Starting phenix.real_space_refine on Tue May 14 19:17:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8reb_19081/05_2024/8reb_19081.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8reb_19081/05_2024/8reb_19081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8reb_19081/05_2024/8reb_19081.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8reb_19081/05_2024/8reb_19081.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8reb_19081/05_2024/8reb_19081.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8reb_19081/05_2024/8reb_19081.pdb" } resolution = 3.4 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 101 5.49 5 Mg 1 5.21 5 S 98 5.16 5 C 17684 2.51 5 N 5093 2.21 5 O 5702 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 17": "OE1" <-> "OE2" Residue "A ASP 62": "OD1" <-> "OD2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A GLU 122": "OE1" <-> "OE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A ASP 199": "OD1" <-> "OD2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A ASP 212": "OD1" <-> "OD2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 250": "OD1" <-> "OD2" Residue "A ASP 258": "OD1" <-> "OD2" Residue "A GLU 273": "OE1" <-> "OE2" Residue "A TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 288": "OE1" <-> "OE2" Residue "B GLU 7": "OE1" <-> "OE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B ASP 77": "OD1" <-> "OD2" Residue "B ASP 96": "OD1" <-> "OD2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "C TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 7": "OE1" <-> "OE2" Residue "C ASP 14": "OD1" <-> "OD2" Residue "C ASP 23": "OD1" <-> "OD2" Residue "C TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 67": "OE1" <-> "OE2" Residue "C TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 132": "OD1" <-> "OD2" Residue "C PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 189": "OD1" <-> "OD2" Residue "C PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 365": "OE1" <-> "OE2" Residue "C GLU 382": "OE1" <-> "OE2" Residue "C ASP 393": "OD1" <-> "OD2" Residue "C ASP 434": "OD1" <-> "OD2" Residue "C GLU 472": "OE1" <-> "OE2" Residue "C GLU 504": "OE1" <-> "OE2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C GLU 588": "OE1" <-> "OE2" Residue "C ASP 596": "OD1" <-> "OD2" Residue "C TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 624": "OD1" <-> "OD2" Residue "C GLU 625": "OE1" <-> "OE2" Residue "C GLU 641": "OE1" <-> "OE2" Residue "C ASP 675": "OD1" <-> "OD2" Residue "C ASP 696": "OD1" <-> "OD2" Residue "C GLU 705": "OE1" <-> "OE2" Residue "C ASP 711": "OD1" <-> "OD2" Residue "C TYR 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 738": "OE1" <-> "OE2" Residue "C ASP 739": "OD1" <-> "OD2" Residue "C TYR 742": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 825": "OE1" <-> "OE2" Residue "C ASP 853": "OD1" <-> "OD2" Residue "C ASP 866": "OD1" <-> "OD2" Residue "C GLU 876": "OE1" <-> "OE2" Residue "C GLU 940": "OE1" <-> "OE2" Residue "C GLU 1020": "OE1" <-> "OE2" Residue "C GLU 1030": "OE1" <-> "OE2" Residue "C ASP 1041": "OD1" <-> "OD2" Residue "C TYR 1053": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1083": "OE1" <-> "OE2" Residue "C ASP 1095": "OD1" <-> "OD2" Residue "C GLU 1143": "OE1" <-> "OE2" Residue "C ASP 1160": "OD1" <-> "OD2" Residue "C GLU 1167": "OE1" <-> "OE2" Residue "C ASP 1203": "OD1" <-> "OD2" Residue "C GLU 1219": "OE1" <-> "OE2" Residue "C ASP 1241": "OD1" <-> "OD2" Residue "C PHE 1265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 1310": "OD1" <-> "OD2" Residue "C GLU 1316": "OE1" <-> "OE2" Residue "D PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "D ASP 28": "OD1" <-> "OD2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 54": "OD1" <-> "OD2" Residue "D TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D GLU 203": "OE1" <-> "OE2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D GLU 235": "OE1" <-> "OE2" Residue "D PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 348": "OD1" <-> "OD2" Residue "D ASP 413": "OD1" <-> "OD2" Residue "D GLU 414": "OE1" <-> "OE2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D GLU 497": "OE1" <-> "OE2" Residue "D GLU 562": "OE1" <-> "OE2" Residue "D GLU 656": "OE1" <-> "OE2" Residue "D GLU 658": "OE1" <-> "OE2" Residue "D GLU 660": "OE1" <-> "OE2" Residue "D GLU 666": "OE1" <-> "OE2" Residue "D PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 699": "OD1" <-> "OD2" Residue "D GLU 714": "OE1" <-> "OE2" Residue "D PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 727": "OD1" <-> "OD2" Residue "D GLU 765": "OE1" <-> "OE2" Residue "D GLU 811": "OE1" <-> "OE2" Residue "D GLU 818": "OE1" <-> "OE2" Residue "D GLU 827": "OE1" <-> "OE2" Residue "D ASP 830": "OD1" <-> "OD2" Residue "D GLU 833": "OE1" <-> "OE2" Residue "D ASP 837": "OD1" <-> "OD2" Residue "D GLU 846": "OE1" <-> "OE2" Residue "D TYR 899": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1146": "OE1" <-> "OE2" Residue "D GLU 1152": "OE1" <-> "OE2" Residue "D GLU 1187": "OE1" <-> "OE2" Residue "D GLU 1188": "OE1" <-> "OE2" Residue "D ASP 1219": "OD1" <-> "OD2" Residue "D TYR 1232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1236": "OE1" <-> "OE2" Residue "D ASP 1250": "OD1" <-> "OD2" Residue "D GLU 1276": "OE1" <-> "OE2" Residue "D GLU 1334": "OE1" <-> "OE2" Residue "D GLU 1343": "OE1" <-> "OE2" Residue "D TYR 1365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 65": "OD1" <-> "OD2" Residue "M GLU 173": "OE1" <-> "OE2" Residue "M TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 28681 Number of models: 1 Model: "" Number of chains: 10 Chain: "N" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 875 Classifications: {'DNA': 43} Link IDs: {'rna3p': 42} Chain breaks: 1 Chain: "R" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 3, 'rna3p_pyr': 3} Link IDs: {'rna3p': 5} Chain: "T" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1072 Classifications: {'DNA': 52} Link IDs: {'rna3p': 51} Chain: "A" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2365 Classifications: {'peptide': 308} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 14, 'TRANS': 293} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "B" Number of atoms: 1735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1735 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 225} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ASP:plan': 3, 'ARG:plan': 5, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 10080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10080 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1284} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 509 Unresolved non-hydrogen angles: 619 Unresolved non-hydrogen dihedrals: 432 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 5, 'GLU:plan': 22, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 338 Chain: "D" Number of atoms: 9682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1330, 9682 Classifications: {'peptide': 1330} Incomplete info: {'truncation_to_alanine': 172} Link IDs: {'PTRANS': 53, 'TRANS': 1276} Chain breaks: 5 Unresolved non-hydrogen bonds: 691 Unresolved non-hydrogen angles: 840 Unresolved non-hydrogen dihedrals: 585 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 15, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 18, 'PHE:plan': 9, 'GLU:plan': 31, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 441 Chain: "E" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 546 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "M" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2194 Classifications: {'peptide': 350} Incomplete info: {'truncation_to_alanine': 176} Link IDs: {'PTRANS': 15, 'TRANS': 334} Chain breaks: 1 Unresolved non-hydrogen bonds: 582 Unresolved non-hydrogen angles: 739 Unresolved non-hydrogen dihedrals: 457 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 9, 'ARG:plan': 10, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 22, 'PHE:plan': 2, 'GLU:plan': 26, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 341 Chain: "D" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 16779 SG CYS D 70 106.543 114.667 92.090 1.00 66.62 S ATOM 16908 SG CYS D 88 104.966 114.784 95.832 1.00 66.10 S ATOM 22401 SG CYS D 814 100.730 47.899 85.807 1.00 47.44 S ATOM 23021 SG CYS D 898 98.212 47.559 85.093 1.00 25.73 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY M 166 " occ=0.71 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.71 Time building chain proxies: 15.01, per 1000 atoms: 0.52 Number of scatterers: 28681 At special positions: 0 Unit cell: (140.98, 172.78, 166.42, 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 2 29.99 S 98 16.00 P 101 15.00 Mg 1 11.99 O 5702 8.00 N 5093 7.00 C 17684 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: 12.85 Conformation dependent library (CDL) restraints added in 4.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 70 " pdb=" ZN D1503 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1503 " - pdb=" SG CYS D 814 " 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6748 Finding SS restraints... Secondary structure from input PDB file: 125 helices and 45 sheets defined 39.3% alpha, 14.2% beta 40 base pairs and 81 stacking pairs defined. Time for finding SS restraints: 10.46 Creating SS restraints... Processing helix chain 'A' and resid 34 through 50 removed outlier: 3.857A pdb=" N THR A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.743A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 115 No H-bonds generated for 'chain 'A' and resid 113 through 115' Processing helix chain 'A' and resid 159 through 164 removed outlier: 3.957A pdb=" N ASP A 164 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 Processing helix chain 'A' and resid 263 through 273 removed outlier: 4.018A pdb=" N ASN A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N CYS A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 282 removed outlier: 3.592A pdb=" N LEU A 281 " --> pdb=" O TYR A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.773A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 74 removed outlier: 3.832A pdb=" N GLY B 73 " --> pdb=" O THR B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 removed outlier: 3.663A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 164 through 169 Processing helix chain 'B' and resid 212 through 227 Processing helix chain 'B' and resid 228 through 233 Processing helix chain 'C' and resid 4 through 9 removed outlier: 3.689A pdb=" N LYS C 9 " --> pdb=" O TYR C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 40 Processing helix chain 'C' and resid 48 through 57 Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 159 through 163 removed outlier: 3.738A pdb=" N LYS C 163 " --> pdb=" O ASP C 160 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 removed outlier: 4.196A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 290 through 294 removed outlier: 3.544A pdb=" N GLY C 294 " --> pdb=" O TYR C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 347 through 354 Processing helix chain 'C' and resid 358 through 371 Processing helix chain 'C' and resid 379 through 389 Processing helix chain 'C' and resid 398 through 409 Processing helix chain 'C' and resid 422 through 438 removed outlier: 4.018A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 455 through 479 removed outlier: 3.605A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ARG C 478 " --> pdb=" O ALA C 474 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU C 479 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 482 No H-bonds generated for 'chain 'C' and resid 480 through 482' Processing helix chain 'C' and resid 494 through 508 removed outlier: 4.330A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 528 removed outlier: 3.593A pdb=" N SER C 522 " --> pdb=" O ASN C 518 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU C 523 " --> pdb=" O ASN C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.963A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 removed outlier: 3.529A pdb=" N ASN C 613 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.631A pdb=" N LEU C 667 " --> pdb=" O GLY C 664 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 668 " --> pdb=" O ALA C 665 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 664 through 668' Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 4.106A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 860 through 865 removed outlier: 4.146A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 982 removed outlier: 3.805A pdb=" N GLU C 947 " --> pdb=" O LYS C 943 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.729A pdb=" N TRP C 997 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU C1000 " --> pdb=" O ARG C 996 " (cutoff:3.500A) Processing helix chain 'C' and resid 1003 through 1009 Processing helix chain 'C' and resid 1009 through 1037 Processing helix chain 'C' and resid 1081 through 1085 Processing helix chain 'C' and resid 1099 through 1103 Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 4.299A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.708A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1176 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1292 Processing helix chain 'C' and resid 1297 through 1311 removed outlier: 3.954A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.519A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 70 through 74 removed outlier: 4.079A pdb=" N LYS D 74 " --> pdb=" O LEU D 71 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 100 Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 122 through 128 Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.588A pdb=" N ILE D 135 " --> pdb=" O PRO D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.765A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.707A pdb=" N LYS D 215 " --> pdb=" O GLU D 211 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY D 231 " --> pdb=" O PHE D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 263 through 284 removed outlier: 3.949A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.790A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 574 through 581 removed outlier: 3.786A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 599 through 612 Processing helix chain 'D' and resid 614 through 636 Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 703 removed outlier: 4.172A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 Processing helix chain 'D' and resid 733 through 741 Processing helix chain 'D' and resid 768 through 805 removed outlier: 3.755A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 Processing helix chain 'D' and resid 865 through 875 Processing helix chain 'D' and resid 884 through 888 removed outlier: 3.622A pdb=" N CYS D 888 " --> pdb=" O VAL D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 925 removed outlier: 3.739A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 1140 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1225 through 1245 removed outlier: 3.543A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1259 removed outlier: 3.743A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1293 Processing helix chain 'D' and resid 1295 through 1299 removed outlier: 3.743A