e-01 2.50e+01 3.87e+01 chirality pdb=" CA PRO C 259 " pdb=" N PRO C 259 " pdb=" C PRO C 259 " pdb=" CB PRO C 259 " both_signs ideal model delta sigma weight residual False 2.72 1.98 0.74 2.00e-01 2.50e+01 1.36e+01 chirality pdb=" CB THR K 25 " pdb=" CA THR K 25 " pdb=" OG1 THR K 25 " pdb=" CG2 THR K 25 " both_signs ideal model delta sigma weight residual False 2.55 1.89 0.66 2.00e-01 2.50e+01 1.08e+01 ... (remaining 5130 not shown) Planarity restraints: 5869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B1056 " 0.036 2.00e-02 2.50e+03 7.47e-02 5.58e+01 pdb=" C ASP B1056 " -0.129 2.00e-02 2.50e+03 pdb=" O ASP B1056 " 0.048 2.00e-02 2.50e+03 pdb=" N ARG B1057 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B1058 " -0.033 2.00e-02 2.50e+03 6.57e-02 4.32e+01 pdb=" C LEU B1058 " 0.114 2.00e-02 2.50e+03 pdb=" O LEU B1058 " -0.041 2.00e-02 2.50e+03 pdb=" N PHE B1059 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 721 " 0.031 2.00e-02 2.50e+03 6.41e-02 4.11e+01 pdb=" C PRO A 721 " -0.111 2.00e-02 2.50e+03 pdb=" O PRO A 721 " 0.041 2.00e-02 2.50e+03 pdb=" N ARG A 722 " 0.038 2.00e-02 2.50e+03 ... (remaining 5866 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.15: 28 2.15 - 2.84: 11447 2.84 - 3.53: 43831 3.53 - 4.21: 81060 4.21 - 4.90: 140731 Nonbonded interactions: 277097 Sorted by model distance: nonbonded pdb=" C7 DT T 0 " pdb=" O6 DG U 1 " model vdw 1.468 3.460 nonbonded pdb=" OH TYR M 69 " pdb=" O ASP I 16 " model vdw 1.721 2.440 nonbonded pdb=" NH1 ARG A 429 " pdb=" OP1 DG T 1 " model vdw 1.729 2.520 nonbonded pdb=" OD2 ASP B 543 " pdb=" N CYS M 81 " model vdw 1.815 2.520 nonbonded pdb=" O ASN B 536 " pdb=" N GLU N 119 " model vdw 1.836 2.520 ... (remaining 277092 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.96 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.020 Extract box with map and model: 8.820 Check model and map are aligned: 0.480 Set scattering table: 0.270 Process input model: 96.110 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.120 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6426 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 : 0.010 0.110 34192 Z= 0.629 Angle : 1.484 20.249 46384 Z= 1.043 Chirality : 0.101 1.244 5133 Planarity : 0.008 0.116 5869 Dihedral : 16.478 90.183 13046 Min Nonbonded Distance : 1.468 Molprobity Statistics. All-atom Clashscore : 33.53 Ramachandran Plot: Outliers : 0.44 % Allowed : 9.11 % Favored : 90.44 % Rotamer: Outliers : 6.11 % Allowed : 7.53 % Favored : 86.37 % Cbeta Deviations : 2.19 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.43 (0.12), residues: 4050 helix: -1.83 (0.13), residues: 1209 sheet: -1.87 (0.19), residues: 646 loop : -2.73 (0.12), residues: 2195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 9 HIS 0.021 0.002 HIS C 166 PHE 0.050 0.002 PHE B 75 TYR 0.046 0.002 TYR B 826 ARG 0.010 0.001 ARG G 183 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1071 residues out of total 3588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 852 time to evaluate : 3.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.6255 (mt) cc_final: 0.5857 (mt) REVERT: A 412 ASP cc_start: 0.3599 (OUTLIER) cc_final: 0.3390 (m-30) REVERT: A 618 TYR cc_start: 0.8352 (t80) cc_final: 0.8079 (t80) REVERT: A 635 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7111 (mpp) REVERT: A 664 LYS cc_start: 0.4223 (OUTLIER) cc_final: 0.3608 (ptpp) REVERT: A 1044 TYR cc_start: 0.7476 (t80) cc_final: 0.7007 (t80) REVERT: A 1239 MET cc_start: 0.4380 (ptt) cc_final: 0.2919 (tpp) REVERT: A 1268 VAL cc_start: 0.5184 (OUTLIER) cc_final: 0.4927 (t) REVERT: A 1606 HIS cc_start: 0.5936 (OUTLIER) cc_final: 0.5608 (t-90) REVERT: B 31 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7894 (mt0) REVERT: B 338 SER cc_start: 0.6977 (OUTLIER) cc_final: 0.6659 (m) REVERT: B 364 ASP cc_start: 0.7603 (m-30) cc_final: 0.7213 (m-30) REVERT: B 524 PHE cc_start: 0.5075 (m-80) cc_final: 0.4551 (t80) REVERT: B 584 LEU cc_start: 0.8081 (mt) cc_final: 0.7476 (mt) REVERT: B 659 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6978 (tt0) REVERT: B 691 MET cc_start: 0.7647 (mtp) cc_final: 0.7173 (mtp) REVERT: K 60 MET cc_start: 0.6864 (mmm) cc_final: 0.6427 (mmm) REVERT: N 60 HIS cc_start: -0.0449 (OUTLIER) cc_final: -0.1121 (p-80) REVERT: G 98 VAL cc_start: 0.1008 (OUTLIER) cc_final: 0.0027 (m) outliers start: 219 outliers final: 56 residues processed: 995 average time/residue: 0.5039 time to fit residues: 785.7362 Evaluate side-chains 591 residues out of total 3588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 525 time to evaluate : 3.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 454 ASN Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 664 LYS Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 1051 GLN Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1269 LEU Chi-restraints excluded: chain A residue 1505 VAL Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1509 HIS Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1606 HIS Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 260 SER Chi-restraints excluded: chain B residue 307 CYS Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 461 ASN Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 542 ILE Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 828 TYR Chi-restraints excluded: chain B residue 864 PHE Chi-restraints excluded: chain B residue 1025 PRO Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1056 ASP Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 1105 ASP Chi-restraints excluded: chain B residue 1109 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain E residue 185 ILE Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 9 THR Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain N residue 60 HIS Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 83 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 342 optimal weight: 0.4980 chunk 307 optimal weight: 0.8980 chunk 170 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 164 optimal weight: 0.7980 chunk 318 optimal weight: 5.9990 chunk 123 optimal weight: 0.9980 chunk 193 optimal weight: 0.8980 chunk 236 optimal weight: 0.8980 chunk 368 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS A 80 HIS A 347 GLN A 397 HIS A 478 GLN A 486 ASN A 586 ASN A 595 ASN A 600 GLN A 617 GLN A 632 GLN A 704 ASN A 728 ASN A 753 HIS ** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 847 GLN A 850 HIS A 859 ASN A 877 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 ASN A 918 GLN A1043 ASN A1051 GLN A1068 HIS A1076 GLN A1109 ASN A1118 GLN A1177 GLN A1313 GLN A1329 GLN A1579 ASN A1683 GLN A1690 HIS B 9 ASN B 18 HIS B 31 GLN B 97 ASN ** B 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 ASN ** B 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 ASN B 468 HIS B 473 HIS B 639 GLN B 734 ASN B 846 ASN B 887 HIS ** B 941 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 945 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1004 HIS B1097 ASN C 32 ASN C 151 HIS C 165 ASN C 181 GLN ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 129 GLN J 61 ASN ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 88 GLN ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 HIS I 117 ASN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 34192 Z= 0.237 Angle : 0.739 11.596 46384 Z= 0.386 Chirality : 0.047 0.205 5133 Planarity : 0.006 0.066 5869 Dihedral : 12.225 86.108 5054 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.14 % Favored : 92.74 % Rotamer: Outliers : 3.90 % Allowed : 14.55 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.42 (0.12), residues: 4050 helix: -0.72 (0.14), residues: 1212 sheet: -1.48 (0.19), residues: 671 loop : -2.21 (0.12), residues: 2167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 494 HIS 0.008 0.001 HIS A 967 PHE 0.033 0.002 PHE E 73 TYR 0.029 0.002 TYR A 754 ARG 0.011 0.001 ARG A1085 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 3588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 574 time to evaluate : 3.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 ASP cc_start: 0.3291 (OUTLIER) cc_final: 0.3082 (m-30) REVERT: A 454 ASN cc_start: 0.7874 (p0) cc_final: 0.7599 (p0) REVERT: A 635 MET cc_start: 0.7366 (OUTLIER) cc_final: 0.6867 (mpp) REVERT: A 676 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8288 (mp) REVERT: A 1239 MET cc_start: 0.4665 (ptt) cc_final: 0.3231 (tpp) REVERT: A 1534 MET cc_start: 0.4139 (mtp) cc_final: 0.3710 (mtt) REVERT: B 94 LYS cc_start: 0.7595 (tptp) cc_final: 0.7129 (tttm) REVERT: B 158 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6912 (mt-10) REVERT: B 290 MET cc_start: 0.5288 (mmm) cc_final: 0.5065 (mmp) REVERT: B 430 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7064 (t80) REVERT: B 659 GLN cc_start: 0.7222 (OUTLIER) cc_final: 0.6828 (tt0) REVERT: B 1103 ARG cc_start: 0.6706 (tpm170) cc_final: 0.6456 (tpp-160) REVERT: C 298 ARG cc_start: 0.7370 (tpp-160) cc_final: 0.7158 (tpm170) REVERT: H 18 GLU cc_start: 0.6995 (pm20) cc_final: 0.6389 (pm20) REVERT: H 66 GLU cc_start: 0.6968 (mm-30) cc_final: 0.6762 (mm-30) REVERT: L 54 VAL cc_start: 0.8055 (OUTLIER) cc_final: 0.7821 (t) REVERT: I 107 GLU cc_start: 0.6192 (mm-30) cc_final: 0.5842 (mm-30) outliers start: 140 outliers final: 66 residues processed: 667 average time/residue: 0.4582 time to fit residues: 497.5567 Evaluate side-chains 534 residues out of total 3588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 461 time to evaluate : 4.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 664 LYS Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 803 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 995 HIS Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1505 VAL Chi-restraints excluded: chain A residue 1529 VAL Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1642 SER Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 158 GLU Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 430 PHE Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 659 GLN Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1035 ILE Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 1133 ASP Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain E residue 197 SER Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain M residue 67 LEU Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 92 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 204 optimal weight: 8.9990 chunk 114 optimal weight: 7.9990 chunk 306 optimal weight: 0.9990 chunk 251 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 369 optimal weight: 7.9990 chunk 399 optimal weight: 10.0000 chunk 328 optimal weight: 10.0000 chunk 366 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 296 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 541 HIS A 564 HIS A 578 HIS A 597 HIS A 700 HIS A 736 GLN ** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 ASN ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1043 ASN ** A1316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN B 219 HIS B 330 GLN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 461 ASN B 501 HIS B 513 HIS B 639 GLN C 42 GLN C 127 GLN C 143 GLN C 151 HIS C 194 HIS ** C 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 31 GLN K 85 GLN L 26 ASN N 60 HIS ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 108 ASN I 92 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 34192 Z= 0.508 Angle : 0.876 13.234 46384 Z= 0.457 Chirality : 0.053 0.231 5133 Planarity : 0.007 0.072 5869 Dihedral : 11.946 86.339 4993 Min Nonbonded Distance : 1.230 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.09 % Favored : 90.81 % Rotamer: Outliers : 5.63 % Allowed : 15.58 % Favored : 78.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -2.47 (0.12), residues: 4050 helix: -0.85 (0.14), residues: 1230 sheet: -1.35 (0.19), residues: 646 loop : -2.24 (0.12), residues: 2174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 9 HIS 0.035 0.002 HIS I 92 PHE 0.038 0.003 PHE E 73 TYR 0.028 0.003 TYR A 754 ARG 0.009 0.001 ARG C 279 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 3588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 534 time to evaluate : 4.