pdb=" N VAL D1298 " --> pdb=" O ASN D1295 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1314 removed outlier: 3.961A pdb=" N LEU D1314 " --> pdb=" O THR D1310 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.551A pdb=" N VAL D1331 " --> pdb=" O GLU D1327 " (cutoff:3.500A) Processing helix chain 'D' and resid 1346 through 1353 removed outlier: 3.991A pdb=" N ASN D1350 " --> pdb=" O GLY D1346 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1376 removed outlier: 4.170A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 13 Processing helix chain 'E' and resid 17 through 33 removed outlier: 4.019A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY E 33 " --> pdb=" O GLN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 60 through 75 Processing helix chain 'M' and resid 119 through 130 removed outlier: 3.539A pdb=" N LEU M 130 " --> pdb=" O TRP M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 147 removed outlier: 3.740A pdb=" N ALA M 147 " --> pdb=" O SER M 143 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 166 Processing helix chain 'M' and resid 171 through 183 Processing helix chain 'M' and resid 194 through 205 removed outlier: 3.633A pdb=" N GLN M 205 " --> pdb=" O ILE M 201 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 218 removed outlier: 4.033A pdb=" N LEU M 218 " --> pdb=" O GLU M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 224 through 230 Processing helix chain 'M' and resid 234 through 240 Processing helix chain 'M' and resid 242 through 255 removed outlier: 3.538A pdb=" N GLU M 248 " --> pdb=" O GLU M 244 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN M 251 " --> pdb=" O LYS M 247 " (cutoff:3.500A) Processing helix chain 'M' and resid 325 through 351 Processing helix chain 'M' and resid 351 through 356 removed outlier: 4.295A pdb=" N PHE M 355 " --> pdb=" O GLN M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 375 removed outlier: 3.556A pdb=" N ILE M 370 " --> pdb=" O VAL M 366 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 385 Processing helix chain 'M' and resid 416 through 430 Processing helix chain 'M' and resid 438 through 450 Processing helix chain 'M' and resid 454 through 466 removed outlier: 3.895A pdb=" N VAL M 458 " --> pdb=" O ALA M 454 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA M 459 " --> pdb=" O ARG M 455 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU M 465 " --> pdb=" O TYR M 461 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 removed outlier: 8.777A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 105 removed outlier: 3.702A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.599A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 15 through 19 removed outlier: 6.513A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N THR B 196 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL B 192 " --> pdb=" O THR B 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 52 through 61 removed outlier: 3.982A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN B 147 " --> pdb=" O ALA B 55 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 111 removed outlier: 3.541A pdb=" N CYS B 131 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AB1, first strand: chain 'C' and resid 13 through 14 removed outlier: 5.822A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.941A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 68 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU C 102 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASP C 116 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE C 104 " --> pdb=" O VAL C 114 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.941A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU C 68 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 144 through 145 Processing sheet with id=AB5, first strand: chain 'C' and resid 451 through 454 Processing sheet with id=AB6, first strand: chain 'C' and resid 154 through 158 Processing sheet with id=AB7, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AB8, first strand: chain 'C' and resid 255 through 257 removed outlier: 7.081A pdb=" N ILE C 255 " --> pdb=" O TYR C 262 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 296 through 297 removed outlier: 4.638A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 580 through 581 removed outlier: 5.995A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC3, first strand: chain 'C' and resid 634 through 636 Processing sheet with id=AC4, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.445A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET C 768 " --> pdb=" O ASP C 785 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 723 through 727 removed outlier: 6.644A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 757 through 758 Processing sheet with id=AC7, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC8, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.376A pdb=" N ILE C 816 " --> pdb=" O LYS C1078 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N ASN C1080 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 830 through 841 removed outlier: 6.319A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 830 through 841 Processing sheet with id=AD2, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD3, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.723A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246 Processing sheet with id=AD5, first strand: chain 'C' and resid 1335 through 1338 Processing sheet with id=AD6, first strand: chain 'D' and resid 104 through 111 removed outlier: 8.651A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 145 through 147 removed outlier: 4.134A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AD9, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AE1, first strand: chain 'D' and resid 809 through 811 Processing sheet with id=AE2, first strand: chain 'D' and resid 820 through 822 Processing sheet with id=AE3, first strand: chain 'D' and resid 825 through 827 removed outlier: 7.070A pdb=" N GLU D 827 " --> pdb=" O VAL D 831 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N VAL D 831 " --> pdb=" O GLU D 827 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 848 through 849 removed outlier: 7.017A pdb=" N VAL D 848 " --> pdb=" O LEU D 857 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 957 through 961 Processing sheet with id=AE6, first strand: chain 'D' and resid 966 through 967 removed outlier: 5.056A pdb=" N LEU D 973 " --> pdb=" O LEU D1003 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU D1003 " --> pdb=" O LEU D 973 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA D1001 " --> pdb=" O ILE D 975 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 1059 through 1062 removed outlier: 3.863A pdb=" N LEU D1059 " --> pdb=" O VAL D1107 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ALA D1105 " --> pdb=" O VAL D1061 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 1277 through 1278 Processing sheet with id=AE9, first strand: chain 'M' and resid 277 through 278 removed outlier: 7.148A pdb=" N LEU M 277 " --> pdb=" O HIS M 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 1151 hydrogen bonds defined for protein. 3225 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 103 hydrogen bonds 202 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 81 stacking parallelities Total time for adding SS restraints: 17.92 Time building geometry restraints manager: 13.