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 ASP cc_start: 0.3888 (OUTLIER) cc_final: 0.3434 (m-30) REVERT: A 635 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.6944 (mpp) REVERT: A 676 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8254 (mp) REVERT: A 933 LYS cc_start: 0.6908 (OUTLIER) cc_final: 0.6645 (ptpt) REVERT: A 935 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7792 (mp) REVERT: A 1313 GLN cc_start: 0.4017 (OUTLIER) cc_final: 0.3780 (pt0) REVERT: A 1534 MET cc_start: 0.4525 (mtp) cc_final: 0.4276 (mtt) REVERT: A 1587 GLU cc_start: 0.5931 (OUTLIER) cc_final: 0.5632 (tp30) REVERT: B 69 LYS cc_start: 0.5871 (OUTLIER) cc_final: 0.5099 (tttm) REVERT: B 94 LYS cc_start: 0.7924 (tptp) cc_final: 0.7401 (tttm) REVERT: B 197 LYS cc_start: 0.7846 (tppt) cc_final: 0.7622 (ptpt) REVERT: B 691 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7320 (mtp) REVERT: B 835 GLU cc_start: 0.6091 (OUTLIER) cc_final: 0.5689 (mt-10) REVERT: H 18 GLU cc_start: 0.7848 (pm20) cc_final: 0.7178 (pm20) outliers start: 202 outliers final: 104 residues processed: 672 average time/residue: 0.4816 time to fit residues: 516.2950 Evaluate side-chains 572 residues out of total 3588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 458 time to evaluate : 4.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 412 ASP Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 664 LYS Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 931 SER Chi-restraints excluded: chain A residue 933 LYS Chi-restraints excluded: chain A residue 935 LEU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1297 ILE Chi-restraints excluded: chain A residue 1313 GLN Chi-restraints excluded: chain A residue 1523 LEU Chi-restraints excluded: chain A residue 1529 VAL Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1587 GLU Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 1642 SER Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain A residue 1705 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 188 ASN Chi-restraints excluded: chain B residue 205 TYR Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 314 VAL Chi-restraints excluded: chain B residue 330 GLN Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 678 ASP Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 821 TYR Chi-restraints excluded: chain B residue 835 GLU Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain B residue 1007 SER Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 1133 ASP Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain F residue 58 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 33 ASP Chi-restraints excluded: chain J residue 53 VAL Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 73 THR Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain L residue 49 THR Chi-restraints excluded: chain N residue 60 HIS Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain N residue 130 LEU Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 99 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 364 optimal weight: 10.0000 chunk 277 optimal weight: 0.0980 chunk 191 optimal weight: 7.9990 chunk 40 optimal weight: 9.9990 chunk 176 optimal weight: 1.9990 chunk 248 optimal weight: 4.9990 chunk 370 optimal weight: 20.0000 chunk 392 optimal weight: 0.6980 chunk 193 optimal weight: 0.8980 chunk 351 optimal weight: 0.0980 chunk 105 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 HIS ** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1052 HIS ** A1316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 297 GLN B 330 GLN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 639 GLN B 945 HIS C 48 ASN C 143 GLN C 290 ASN ** E 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 133 GLN K 31 GLN K 97 GLN N 60 HIS ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34192 Z= 0.196 Angle : 0.660 12.492 46384 Z= 0.341 Chirality : 0.045 0.199 5133 Planarity : 0.005 0.070 5869 Dihedral : 11.447 86.690 4985 Min Nonbonded Distance : 1.424 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.01 % Favored : 92.91 % Rotamer: Outliers : 3.65 % Allowed : 18.43 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.13), residues: 4050 helix: -0.15 (0.15), residues: 1223 sheet: -1.21 (0.19), residues: 650 loop : -1.97 (0.13), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 592 HIS 0.029 0.001 HIS N 60 PHE 0.025 0.001 PHE B 326 TYR 0.034 0.002 TYR E 8 ARG 0.009 0.001 ARG A 101 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 494 time to evaluate : 4.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 676 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8020 (mp) REVERT: A 963 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7413 (mt-10) REVERT: A 1024 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8238 (mp) REVERT: A 1534 MET cc_start: 0.4560 (mtp) cc_final: 0.4157 (mtt) REVERT: A 1587 GLU cc_start: 0.5784 (OUTLIER) cc_final: 0.5549 (tp30) REVERT: A 1716 LYS cc_start: 0.7112 (tppt) cc_final: 0.6870 (ttpt) REVERT: B 17 LYS cc_start: 0.8303 (ptpp) cc_final: 0.8080 (ptpp) REVERT: B 94 LYS cc_start: 0.7709 (tptp) cc_final: 0.7284 (tttm) REVERT: B 290 MET cc_start: 0.6004 (mmm) cc_final: 0.5730 (tpp) REVERT: B 411 MET cc_start: 0.4655 (mmm) cc_final: 0.4449 (mmm) REVERT: E 92 GLN cc_start: 0.6146 (mm110) cc_final: 0.4655 (mm-40) REVERT: H 78 THR cc_start: 0.8159 (p) cc_final: 0.7846 (t) REVERT: H 128 ASP cc_start: 0.6420 (t70) cc_final: 0.6162 (t70) REVERT: K 60 MET cc_start: 0.7313 (mmm) cc_final: 0.6966 (mmm) REVERT: M 39 MET cc_start: 0.3151 (mmp) cc_final: 0.1981 (mmm) REVERT: I 107 GLU cc_start: 0.6183 (mm-30) cc_final: 0.5977 (mm-30) outliers start: 131 outliers final: 89 residues processed: 585 average time/residue: 0.4713 time to fit residues: 447.5706 Evaluate side-chains 537 residues out of total 3588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 445 time to evaluate : 3.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 592 ASP Chi-restraints excluded: chain A residue 664 LYS Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 995 HIS Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1024 LEU Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1505 VAL Chi-restraints excluded: chain A residue 1512 ILE Chi-restraints excluded: chain A residue 1587 GLU Chi-restraints excluded: chain A residue 1642 SER Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 585 ARG Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 821 TYR Chi-restraints excluded: chain B residue 864 PHE Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain B residue 1007 SER Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1133 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 123 GLU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain E residue 13 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain N residue 116 ARG Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 99 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 326 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 5 optimal weight: 10.0000 chunk 292 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 334 optimal weight: 3.9990 chunk 271 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 200 optimal weight: 0.9990 chunk 352 optimal weight: 0.4980 chunk 99 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 143 GLN C 151 HIS ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 GLN K 31 GLN K 97 GLN K 124 GLN ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 34192 Z= 0.224 Angle : 0.640 10.249 46384 Z= 0.330 Chirality : 0.045 0.200 5133 Planarity : 0.005 0.070 5869 Dihedral : 11.167 87.470 4972 Min Nonbonded Distance : 1.482 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.83 % Favored : 92.10 % Rotamer: Outliers : 4.29 % Allowed : 18.85 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.13), residues: 4050 helix: 0.08 (0.15), residues: 1227 sheet: -1.14 (0.19), residues: 653 loop : -1.92 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 592 HIS 0.004 0.001 HIS C 151 PHE 0.037 0.001 PHE E 73 TYR 0.032 0.002 TYR A 754 ARG 0.006 0.000 ARG B 187 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 469 time to evaluate : 3.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLN cc_start: 0.5795 (OUTLIER) cc_final: 0.5351 (mp10) REVERT: A 423 LYS cc_start: 0.5761 (OUTLIER) cc_final: 0.5544 (mmtt) REVERT: A 460 MET cc_start: 0.8295 (tpp) cc_final: 0.8079 (tpp) REVERT: A 676 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8054 (mp) REVERT: A 1534 MET cc_start: 0.4834 (mtp) cc_final: 0.4557 (mtt) REVERT: B 17 LYS cc_start: 0.8279 (ptpp) cc_final: 0.8036 (ptpp) REVERT: B 94 LYS cc_start: 0.7736 (tptp) cc_final: 0.7275 (tttm) REVERT: B 691 MET cc_start: 0.7845 (OUTLIER) cc_final: 0.7508 (mtm) REVERT: B 826 TYR cc_start: 0.7168 (p90) cc_final: 0.6581 (p90) REVERT: C 65 MET cc_start: 0.7924 (ttm) cc_final: 0.7617 (ttm) REVERT: H 18 GLU cc_start: 0.8007 (pm20) cc_final: 0.7725 (pt0) REVERT: H 78 THR cc_start: 0.8138 (p) cc_final: 0.7862 (t) REVERT: K 31 GLN cc_start: 0.7136 (tt0) cc_final: 0.6788 (mt0) REVERT: K 60 MET cc_start: 0.7405 (mmm) cc_final: 0.7106 (mmm) REVERT: K 90 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8317 (mt) REVERT: G 104 ASP cc_start: 0.2263 (OUTLIER) cc_final: 0.1798 (t70) REVERT: M 39 MET cc_start: 0.3256 (OUTLIER) cc_final: 0.1933 (mmm) REVERT: M 99 MET cc_start: 0.3242 (tpt) cc_final: 0.2857 (tpt) outliers start: 154 outliers final: 102 residues processed: 578 average time/residue: 0.4618 time to fit residues: 432.0569 Evaluate side-chains 549 residues out of total 3588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 440 time to evaluate : 3.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 555 THR Chi-restraints excluded: chain A residue 601 SER Chi-restraints excluded: chain A residue 664 LYS Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 995 HIS Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1498 MET Chi-restraints excluded: chain A residue 1505 VAL Chi-restraints excluded: chain A residue 1512 ILE Chi-restraints excluded: chain A residue 1642 SER Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 466 LEU Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 821 TYR Chi-restraints excluded: chain B residue 864 PHE Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 1133 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 86 THR Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 90 LEU Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain N residue 60 HIS Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 104 ASP Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain M residue 39 MET Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 99 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 132 optimal weight: 10.0000 chunk 353 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 230 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 392 optimal weight: 0.0970 chunk 326 optimal weight: 0.3980 chunk 181 optimal weight: 1.9990 chunk 32 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 206 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 790 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1717 GLN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 889 GLN C 151 HIS C 290 ASN J 26 GLN K 124 GLN ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 87 HIS ** M 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.5668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 34192 Z= 0.234 Angle : 0.642 14.190 46384 Z= 0.330 Chirality : 0.045 0.216 5133 Planarity : 0.005 0.068 5869 Dihedral : 11.042 87.899 4967 Min Nonbonded Distance : 1.485 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.05 % Favored : 91.88 % Rotamer: Outliers : 4.18 % Allowed : 19.18 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.13), residues: 4050 helix: 0.16 (0.15), residues: 1226 sheet: -1.08 (0.19), residues: 670 loop : -1.83 (0.13), residues: 2154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1174 HIS 0.005 0.001 HIS B 213 PHE 0.028 0.001 PHE E 73 TYR 0.026 0.002 TYR A 754 ARG 0.013 0.000 ARG A1122 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 459 time to evaluate : 4.