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8931 1.33 - 1.46: 4565 1.46 - 1.58: 15433 1.58 - 1.70: 202 1.70 - 1.82: 170 Bond restraints: 29301 Sorted by residual: bond pdb=" CG PRO M 258 " pdb=" CD PRO M 258 " ideal model delta sigma weight residual 1.503 1.304 0.199 3.40e-02 8.65e+02 3.42e+01 bond pdb=" N PRO M 258 " pdb=" CA PRO M 258 " ideal model delta sigma weight residual 1.469 1.429 0.039 1.28e-02 6.10e+03 9.39e+00 bond pdb=" CG PRO D1139 " pdb=" CD PRO D1139 " ideal model delta sigma weight residual 1.503 1.401 0.102 3.40e-02 8.65e+02 8.93e+00 bond pdb=" N PRO M 258 " pdb=" CD PRO M 258 " ideal model delta sigma weight residual 1.473 1.513 -0.040 1.40e-02 5.10e+03 8.18e+00 bond pdb=" CB PRO M 258 " pdb=" CG PRO M 258 " ideal model delta sigma weight residual 1.492 1.618 -0.126 5.00e-02 4.00e+02 6.35e+00 ... (remaining 29296 not shown) Histogram of bond angle deviations from ideal: 88.97 - 97.98: 4 97.98 - 107.00: 1347 107.00 - 116.02: 18816 116.02 - 125.04: 19473 125.04 - 134.06: 610 Bond angle restraints: 40250 Sorted by residual: angle pdb=" CA PRO M 258 " pdb=" N PRO M 258 " pdb=" CD PRO M 258 " ideal model delta sigma weight residual 112.00 94.43 17.57 1.40e+00 5.10e-01 1.58e+02 angle pdb=" N PRO M 258 " pdb=" CD PRO M 258 " pdb=" CG PRO M 258 " ideal model delta sigma weight residual 103.20 88.97 14.23 1.50e+00 4.44e-01 9.01e+01 angle pdb=" CA PRO D1139 " pdb=" N PRO D1139 " pdb=" CD PRO D1139 " ideal model delta sigma weight residual 112.00 101.82 10.18 1.40e+00 5.10e-01 5.28e+01 angle pdb=" N ILE A 159 " pdb=" CA ILE A 159 " pdb=" C ILE A 159 " ideal model delta sigma weight residual 113.53 107.94 5.59 9.80e-01 1.04e+00 3.25e+01 angle pdb=" C ASP D 67 " pdb=" CA ASP D 67 " pdb=" CB ASP D 67 " ideal model delta sigma weight residual 116.54 110.16 6.38 1.15e+00 7.56e-01 3.07e+01 ... (remaining 40245 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.34: 16635 34.34 - 68.68: 918 68.68 - 103.02: 42 103.02 - 137.36: 2 137.36 - 171.70: 2 Dihedral angle restraints: 17599 sinusoidal: 7140 harmonic: 10459 Sorted by residual: dihedral pdb=" CA LEU D1138 " pdb=" C LEU D1138 " pdb=" N PRO D1139 " pdb=" CA PRO D1139 " ideal model delta harmonic sigma weight residual 180.00 141.02 38.98 0 5.00e+00 4.00e-02 6.08e+01 dihedral pdb=" CA PHE C 15 " pdb=" C PHE C 15 " pdb=" N GLY C 16 " pdb=" CA GLY C 16 " ideal model delta harmonic sigma weight residual 180.00 157.59 22.41 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA PHE D 338 " pdb=" C PHE D 338 " pdb=" N ARG D 339 " pdb=" CA ARG D 339 " ideal model delta harmonic sigma weight residual -180.00 -158.78 -21.22 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 17596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3787 0.050 - 0.100: 797 0.100 - 0.150: 188 0.150 - 0.200: 15 0.200 - 0.250: 1 Chirality restraints: 4788 Sorted by residual: chirality pdb=" CB ILE D 159 " pdb=" CA ILE D 159 " pdb=" CG1 ILE D 159 " pdb=" CG2 ILE D 159 " both_signs ideal model delta sigma weight residual False 2.64 2.90 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CG LEU D 324 " pdb=" CB LEU D 324 " pdb=" CD1 LEU D 324 " pdb=" CD2 LEU D 324 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.55e-01 chirality pdb=" CB ILE M 144 " pdb=" CA ILE M 144 " pdb=" CG1 ILE M 144 " pdb=" CG2 ILE M 144 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.06e-01 ... (remaining 4785 not shown) Planarity restraints: 4929 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D1138 " 0.131 5.00e-02 4.00e+02 1.90e-01 5.80e+01 pdb=" N PRO D1139 " -0.329 5.00e-02 4.00e+02 pdb=" CA PRO D1139 " 0.109 5.00e-02 4.00e+02 pdb=" CD PRO D1139 " 0.089 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP M 257 " 0.100 5.00e-02 4.00e+02 1.36e-01 2.95e+01 pdb=" N PRO M 258 " -0.234 5.00e-02 4.00e+02 pdb=" CA PRO M 258 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO M 258 " 0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE M 273 " -0.069 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO M 274 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO M 274 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO M 274 " -0.056 5.00e-02 4.00e+02 ... (remaining 4926 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 228 2.58 - 3.16: 24131 3.16 - 3.74: 44604 3.74 - 4.32: 58615 4.32 - 4.90: 97701 Nonbonded interactions: 225279 Sorted by model distance: nonbonded pdb=" O3' G R 4 " pdb="MG MG D1501 " model vdw 2.006 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1501 " model vdw 2.037 2.170 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1501 " model vdw 2.091 2.170 nonbonded pdb=" OG SER D 326 " pdb=" OD1 ASP D 329 " model vdw 2.141 2.440 nonbonded pdb=" NH1 ARG D 799 " pdb=" OE2 GLU D1146 " model vdw 2.153 2.520 ... (remaining 225274 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.450 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 94.210 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.150 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3518 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 : 0.005 0.199 29301 Z= 0.324 Angle : 0.711 17.573 40250 Z= 0.386 Chirality : 0.043 0.250 4788 Planarity : 0.006 0.190 4929 Dihedral : 19.202 171.697 10851 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.67 % Favored : 93.30 % Rotamer: Outliers : 0.38 % Allowed : 29.98 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3612 helix: 0.95 (0.15), residues: 1276 sheet: 0.46 (0.27), residues: 396 loop : -1.55 (0.14), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 183 HIS 0.005 0.001 HIS D 113 PHE 0.015 0.002 PHE M 355 TYR 0.036 0.002 TYR C1053 ARG 0.008 0.001 ARG M 184 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 3113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 760 time to evaluate : 2.713 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.4880 (m-80) cc_final: 0.4605 (m-10) REVERT: A 223 ILE cc_start: 0.5677 (mt) cc_final: 0.5458 (mt) REVERT: B 236 ASP cc_start: 0.5041 (t0) cc_final: 0.4717 (t0) REVERT: C 189 ASP cc_start: 0.4148 (t70) cc_final: 0.3929 (t0) REVERT: C 726 TYR cc_start: 0.3265 (t80) cc_final: 0.2905 (t80) REVERT: D 1040 MET cc_start: 0.2818 (tpt) cc_final: 0.2010 (tpt) REVERT: D 1357 ILE cc_start: 0.1264 (pt) cc_final: 0.0823 (pt) REVERT: E 54 ILE cc_start: 0.3741 (mt) cc_final: 0.3363 (mt) REVERT: M 270 GLU cc_start: 0.5301 (tp30) cc_final: 0.4568 (tm-30) REVERT: M 365 MET cc_start: 0.0162 (pmm) cc_final: -0.1949 (ppp) outliers start: 10 outliers final: 0 residues processed: 767 average time/residue: 0.4652 time to fit residues: 540.9738 Evaluate side-chains 468 residues out of total 3113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 468 time to evaluate : 3.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 313 optimal weight: 9.9990 chunk 281 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 96 optimal weight: 0.0170 chunk 189 optimal weight: 0.8980 chunk 150 optimal weight: 0.9990 chunk 290 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 176 optimal weight: 9.9990 chunk 216 optimal weight: 0.0970 chunk 336 optimal weight: 9.9990 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN C 314 ASN ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN ** C 761 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 ASN C1108 ASN C1111 GLN ** C1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1244 HIS ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN D 266 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 594 GLN D 665 GLN D1238 GLN D1249 ASN ** D1259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1350 ASN M 121 GLN ** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4018 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29301 Z= 0.211 Angle : 0.703 11.444 40250 Z= 0.355 Chirality : 0.044 0.196 4788 Planarity : 0.005 0.126 4929 Dihedral : 16.271 171.910 5044 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.76 % Favored : 94.21 % Rotamer: Outliers : 4.72 % Allowed : 29.91 % Favored : 65.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.14), residues: 3612 helix: 0.87 (0.15), residues: 1333 sheet: 0.52 (0.27), residues: 385 loop : -1.49 (0.14), residues: 1894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 183 HIS 0.017 0.002 HIS D 80 PHE 0.025 0.002 PHE M 355 TYR 0.032 0.002 TYR D 349 ARG 0.011 0.001 ARG D 133 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 3113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 502 time to evaluate : 3.299 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 THR cc_start: 0.2946 (OUTLIER) cc_final: 0.1561 (p) REVERT: A 316 MET cc_start: 0.4744 (ppp) cc_final: 0.4491 (ppp) REVERT: C 47 TYR cc_start: 0.2789 (OUTLIER) cc_final: 0.2348 (p90) REVERT: C 900 LYS cc_start: 0.5208 (OUTLIER) cc_final: 0.4595 (mttt) REVERT: C 1022 LYS cc_start: 0.7890 (mttp) cc_final: 0.7555 (mmmt) REVERT: D 43 THR cc_start: 0.2773 (OUTLIER) cc_final: 0.2562 (m) REVERT: D 1040 MET cc_start: 0.2669 (tpt) cc_final: 0.2035 (tpt) REVERT: M 270 GLU cc_start: 0.5462 (tp30) cc_final: 0.4657 (tm-30) REVERT: M 363 LYS cc_start: 0.4223 (mmmt) cc_final: 0.3930 (mmmt) REVERT: M 365 MET cc_start: 0.0603 (pmm) cc_final: -0.1409 (ppp) outliers start: 123 outliers final: 45 residues processed: 596 average time/residue: 0.4271 time to fit residues: 399.5842 Evaluate side-chains 462 residues out of total 3113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 413 time to evaluate : 3.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 71 LYS Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 123 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 735 LYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 793 GLU Chi-restraints excluded: chain C residue 819 SER Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 833 ILE Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 930 ASP Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 1154 ASP Chi-restraints excluded: chain C residue 1176 LEU Chi-restraints excluded: chain C residue 1201 LEU Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1302 THR Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 423 LEU Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 484 MET Chi-restraints excluded: chain D residue 590 SER Chi-restraints excluded: chain D residue 619 ILE Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1351 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 187 optimal weight: 0.0980 chunk 104 optimal weight: 2.9990 chunk 280 optimal weight: 8.9990 chunk 229 optimal weight: 9.9990 chunk 92 optimal weight: 20.0000 chunk 337 optimal weight: 20.0000 chunk 364 optimal weight: 50.0000 chunk 300 optimal weight: 0.3980 chunk 334 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 270 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 GLN C 659 GLN C 686 GLN C 725 GLN C 762 ASN C 932 GLN C1108 ASN ** C1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1244 HIS C1257 GLN D 309 ASN D 364 HIS D 365 GLN ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1218 HIS D1249 ASN ** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4532 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29301 Z= 0.214 Angle : 0.693 11.082 40250 Z= 0.349 Chirality : 0.044 0.230 4788 Planarity : 0.005 0.105 4929 Dihedral : 16.155 170.729 5044 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.73 % Favored : 94.21 % Rotamer: Outliers : 4.95 % Allowed : 29.87 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.14), residues: 3612 helix: 0.79 (0.14), residues: 1342 sheet: 0.60 (0.26), residues: 373 loop : -1.48 (0.14), residues: 1897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP D 580 HIS 0.013 0.002 HIS D 80 PHE 0.026 0.002 PHE C 629 TYR 0.032 0.002 TYR D 589 ARG 0.009 0.001 ARG D 744 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 473 time to evaluate : 3.019 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: 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: symmetry clash REVERT: A 77 ASP cc_start: 0.3875 (OUTLIER) cc_final: 0.3652 (t70) REVERT: C 47 TYR cc_start: 0.3596 (OUTLIER) cc_final: 0.2937 (p90) REVERT: C 68 LEU cc_start: 0.6848 (tp) cc_final: 0.6297 (tt) REVERT: C 409 LEU cc_start: 0.5281 (OUTLIER) cc_final: 0.4895 (tp) REVERT: C 430 LYS cc_start: 0.3158 (mmtt) cc_final: 0.2861 (mmtt) REVERT: C 900 LYS cc_start: 0.5539 (OUTLIER) cc_final: 0.4781 (mttt) REVERT: C 1022 LYS cc_start: 0.7896 (mttp) cc_final: 0.7655 (mmmt) REVERT: D 894 VAL cc_start: 0.4728 (OUTLIER) cc_final: 0.4406 (t) REVERT: D 1040 MET cc_start: 0.2656 (tpt) cc_final: 0.2157 (tpt) REVERT: M 270 GLU cc_start: 0.5667 (tp30) cc_final: 0.5399 (tp30) REVERT: M 363 LYS cc_start: 0.4345 (mmmt) cc_final: 0.4132 (mmmt) REVERT: M 365 MET cc_start: 0.0187 (pmm) cc_final: -0.1908 (ppp) outliers start: 129 outliers final: 55 residues processed: 566 average time/residue: 0.4001 time to fit residues: 362.7807 Evaluate side-chains 467 residues out of total 3113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 407 time to evaluate : 3.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 SER Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 231 PHE Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 655 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 831 ILE Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1154 ASP Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 146 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 309 ASN Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 772 TYR Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 869 CYS Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1249 ASN Chi-restraints excluded: chain D residue 1253 ILE Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain M residue 210 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 333 optimal weight: 5.9990 chunk 253 optimal weight: 0.0970 chunk 175 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 161 optimal weight: 8.9990 chunk 226 optimal weight: 7.9990 chunk 338 optimal weight: 20.0000 chunk 358 optimal weight: 20.0000 chunk 176 optimal weight: 3.9990 chunk 321 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 ASN B 75 GLN B 93 GLN C 314 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1257 GLN ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 ASN D 430 HIS ** D 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 265 GLN ** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6401 moved from start: 0.9295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.187 29301 Z= 0.459 Angle : 0.973 20.387 40250 Z= 0.506 Chirality : 0.055 0.629 4788 Planarity : 0.008 0.150 4929 Dihedral : 16.591 167.024 5044 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 23.