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 GLN cc_start: 0.5546 (OUTLIER) cc_final: 0.5052 (mp10) REVERT: A 302 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6598 (mm) REVERT: A 423 LYS cc_start: 0.5744 (OUTLIER) cc_final: 0.5435 (mmtt) REVERT: A 557 HIS cc_start: 0.7964 (OUTLIER) cc_final: 0.7732 (p90) REVERT: A 586 ASN cc_start: 0.7903 (t160) cc_final: 0.7522 (t0) REVERT: A 635 MET cc_start: 0.8280 (OUTLIER) cc_final: 0.7040 (mpp) REVERT: A 676 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.8110 (mp) REVERT: B 94 LYS cc_start: 0.7741 (tptp) cc_final: 0.7367 (tptm) REVERT: B 235 MET cc_start: 0.6010 (OUTLIER) cc_final: 0.5762 (ptp) REVERT: B 691 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7531 (mtm) REVERT: C 65 MET cc_start: 0.7863 (ttm) cc_final: 0.7566 (ttm) REVERT: C 184 LEU cc_start: 0.5453 (OUTLIER) cc_final: 0.4755 (tt) REVERT: H 18 GLU cc_start: 0.8053 (pm20) cc_final: 0.7743 (pt0) REVERT: H 78 THR cc_start: 0.8121 (p) cc_final: 0.7891 (t) REVERT: M 39 MET cc_start: 0.3365 (OUTLIER) cc_final: 0.2221 (mmm) outliers start: 150 outliers final: 110 residues processed: 565 average time/residue: 0.4574 time to fit residues: 422.4457 Evaluate side-chains 561 residues out of total 3588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 441 time to evaluate : 3.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 664 LYS Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 995 HIS Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1293 VAL Chi-restraints excluded: chain A residue 1314 VAL Chi-restraints excluded: chain A residue 1498 MET Chi-restraints excluded: chain A residue 1505 VAL Chi-restraints excluded: chain A residue 1512 ILE Chi-restraints excluded: chain A residue 1529 VAL Chi-restraints excluded: chain A residue 1642 SER Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 821 TYR Chi-restraints excluded: chain B residue 864 PHE Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 1133 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 166 HIS Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 121 ASP Chi-restraints excluded: chain F residue 125 ILE Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 127 SER Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain M residue 39 MET Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 99 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 378 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 223 optimal weight: 3.9990 chunk 286 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 330 optimal weight: 5.9990 chunk 219 optimal weight: 0.8980 chunk 391 optimal weight: 20.0000 chunk 244 optimal weight: 3.9990 chunk 238 optimal weight: 0.6980 chunk 180 optimal weight: 10.0000 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 616 GLN A 652 HIS A 790 GLN A 870 ASN ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1270 ASN ** A1316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 851 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS C 166 HIS E 30 GLN ** E 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 GLN K 31 GLN ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 63 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.6019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 34192 Z= 0.312 Angle : 0.689 11.167 46384 Z= 0.355 Chirality : 0.047 0.221 5133 Planarity : 0.005 0.068 5869 Dihedral : 11.086 88.141 4966 Min Nonbonded Distance : 1.477 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.54 % Favored : 91.38 % Rotamer: Outliers : 4.68 % Allowed : 19.68 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.13), residues: 4050 helix: 0.06 (0.15), residues: 1221 sheet: -1.01 (0.20), residues: 654 loop : -1.83 (0.13), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 40 HIS 0.008 0.001 HIS I 98 PHE 0.033 0.002 PHE E 73 TYR 0.026 0.002 TYR A 754 ARG 0.008 0.001 ARG C 303 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 3588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 467 time to evaluate : 4.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.6492 (tp40) cc_final: 0.5866 (mp10) REVERT: A 163 GLN cc_start: 0.5279 (OUTLIER) cc_final: 0.4742 (mp10) REVERT: A 423 LYS cc_start: 0.5732 (OUTLIER) cc_final: 0.5466 (mmtt) REVERT: A 557 HIS cc_start: 0.8052 (OUTLIER) cc_final: 0.7699 (p90) REVERT: A 586 ASN cc_start: 0.8075 (t160) cc_final: 0.7715 (t0) REVERT: A 635 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7088 (mpp) REVERT: A 676 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8154 (mp) REVERT: A 926 PRO cc_start: 0.6025 (Cg_endo) cc_final: 0.5792 (Cg_exo) REVERT: A 1129 GLU cc_start: 0.5453 (mp0) cc_final: 0.5224 (mp0) REVERT: B 94 LYS cc_start: 0.7798 (tptp) cc_final: 0.7419 (tptm) REVERT: B 235 MET cc_start: 0.6221 (OUTLIER) cc_final: 0.5845 (ptp) REVERT: B 691 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7449 (mtp) REVERT: B 977 GLU cc_start: 0.6784 (tp30) cc_final: 0.6581 (tp30) REVERT: C 65 MET cc_start: 0.7897 (ttm) cc_final: 0.7641 (ttm) REVERT: C 124 TYR cc_start: 0.8895 (m-80) cc_final: 0.8683 (m-80) REVERT: F 104 ILE cc_start: 0.6792 (mm) cc_final: 0.6460 (mt) REVERT: F 106 ILE cc_start: 0.7765 (mp) cc_final: 0.7512 (mp) REVERT: H 18 GLU cc_start: 0.8197 (pm20) cc_final: 0.7933 (pt0) REVERT: L 41 TYR cc_start: 0.7338 (OUTLIER) cc_final: 0.6329 (m-80) REVERT: M 39 MET cc_start: 0.3530 (OUTLIER) cc_final: 0.2533 (mmm) outliers start: 168 outliers final: 119 residues processed: 588 average time/residue: 0.4623 time to fit residues: 441.6779 Evaluate side-chains 577 residues out of total 3588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 449 time to evaluate : 3.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 664 LYS Chi-restraints excluded: chain A residue 676 LEU Chi-restraints excluded: chain A residue 701 ILE Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 730 ASP Chi-restraints excluded: chain A residue 749 LEU Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 790 GLN Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 898 VAL Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 995 HIS Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1121 LEU Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1293 VAL Chi-restraints excluded: chain A residue 1314 VAL Chi-restraints excluded: chain A residue 1498 MET Chi-restraints excluded: chain A residue 1512 ILE Chi-restraints excluded: chain A residue 1529 VAL Chi-restraints excluded: chain A residue 1631 VAL Chi-restraints excluded: chain A residue 1642 SER Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 235 MET Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 436 THR Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 648 GLU Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 666 LEU Chi-restraints excluded: chain B residue 691 MET Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 821 TYR Chi-restraints excluded: chain B residue 864 PHE Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain B residue 965 MET Chi-restraints excluded: chain B residue 1007 SER Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 1133 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 287 ILE Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 33 GLU Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 127 SER Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain N residue 60 HIS Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain M residue 39 MET Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 83 VAL Chi-restraints excluded: chain I residue 99 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 242 optimal weight: 0.0970 chunk 156 optimal weight: 0.8980 chunk 233 optimal weight: 0.6980 chunk 117 optimal weight: 0.0170 chunk 76 optimal weight: 8.9990 chunk 75 optimal weight: 0.7980 chunk 248 optimal weight: 7.9990 chunk 266 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 307 optimal weight: 2.9990 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 790 GLN ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 895 GLN ** A1316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1509 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1610 ASN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 330 GLN ** B 972 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS K 124 GLN ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.6188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 34192 Z= 0.170 Angle : 0.620 12.997 46384 Z= 0.317 Chirality : 0.044 0.223 5133 Planarity : 0.005 0.068 5869 Dihedral : 10.848 89.551 4963 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.14 % Favored : 92.79 % Rotamer: Outliers : 3.37 % Allowed : 21.24 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.13), residues: 4050 helix: 0.47 (0.15), residues: 1216 sheet: -0.94 (0.20), residues: 649 loop : -1.70 (0.13), residues: 2185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1174 HIS 0.004 0.001 HIS A1509 PHE 0.025 0.001 PHE E 73 TYR 0.024 0.001 TYR A 754 ARG 0.007 0.000 ARG F 107 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 3588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 473 time to evaluate : 4.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.6346 (tp40) cc_final: 0.5768 (mp10) REVERT: A 163 GLN cc_start: 0.5348 (OUTLIER) cc_final: 0.4869 (mp10) REVERT: A 302 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6755 (mm) REVERT: A 423 LYS cc_start: 0.5490 (OUTLIER) cc_final: 0.5167 (mmtt) REVERT: A 557 HIS cc_start: 0.7889 (OUTLIER) cc_final: 0.7613 (p90) REVERT: A 586 ASN cc_start: 0.7946 (t160) cc_final: 0.7606 (t0) REVERT: A 635 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.6933 (mpp) REVERT: A 926 PRO cc_start: 0.5907 (Cg_endo) cc_final: 0.5665 (Cg_exo) REVERT: A 1189 LEU cc_start: 0.6949 (mm) cc_final: 0.6633 (tp) REVERT: B 94 LYS cc_start: 0.7722 (tptp) cc_final: 0.7311 (tttm) REVERT: B 111 ARG cc_start: 0.6865 (OUTLIER) cc_final: 0.6585 (ptt180) REVERT: B 235 MET cc_start: 0.6141 (ptp) cc_final: 0.5760 (ptp) REVERT: B 977 GLU cc_start: 0.6381 (tp30) cc_final: 0.6134 (tp30) REVERT: C 65 MET cc_start: 0.7809 (ttm) cc_final: 0.7563 (ttm) REVERT: F 104 ILE cc_start: 0.6660 (mm) cc_final: 0.6413 (mt) REVERT: F 106 ILE cc_start: 0.7745 (mp) cc_final: 0.7529 (mp) REVERT: H 18 GLU cc_start: 0.8151 (pm20) cc_final: 0.7881 (pt0) REVERT: L 18 ILE cc_start: 0.8654 (mp) cc_final: 0.8449 (mt) REVERT: L 41 TYR cc_start: 0.7125 (OUTLIER) cc_final: 0.6257 (m-80) REVERT: N 137 PRO cc_start: -0.0583 (Cg_exo) cc_final: -0.0863 (Cg_endo) REVERT: M 39 MET cc_start: 0.3444 (OUTLIER) cc_final: 0.2328 (mmm) outliers start: 121 outliers final: 81 residues processed: 555 average time/residue: 0.4702 time to fit residues: 426.9548 Evaluate side-chains 534 residues out of total 3588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 445 time to evaluate : 4.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 664 LYS Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 995 HIS Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1098 GLU Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1293 VAL Chi-restraints excluded: chain A residue 1314 VAL Chi-restraints excluded: chain A residue 1498 MET Chi-restraints excluded: chain A residue 1512 ILE Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 821 TYR Chi-restraints excluded: chain B residue 864 PHE Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain B residue 965 MET Chi-restraints excluded: chain B residue 1007 SER Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1133 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 218 ILE Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 127 SER Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain N residue 60 HIS Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain M residue 39 MET Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 83 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 355 optimal weight: 7.9990 chunk 374 optimal weight: 7.9990 chunk 342 optimal weight: 0.9990 chunk 364 optimal weight: 0.0970 chunk 219 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 chunk 286 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 329 optimal weight: 0.9990 chunk 344 optimal weight: 0.9990 chunk 363 optimal weight: 0.0370 overall best weight: 0.6262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 877 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1579 ASN ** B 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 GLN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 151 HIS K 124 GLN ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.6299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 34192 Z= 0.176 Angle : 0.624 13.810 46384 Z= 0.318 Chirality : 0.044 0.262 5133 Planarity : 0.005 0.068 5869 Dihedral : 10.719 89.658 4959 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.21 % Favored : 92.72 % Rotamer: Outliers : 3.01 % Allowed : 21.83 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.13), residues: 4050 helix: 0.59 (0.15), residues: 1223 sheet: -0.91 (0.20), residues: 663 loop : -1.61 (0.13), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1174 HIS 0.005 0.001 HIS B 335 PHE 0.035 0.001 PHE E 73 TYR 0.022 0.001 TYR A 754 ARG 0.008 0.000 ARG C 303 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 459 time to evaluate : 3.