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.89 % Favored : 93.00 % Rotamer: Outliers : 7.48 % Allowed : 27.72 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.13), residues: 3612 helix: 0.00 (0.14), residues: 1346 sheet: -0.03 (0.27), residues: 381 loop : -1.71 (0.13), residues: 1885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.005 TRP D 580 HIS 0.018 0.003 HIS D1252 PHE 0.035 0.004 PHE C 53 TYR 0.041 0.004 TYR D 589 ARG 0.022 0.001 ARG D 250 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 3113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 486 time to evaluate : 2.995 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: symmetry clash REVERT: A 8 PHE cc_start: 0.6521 (m-10) cc_final: 0.6264 (m-80) REVERT: A 57 THR cc_start: 0.6948 (p) cc_final: 0.6380 (m) REVERT: A 142 MET cc_start: 0.6571 (ppp) cc_final: 0.5981 (ppp) REVERT: B 37 HIS cc_start: 0.8126 (OUTLIER) cc_final: 0.7210 (t-90) REVERT: C 1022 LYS cc_start: 0.7877 (mttp) cc_final: 0.7607 (mmmt) REVERT: C 1108 ASN cc_start: 0.7284 (OUTLIER) cc_final: 0.7060 (p0) REVERT: D 1040 MET cc_start: 0.2774 (tpt) cc_final: 0.1973 (tpt) REVERT: D 1287 ILE cc_start: 0.4900 (OUTLIER) cc_final: 0.4557 (mt) REVERT: M 270 GLU cc_start: 0.6448 (tp30) cc_final: 0.5866 (tp30) REVERT: M 455 ARG cc_start: 0.5010 (tpt90) cc_final: 0.2558 (tmm160) outliers start: 195 outliers final: 77 residues processed: 639 average time/residue: 0.4007 time to fit residues: 411.8943 Evaluate side-chains 446 residues out of total 3113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 366 time to evaluate : 3.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 207 THR Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 127 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 493 ILE Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 719 LYS Chi-restraints excluded: chain C residue 785 ASP Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 840 SER Chi-restraints excluded: chain C residue 871 VAL Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 1018 TYR Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1108 ASN Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1154 ASP Chi-restraints excluded: chain C residue 1157 GLN Chi-restraints excluded: chain C residue 1227 VAL Chi-restraints excluded: chain C residue 1234 LYS Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 329 ASP Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 564 VAL Chi-restraints excluded: chain D residue 708 ASN Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 765 GLU Chi-restraints excluded: chain D residue 767 LEU Chi-restraints excluded: chain D residue 811 GLU Chi-restraints excluded: chain D residue 840 LEU Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1253 ILE Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1344 LEU Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 61 ASN Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 201 ILE Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 355 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 298 optimal weight: 0.1980 chunk 203 optimal weight: 8.9990 chunk 5 optimal weight: 10.0000 chunk 267 optimal weight: 5.9990 chunk 147 optimal weight: 0.9980 chunk 306 optimal weight: 0.6980 chunk 247 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 321 optimal weight: 9.9990 chunk 90 optimal weight: 0.0980 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 737 ASN ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1070 HIS C1108 ASN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1257 GLN D 276 ASN D 469 HIS ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 921 GLN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1366 HIS ** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.9776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 29301 Z= 0.210 Angle : 0.702 14.848 40250 Z= 0.351 Chirality : 0.043 0.197 4788 Planarity : 0.005 0.066 4929 Dihedral : 16.335 169.023 5044 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 18.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.51 % Favored : 94.41 % Rotamer: Outliers : 3.87 % Allowed : 32.98 % Favored : 63.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3612 helix: 0.59 (0.14), residues: 1333 sheet: 0.23 (0.27), residues: 371 loop : -1.57 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 580 HIS 0.009 0.001 HIS D 80 PHE 0.022 0.002 PHE D 892 TYR 0.028 0.002 TYR D 555 ARG 0.010 0.001 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 503 residues out of total 3113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 402 time to evaluate : 3.151 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: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.6840 (ppp) cc_final: 0.6310 (ppp) REVERT: C 900 LYS cc_start: 0.5647 (OUTLIER) cc_final: 0.5060 (mttt) REVERT: D 772 TYR cc_start: 0.6397 (OUTLIER) cc_final: 0.5834 (m-80) REVERT: D 1040 MET cc_start: 0.2385 (tpt) cc_final: 0.1552 (tpt) REVERT: M 270 GLU cc_start: 0.6503 (tp30) cc_final: 0.6011 (tp30) REVERT: M 455 ARG cc_start: 0.4941 (tpt90) cc_final: 0.2529 (tmm160) outliers start: 101 outliers final: 51 residues processed: 485 average time/residue: 0.3994 time to fit residues: 312.8114 Evaluate side-chains 410 residues out of total 3113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 357 time to evaluate : 2.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 185 ASP Chi-restraints excluded: chain C residue 484 LEU Chi-restraints excluded: chain C residue 530 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 651 ASP Chi-restraints excluded: chain C residue 719 LYS Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1154 ASP Chi-restraints excluded: chain C residue 1275 VAL Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 65 VAL Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 355 ILE Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 514 THR Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 721 SER Chi-restraints excluded: chain D residue 772 TYR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1253 ILE Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 355 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 120 optimal weight: 2.9990 chunk 322 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 210 optimal weight: 30.0000 chunk 88 optimal weight: 0.0030 chunk 358 optimal weight: 7.9990 chunk 297 optimal weight: 0.9990 chunk 166 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 188 optimal weight: 8.9990 overall best weight: 3.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 1.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 29301 Z= 0.324 Angle : 0.792 16.874 40250 Z= 0.404 Chirality : 0.047 0.300 4788 Planarity : 0.006 0.093 4929 Dihedral : 16.357 170.501 5044 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.92 % Favored : 93.02 % Rotamer: Outliers : 4.72 % Allowed : 32.02 % Favored : 63.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.14), residues: 3612 helix: 0.45 (0.14), residues: 1330 sheet: 0.09 (0.27), residues: 356 loop : -1.53 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.004 TRP D 115 HIS 0.014 0.002 HIS D 80 PHE 0.029 0.003 PHE C 645 TYR 0.024 0.002 TYR C 3 ARG 0.028 0.001 ARG D 297 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 367 time to evaluate : 3.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.7052 (ppp) cc_final: 0.6662 (ptt) REVERT: B 37 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7463 (t-90) REVERT: C 47 TYR cc_start: 0.6553 (OUTLIER) cc_final: 0.6226 (p90) REVERT: C 430 LYS cc_start: 0.5770 (mmtt) cc_final: 0.5427 (mmtt) REVERT: C 900 LYS cc_start: 0.6212 (OUTLIER) cc_final: 0.5519 (mttt) REVERT: C 1274 GLU cc_start: 0.6949 (mp0) cc_final: 0.6620 (mp0) REVERT: C 1290 MET cc_start: 0.7070 (mtt) cc_final: 0.6768 (mtt) REVERT: D 772 TYR cc_start: 0.6764 (OUTLIER) cc_final: 0.6361 (m-80) REVERT: D 1040 MET cc_start: 0.2235 (tpt) cc_final: 0.1331 (tpt) REVERT: D 1344 LEU cc_start: 0.6642 (mm) cc_final: 0.6399 (mm) REVERT: M 270 GLU cc_start: 0.6766 (tp30) cc_final: 0.6114 (tp30) REVERT: M 455 ARG cc_start: 0.4698 (tpt90) cc_final: 0.2655 (tmm160) outliers start: 123 outliers final: 62 residues processed: 454 average time/residue: 0.3891 time to fit residues: 288.9865 Evaluate side-chains 359 residues out of total 3113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 293 time to evaluate : 3.