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.6337 (tp40) cc_final: 0.5792 (mp10) REVERT: A 163 GLN cc_start: 0.5099 (OUTLIER) cc_final: 0.4578 (mp10) REVERT: A 302 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6842 (mm) REVERT: A 423 LYS cc_start: 0.5561 (OUTLIER) cc_final: 0.5279 (mmtt) REVERT: A 432 MET cc_start: 0.6859 (mtp) cc_final: 0.6430 (mtm) REVERT: A 557 HIS cc_start: 0.7894 (OUTLIER) cc_final: 0.7633 (p90) REVERT: A 586 ASN cc_start: 0.7981 (t160) cc_final: 0.7643 (t0) REVERT: A 635 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7023 (mpp) REVERT: A 926 PRO cc_start: 0.5931 (Cg_endo) cc_final: 0.5711 (Cg_exo) REVERT: A 1189 LEU cc_start: 0.6948 (mm) cc_final: 0.6657 (tp) REVERT: B 94 LYS cc_start: 0.7781 (tptp) cc_final: 0.7493 (tptm) REVERT: B 111 ARG cc_start: 0.6863 (OUTLIER) cc_final: 0.6587 (ptt180) REVERT: B 235 MET cc_start: 0.6181 (ptp) cc_final: 0.5785 (ptp) REVERT: B 999 TYR cc_start: 0.7959 (OUTLIER) cc_final: 0.7280 (t80) REVERT: C 65 MET cc_start: 0.7716 (ttm) cc_final: 0.7475 (ttm) REVERT: F 104 ILE cc_start: 0.6629 (mm) cc_final: 0.6412 (mt) REVERT: F 106 ILE cc_start: 0.7774 (mp) cc_final: 0.7492 (mp) REVERT: H 18 GLU cc_start: 0.8133 (pm20) cc_final: 0.7863 (pt0) REVERT: L 41 TYR cc_start: 0.7165 (OUTLIER) cc_final: 0.6409 (m-80) REVERT: N 137 PRO cc_start: -0.0650 (Cg_exo) cc_final: -0.0886 (Cg_endo) REVERT: M 39 MET cc_start: 0.3629 (OUTLIER) cc_final: 0.2492 (mmm) outliers start: 108 outliers final: 88 residues processed: 533 average time/residue: 0.4732 time to fit residues: 406.2849 Evaluate side-chains 542 residues out of total 3588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 445 time to evaluate : 3.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 TRP Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 664 LYS Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 995 HIS Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1098 GLU Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1293 VAL Chi-restraints excluded: chain A residue 1314 VAL Chi-restraints excluded: chain A residue 1498 MET Chi-restraints excluded: chain A residue 1505 VAL Chi-restraints excluded: chain A residue 1512 ILE Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 299 GLN Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 821 TYR Chi-restraints excluded: chain B residue 864 PHE Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain B residue 965 MET Chi-restraints excluded: chain B residue 999 TYR Chi-restraints excluded: chain B residue 1007 SER Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 1133 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain N residue 60 HIS Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain M residue 39 MET Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 83 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 239 optimal weight: 2.9990 chunk 385 optimal weight: 1.9990 chunk 235 optimal weight: 0.9990 chunk 182 optimal weight: 5.9990 chunk 268 optimal weight: 0.9980 chunk 404 optimal weight: 10.0000 chunk 372 optimal weight: 9.9990 chunk 322 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 248 optimal weight: 5.9990 chunk 197 optimal weight: 0.6980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 454 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 263 GLN ** B 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 643 ASN C 151 HIS K 45 HIS K 124 GLN ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 110 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.6441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 34192 Z= 0.208 Angle : 0.640 14.270 46384 Z= 0.325 Chirality : 0.044 0.253 5133 Planarity : 0.005 0.069 5869 Dihedral : 10.683 89.857 4959 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.56 % Favored : 92.37 % Rotamer: Outliers : 3.01 % Allowed : 21.91 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.13), residues: 4050 helix: 0.62 (0.15), residues: 1219 sheet: -0.87 (0.20), residues: 653 loop : -1.58 (0.13), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1174 HIS 0.005 0.001 HIS A1509 PHE 0.030 0.001 PHE C 288 TYR 0.024 0.002 TYR E 90 ARG 0.013 0.000 ARG A1122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 3588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 455 time to evaluate : 3.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.6361 (tp40) cc_final: 0.5802 (mp10) REVERT: A 163 GLN cc_start: 0.5153 (OUTLIER) cc_final: 0.4673 (mp10) REVERT: A 403 ASP cc_start: 0.6576 (t0) cc_final: 0.6160 (t70) REVERT: A 423 LYS cc_start: 0.5531 (OUTLIER) cc_final: 0.5233 (mmtt) REVERT: A 432 MET cc_start: 0.6980 (mtp) cc_final: 0.6515 (mtm) REVERT: A 557 HIS cc_start: 0.7939 (OUTLIER) cc_final: 0.7669 (p90) REVERT: A 586 ASN cc_start: 0.8039 (t160) cc_final: 0.7697 (t0) REVERT: A 635 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7000 (mpp) REVERT: A 749 LEU cc_start: 0.6752 (tt) cc_final: 0.6358 (tt) REVERT: A 926 PRO cc_start: 0.6017 (Cg_endo) cc_final: 0.5810 (Cg_exo) REVERT: A 1189 LEU cc_start: 0.7019 (mm) cc_final: 0.6708 (tp) REVERT: A 1263 MET cc_start: 0.5562 (ppp) cc_final: 0.4921 (mtt) REVERT: A 1589 PHE cc_start: 0.6497 (m-10) cc_final: 0.6292 (m-10) REVERT: B 111 ARG cc_start: 0.6876 (OUTLIER) cc_final: 0.6561 (ptt180) REVERT: B 235 MET cc_start: 0.6136 (ptp) cc_final: 0.5800 (ptp) REVERT: B 912 ASP cc_start: 0.7925 (OUTLIER) cc_final: 0.7361 (p0) REVERT: B 999 TYR cc_start: 0.7977 (OUTLIER) cc_final: 0.7288 (t80) REVERT: B 1097 ASN cc_start: 0.7304 (OUTLIER) cc_final: 0.7069 (m110) REVERT: C 65 MET cc_start: 0.7735 (ttm) cc_final: 0.7509 (ttm) REVERT: F 104 ILE cc_start: 0.6784 (mm) cc_final: 0.6501 (mt) REVERT: F 106 ILE cc_start: 0.7730 (mp) cc_final: 0.7488 (mp) REVERT: H 18 GLU cc_start: 0.8157 (pm20) cc_final: 0.7901 (pt0) REVERT: L 41 TYR cc_start: 0.7301 (OUTLIER) cc_final: 0.6551 (m-80) REVERT: N 137 PRO cc_start: -0.0744 (Cg_exo) cc_final: -0.0960 (Cg_endo) REVERT: M 39 MET cc_start: 0.3638 (OUTLIER) cc_final: 0.2513 (mmm) outliers start: 108 outliers final: 93 residues processed: 534 average time/residue: 0.4672 time to fit residues: 404.0070 Evaluate side-chains 545 residues out of total 3588 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 442 time to evaluate : 3.