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain C residue 432 LEU Chi-restraints excluded: chain C residue 499 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 719 LYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 802 VAL Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1112 ILE Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1154 ASP Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 441 LEU Chi-restraints excluded: chain D residue 449 LEU Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 772 TYR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1162 ILE Chi-restraints excluded: chain D residue 1169 THR Chi-restraints excluded: chain D residue 1177 ILE Chi-restraints excluded: chain D residue 1226 VAL Chi-restraints excluded: chain D residue 1230 THR Chi-restraints excluded: chain D residue 1253 ILE Chi-restraints excluded: chain D residue 1260 MET Chi-restraints excluded: chain D residue 1273 ASP Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain D residue 1329 THR Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 355 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 346 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 204 optimal weight: 7.9990 chunk 262 optimal weight: 7.9990 chunk 203 optimal weight: 2.9990 chunk 302 optimal weight: 50.0000 chunk 200 optimal weight: 1.9990 chunk 357 optimal weight: 20.0000 chunk 223 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 165 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 266 ASN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 1.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 29301 Z= 0.281 Angle : 0.736 17.211 40250 Z= 0.368 Chirality : 0.045 0.321 4788 Planarity : 0.005 0.090 4929 Dihedral : 16.318 169.654 5044 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.20 % Favored : 93.74 % Rotamer: Outliers : 2.99 % Allowed : 35.05 % Favored : 61.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -0.67 (0.14), residues: 3612 helix: 0.67 (0.14), residues: 1327 sheet: 0.16 (0.27), residues: 367 loop : -1.42 (0.14), residues: 1918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP D 115 HIS 0.010 0.001 HIS D 80 PHE 0.021 0.002 PHE C 505 TYR 0.022 0.002 TYR A 152 ARG 0.012 0.001 ARG D1330 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 320 time to evaluate : 3.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.7936 (mmm) cc_final: 0.7572 (mmt) REVERT: C 47 TYR cc_start: 0.6538 (OUTLIER) cc_final: 0.6226 (p90) REVERT: C 517 GLN cc_start: 0.7819 (tp40) cc_final: 0.7539 (tp40) REVERT: C 742 TYR cc_start: 0.6916 (m-10) cc_final: 0.6301 (m-10) REVERT: C 900 LYS cc_start: 0.6274 (OUTLIER) cc_final: 0.5476 (mttt) REVERT: C 1023 HIS cc_start: 0.8216 (m90) cc_final: 0.7997 (m90) REVERT: D 102 MET cc_start: 0.6150 (mmt) cc_final: 0.5926 (mmt) REVERT: D 400 MET cc_start: 0.7015 (tmm) cc_final: 0.6718 (ttt) REVERT: D 513 MET cc_start: 0.6958 (tpp) cc_final: 0.6546 (ttt) REVERT: D 772 TYR cc_start: 0.6857 (OUTLIER) cc_final: 0.6320 (m-80) REVERT: D 1040 MET cc_start: 0.2346 (tpt) cc_final: 0.1683 (tpt) REVERT: D 1305 ASP cc_start: 0.5125 (m-30) cc_final: 0.4832 (m-30) REVERT: M 154 LEU cc_start: 0.4935 (mt) cc_final: 0.4416 (mt) REVERT: M 270 GLU cc_start: 0.6699 (tp30) cc_final: 0.6232 (tp30) REVERT: M 455 ARG cc_start: 0.5293 (tpt90) cc_final: 0.3077 (tmm160) outliers start: 78 outliers final: 46 residues processed: 379 average time/residue: 0.4039 time to fit residues: 248.3385 Evaluate side-chains 335 residues out of total 3113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 286 time to evaluate : 3.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1154 ASP Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 262 THR Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 772 TYR Chi-restraints excluded: chain D residue 802 ASP Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 910 ASN Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 921 GLN Chi-restraints excluded: chain D residue 1250 ASP Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 155 THR Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 355 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 221 optimal weight: 0.0980 chunk 142 optimal weight: 0.9990 chunk 213 optimal weight: 30.0000 chunk 107 optimal weight: 4.9990 chunk 70 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 227 optimal weight: 6.9990 chunk 243 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 281 optimal weight: 0.0170 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 HIS ** C 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1108 ASN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 1.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29301 Z= 0.193 Angle : 0.701 14.017 40250 Z= 0.347 Chirality : 0.043 0.187 4788 Planarity : 0.005 0.084 4929 Dihedral : 16.273 171.918 5044 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.04 % Favored : 93.94 % Rotamer: Outliers : 2.53 % Allowed : 34.55 % Favored : 62.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3612 helix: 0.94 (0.14), residues: 1316 sheet: 0.31 (0.28), residues: 355 loop : -1.36 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 236 HIS 0.009 0.001 HIS D 80 PHE 0.015 0.002 PHE C 390 TYR 0.028 0.002 TYR C 26 ARG 0.008 0.001 ARG M 196 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 3113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 326 time to evaluate : 3.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.7818 (mmm) cc_final: 0.7503 (mmt) REVERT: B 51 MET cc_start: 0.7089 (tpp) cc_final: 0.6853 (tpp) REVERT: C 47 TYR cc_start: 0.6511 (OUTLIER) cc_final: 0.6235 (p90) REVERT: C 80 PHE cc_start: 0.7477 (OUTLIER) cc_final: 0.6764 (m-80) REVERT: C 517 GLN cc_start: 0.7681 (tp40) cc_final: 0.7145 (tp-100) REVERT: C 523 GLU cc_start: 0.5606 (mt-10) cc_final: 0.5324 (mt-10) REVERT: C 741 MET cc_start: 0.7554 (mmt) cc_final: 0.7177 (mmm) REVERT: C 900 LYS cc_start: 0.6391 (OUTLIER) cc_final: 0.5604 (mttt) REVERT: C 1023 HIS cc_start: 0.8150 (m90) cc_final: 0.7866 (m90) REVERT: D 400 MET cc_start: 0.6965 (tmm) cc_final: 0.6658 (ttt) REVERT: D 513 MET cc_start: 0.6880 (tpp) cc_final: 0.6430 (ttt) REVERT: D 1040 MET cc_start: 0.2445 (tpt) cc_final: 0.1975 (tpt) REVERT: D 1151 LYS cc_start: 0.7827 (mppt) cc_final: 0.7535 (mmtm) REVERT: M 270 GLU cc_start: 0.6757 (tp30) cc_final: 0.6352 (tp30) REVERT: M 455 ARG cc_start: 0.5149 (tpt90) cc_final: 0.3032 (tmm160) outliers start: 66 outliers final: 43 residues processed: 375 average time/residue: 0.3984 time to fit residues: 240.4360 Evaluate side-chains 342 residues out of total 3113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 296 time to evaluate : 3.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1163 THR Chi-restraints excluded: chain C residue 1241 ASP Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 772 TYR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 921 GLN Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 355 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 325 optimal weight: 0.9980 chunk 342 optimal weight: 0.2980 chunk 312 optimal weight: 5.9990 chunk 333 optimal weight: 0.0570 chunk 200 optimal weight: 7.9990 chunk 145 optimal weight: 6.9990 chunk 261 optimal weight: 7.9990 chunk 102 optimal weight: 8.9990 chunk 301 optimal weight: 0.0070 chunk 315 optimal weight: 8.9990 chunk 332 optimal weight: 0.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1244 GLN ** D1249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 387 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 1.