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 TRP Chi-restraints excluded: chain A residue 15 ILE Chi-restraints excluded: chain A residue 70 ASP Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 423 LYS Chi-restraints excluded: chain A residue 437 VAL Chi-restraints excluded: chain A residue 452 ASN Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 535 THR Chi-restraints excluded: chain A residue 557 HIS Chi-restraints excluded: chain A residue 635 MET Chi-restraints excluded: chain A residue 664 LYS Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 754 TYR Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 995 HIS Chi-restraints excluded: chain A residue 1010 SER Chi-restraints excluded: chain A residue 1083 LEU Chi-restraints excluded: chain A residue 1098 GLU Chi-restraints excluded: chain A residue 1114 SER Chi-restraints excluded: chain A residue 1198 LEU Chi-restraints excluded: chain A residue 1218 SER Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1293 VAL Chi-restraints excluded: chain A residue 1314 VAL Chi-restraints excluded: chain A residue 1498 MET Chi-restraints excluded: chain A residue 1505 VAL Chi-restraints excluded: chain A residue 1556 THR Chi-restraints excluded: chain A residue 1642 SER Chi-restraints excluded: chain A residue 1653 VAL Chi-restraints excluded: chain B residue 111 ARG Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 225 ASN Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 275 ASP Chi-restraints excluded: chain B residue 345 MET Chi-restraints excluded: chain B residue 356 LEU Chi-restraints excluded: chain B residue 365 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 458 ASP Chi-restraints excluded: chain B residue 492 GLU Chi-restraints excluded: chain B residue 506 GLU Chi-restraints excluded: chain B residue 601 THR Chi-restraints excluded: chain B residue 655 VAL Chi-restraints excluded: chain B residue 792 LEU Chi-restraints excluded: chain B residue 815 ILE Chi-restraints excluded: chain B residue 821 TYR Chi-restraints excluded: chain B residue 864 PHE Chi-restraints excluded: chain B residue 867 VAL Chi-restraints excluded: chain B residue 912 ASP Chi-restraints excluded: chain B residue 940 LEU Chi-restraints excluded: chain B residue 957 SER Chi-restraints excluded: chain B residue 999 TYR Chi-restraints excluded: chain B residue 1007 SER Chi-restraints excluded: chain B residue 1008 ASP Chi-restraints excluded: chain B residue 1063 ASP Chi-restraints excluded: chain B residue 1097 ASN Chi-restraints excluded: chain B residue 1133 ASP Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 55 HIS Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 330 MET Chi-restraints excluded: chain E residue 60 VAL Chi-restraints excluded: chain E residue 152 THR Chi-restraints excluded: chain E residue 183 PHE Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain H residue 9 ILE Chi-restraints excluded: chain H residue 15 ILE Chi-restraints excluded: chain H residue 37 MET Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 107 GLU Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 7 CYS Chi-restraints excluded: chain J residue 29 TYR Chi-restraints excluded: chain K residue 25 THR Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 54 SER Chi-restraints excluded: chain K residue 127 SER Chi-restraints excluded: chain L residue 22 CYS Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 41 TYR Chi-restraints excluded: chain L residue 43 ILE Chi-restraints excluded: chain N residue 60 HIS Chi-restraints excluded: chain G residue 57 ILE Chi-restraints excluded: chain G residue 181 VAL Chi-restraints excluded: chain M residue 39 MET Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 83 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 255 optimal weight: 6.9990 chunk 343 optimal weight: 0.9980 chunk 98 optimal weight: 7.9990 chunk 296 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 322 optimal weight: 4.9990 chunk 135 optimal weight: 9.9990 chunk 331 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 59 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 877 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 989 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1324 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 HIS C 151 HIS K 124 GLN ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 98 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 = 0.4418 r_free = 0.4418 target = 0.204475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.160232 restraints weight = 41071.409| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.08 r_work: 0.3719 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3589 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.6683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 34192 Z= 0.392 Angle : 0.749 13.127 46384 Z= 0.383 Chirality : 0.049 0.258 5133 Planarity : 0.006 0.067 5869 Dihedral : 10.935 89.749 4959 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.84 % Favored : 91.09 % Rotamer: Outliers : 3.23 % Allowed : 21.75 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.13), residues: 4050 helix: 0.20 (0.15), residues: 1222 sheet: -0.95 (0.20), residues: 644 loop : -1.71 (0.13), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1124 HIS 0.010 0.001 HIS C 213 PHE 0.028 0.002 PHE E 73 TYR 0.038 0.002 TYR B 169 ARG 0.013 0.001 ARG B 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9746.05 seconds wall clock time: 175 minutes 48.08 seconds (10548.08 seconds total)