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29301 Z= 0.183 Angle : 0.690 13.833 40250 Z= 0.339 Chirality : 0.043 0.207 4788 Planarity : 0.005 0.078 4929 Dihedral : 16.213 173.325 5044 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.56 % Favored : 94.41 % Rotamer: Outliers : 1.92 % Allowed : 34.70 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.14), residues: 3612 helix: 1.00 (0.14), residues: 1317 sheet: 0.42 (0.29), residues: 346 loop : -1.34 (0.14), residues: 1949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 236 HIS 0.009 0.001 HIS D 80 PHE 0.023 0.001 PHE D 7 TYR 0.023 0.001 TYR A 152 ARG 0.008 0.000 ARG D1222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 317 time to evaluate : 3.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.7726 (mmm) cc_final: 0.7410 (mmt) REVERT: B 51 MET cc_start: 0.7238 (tpp) cc_final: 0.6886 (tpp) REVERT: C 47 TYR cc_start: 0.6519 (OUTLIER) cc_final: 0.6222 (p90) REVERT: C 80 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.6974 (m-80) REVERT: C 523 GLU cc_start: 0.5616 (mt-10) cc_final: 0.5317 (mt-10) REVERT: C 900 LYS cc_start: 0.6447 (OUTLIER) cc_final: 0.5685 (mttt) REVERT: C 1023 HIS cc_start: 0.8212 (m90) cc_final: 0.7947 (m90) REVERT: D 400 MET cc_start: 0.6894 (tmm) cc_final: 0.6638 (ttt) REVERT: D 500 ILE cc_start: 0.8265 (mp) cc_final: 0.8047 (mt) REVERT: D 1040 MET cc_start: 0.2400 (tpt) cc_final: 0.1976 (tpt) REVERT: M 154 LEU cc_start: 0.4798 (mt) cc_final: 0.4575 (tp) REVERT: M 270 GLU cc_start: 0.6624 (tp30) cc_final: 0.6230 (tp30) outliers start: 50 outliers final: 36 residues processed: 353 average time/residue: 0.3827 time to fit residues: 223.0604 Evaluate side-chains 332 residues out of total 3113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 293 time to evaluate : 3.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 704 MET Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1241 ASP Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 128 LEU Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 412 LEU Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 474 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 772 TYR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 921 GLN Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain M residue 210 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 218 optimal weight: 9.9990 chunk 352 optimal weight: 4.9990 chunk 215 optimal weight: 5.9990 chunk 167 optimal weight: 5.9990 chunk 244 optimal weight: 5.9990 chunk 369 optimal weight: 8.9990 chunk 340 optimal weight: 5.9990 chunk 294 optimal weight: 30.0000 chunk 30 optimal weight: 10.0000 chunk 227 optimal weight: 3.9990 chunk 180 optimal weight: 0.7980 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 760 ASN C1116 HIS C1175 ASN ** C1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1313 HIS ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1249 ASN E 15 ASN M 202 GLN ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 290 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 1.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.128 29301 Z= 0.356 Angle : 0.813 29.572 40250 Z= 0.407 Chirality : 0.047 0.262 4788 Planarity : 0.006 0.124 4929 Dihedral : 16.386 170.931 5044 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.28 % Favored : 92.69 % Rotamer: Outliers : 2.45 % Allowed : 34.43 % Favored : 63.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -0.69 (0.14), residues: 3612 helix: 0.74 (0.14), residues: 1307 sheet: 0.13 (0.28), residues: 357 loop : -1.47 (0.14), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP C 807 HIS 0.011 0.002 HIS D1366 PHE 0.070 0.003 PHE M 354 TYR 0.031 0.002 TYR C 26 ARG 0.015 0.001 ARG A 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7224 Ramachandran restraints generated. 3612 Oldfield, 0 Emsley, 3612 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 3113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 283 time to evaluate : 2.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 HIS cc_start: 0.8225 (OUTLIER) cc_final: 0.7348 (t-90) REVERT: B 51 MET cc_start: 0.7652 (tpp) cc_final: 0.6904 (tpp) REVERT: C 80 PHE cc_start: 0.7879 (OUTLIER) cc_final: 0.7341 (m-80) REVERT: C 430 LYS cc_start: 0.6938 (tptt) cc_final: 0.6683 (mptt) REVERT: D 500 ILE cc_start: 0.8336 (mp) cc_final: 0.8078 (mt) REVERT: D 1040 MET cc_start: 0.3054 (tpt) cc_final: 0.2210 (tpt) outliers start: 64 outliers final: 41 residues processed: 333 average time/residue: 0.4062 time to fit residues: 218.7359 Evaluate side-chains 291 residues out of total 3113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 248 time to evaluate : 3.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 252 ILE Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 37 HIS Chi-restraints excluded: chain B residue 110 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 900 LYS Chi-restraints excluded: chain C residue 967 LEU Chi-restraints excluded: chain C residue 1049 ILE Chi-restraints excluded: chain C residue 1115 THR Chi-restraints excluded: chain C residue 1154 ASP Chi-restraints excluded: chain C residue 1241 ASP Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 70 CYS Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 338 PHE Chi-restraints excluded: chain D residue 408 VAL Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 674 THR Chi-restraints excluded: chain D residue 772 TYR Chi-restraints excluded: chain D residue 858 VAL Chi-restraints excluded: chain D residue 910 ASN Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 918 ILE Chi-restraints excluded: chain D residue 921 GLN Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1320 ILE Chi-restraints excluded: chain E residue 11 GLU Chi-restraints excluded: chain E residue 44 ASP Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain M residue 210 THR Chi-restraints excluded: chain M residue 363 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 371 random chunks: chunk 233 optimal weight: 0.7980 chunk 313 optimal weight: 0.9990 chunk 90 optimal weight: 6.9990 chunk 271 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 81 optimal weight: 8.9990 chunk 294 optimal weight: 30.0000 chunk 123 optimal weight: 5.9990 chunk 302 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 551 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 798 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 504 GLN ** D 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 202 GLN ** M 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.086508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.062160 restraints weight = 114029.279| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 4.26 r_work: 0.3056 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 1.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 29301 Z= 0.239 Angle : 0.738 12.982 40250 Z= 0.366 Chirality : 0.045 0.270 4788 Planarity : 0.005 0.080 4929 Dihedral : 16.319 171.985 5044 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 18.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.20 % Favored : 93.77 % Rotamer: Outliers : 1.80 % Allowed : 35.93 % Favored : 62.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.34 % Cis-general : 0.00 % Twisted Proline : 0.67 % 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: -0.55 (0.14), residues: 3612 helix: 0.90 (0.14), residues: 1314 sheet: 0.12 (0.28), residues: 357 loop : -1.40 (0.14), residues: 1941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 236 HIS 0.008 0.001 HIS D 80 PHE 0.034 0.002 PHE C 390 TYR 0.028 0.002 TYR A 152 ARG 0.017 0.001 ARG C 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7298.01 seconds wall clock time: 132 minutes 55.10 seconds (7975.10 seconds total)