Starting phenix.real_space_refine on Fri Mar 22 10:26:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c17_30268/03_2024/7c17_30268.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c17_30268/03_2024/7c17_30268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c17_30268/03_2024/7c17_30268.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c17_30268/03_2024/7c17_30268.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c17_30268/03_2024/7c17_30268.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7c17_30268/03_2024/7c17_30268.pdb" } resolution = 4.22 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: 8 Type Number sf(0) Gaussians Ag 1 8.66 5 Zn 2 6.06 5 P 103 5.49 5 Mg 1 5.21 5 S 137 5.16 5 C 20403 2.51 5 N 5838 2.21 5 O 6576 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 12": "NH1" <-> "NH2" Residue "A GLU 17": "OE1" <-> "OE2" Residue "A GLU 29": "OE1" <-> "OE2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "B ARG 33": "NH1" <-> "NH2" Residue "B ARG 150": "NH1" <-> "NH2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "C ARG 10": "NH1" <-> "NH2" Residue "C GLU 40": "OE1" <-> "OE2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C GLU 187": "OE1" <-> "OE2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C GLU 278": "OE1" <-> "OE2" Residue "C GLU 349": "OE1" <-> "OE2" Residue "C ARG 359": "NH1" <-> "NH2" Residue "C ARG 368": "NH1" <-> "NH2" Residue "C ARG 371": "NH1" <-> "NH2" Residue "C ARG 378": "NH1" <-> "NH2" Residue "C GLU 386": "OE1" <-> "OE2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "C GLU 441": "OE1" <-> "OE2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C GLU 472": "OE1" <-> "OE2" Residue "C ARG 478": "NH1" <-> "NH2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C ARG 540": "NH1" <-> "NH2" Residue "C GLU 546": "OE1" <-> "OE2" Residue "C ARG 637": "NH1" <-> "NH2" Residue "C ARG 687": "NH1" <-> "NH2" Residue "C ARG 779": "NH1" <-> "NH2" Residue "C GLU 813": "OE1" <-> "OE2" Residue "C ARG 827": "NH1" <-> "NH2" Residue "C GLU 876": "OE1" <-> "OE2" Residue "C GLU 892": "OE1" <-> "OE2" Residue "C ARG 936": "NH1" <-> "NH2" Residue "C ARG 944": "NH1" <-> "NH2" Residue "C GLU 950": "OE1" <-> "OE2" Residue "C GLU 1005": "OE1" <-> "OE2" Residue "C GLU 1006": "OE1" <-> "OE2" Residue "C ARG 1033": "NH1" <-> "NH2" Residue "C ARG 1059": "NH1" <-> "NH2" Residue "C ARG 1142": "NH1" <-> "NH2" Residue "C ARG 1156": "NH1" <-> "NH2" Residue "C GLU 1167": "OE1" <-> "OE2" Residue "C ARG 1246": "NH1" <-> "NH2" Residue "C ARG 1269": "NH1" <-> "NH2" Residue "C GLU 1272": "OE1" <-> "OE2" Residue "C GLU 1289": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D ARG 47": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D ARG 220": "NH1" <-> "NH2" Residue "D ARG 259": "NH1" <-> "NH2" Residue "D ARG 270": "NH1" <-> "NH2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D GLU 375": "OE1" <-> "OE2" Residue "D ARG 388": "NH1" <-> "NH2" Residue "D GLU 404": "OE1" <-> "OE2" Residue "D ARG 417": "NH1" <-> "NH2" Residue "D ARG 431": "NH1" <-> "NH2" Residue "D GLU 479": "OE1" <-> "OE2" Residue "D ARG 535": "NH1" <-> "NH2" Residue "D ARG 547": "NH1" <-> "NH2" Residue "D GLU 556": "OE1" <-> "OE2" Residue "D ARG 634": "NH1" <-> "NH2" Residue "D GLU 648": "OE1" <-> "OE2" Residue "D GLU 660": "OE1" <-> "OE2" Residue "D GLU 666": "OE1" <-> "OE2" Residue "D ARG 678": "NH1" <-> "NH2" Residue "D ARG 692": "NH1" <-> "NH2" Residue "D ARG 744": "NH1" <-> "NH2" Residue "D ARG 842": "NH1" <-> "NH2" Residue "D ARG 860": "NH1" <-> "NH2" Residue "D GLU 925": "OE1" <-> "OE2" Residue "D ARG 1149": "NH1" <-> "NH2" Residue "D GLU 1215": "OE1" <-> "OE2" Residue "D ARG 1222": "NH1" <-> "NH2" Residue "D ARG 1242": "NH1" <-> "NH2" Residue "D ARG 1258": "NH1" <-> "NH2" Residue "D ARG 1284": "NH1" <-> "NH2" Residue "D ARG 1369": "NH1" <-> "NH2" Residue "E ARG 26": "NH1" <-> "NH2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "F ARG 93": "NH1" <-> "NH2" Residue "F ARG 103": "NH1" <-> "NH2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "F GLU 114": "OE1" <-> "OE2" Residue "F GLU 124": "OE1" <-> "OE2" Residue "F GLU 247": "OE1" <-> "OE2" Residue "F GLU 293": "OE1" <-> "OE2" Residue "F GLU 349": "OE1" <-> "OE2" Residue "F GLU 356": "OE1" <-> "OE2" Residue "F ARG 364": "NH1" <-> "NH2" Residue "F GLU 420": "OE1" <-> "OE2" Residue "F ARG 465": "NH1" <-> "NH2" Residue "F ARG 476": "NH1" <-> "NH2" Residue "F ARG 554": "NH1" <-> "NH2" Residue "F ARG 584": "NH1" <-> "NH2" Residue "F GLU 605": "OE1" <-> "OE2" Residue "F ARG 608": "NH1" <-> "NH2" Residue "G ARG 37": "NH1" <-> "NH2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 86": "OE1" <-> "OE2" Residue "G ARG 102": "NH1" <-> "NH2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H GLU 22": "OE1" <-> "OE2" Residue "H ARG 54": "NH1" <-> "NH2" Residue "H GLU 61": "OE1" <-> "OE2" Residue "H ARG 82": "NH1" <-> "NH2" Residue "H ARG 102": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33061 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2307 Classifications: {'peptide': 303} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 289} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 27 Chain: "B" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1692 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 217} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "C" Number of atoms: 10450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1338, 10450 Classifications: {'peptide': 1338} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1281} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 63 Chain: "D" Number of atoms: 10168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1331, 10168 Classifications: {'peptide': 1331} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1275} Chain breaks: 2 Unresolved non-hydrogen bonds: 192 Unresolved non-hydrogen angles: 241 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASP:plan': 4, 'PHE:plan': 2, 'GLU:plan': 10, 'ARG:plan': 17} Unresolved non-hydrogen planarities: 145 Chain: "E" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 73} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 3726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3726 Classifications: {'peptide': 465} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 14, 'TRANS': 450} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 3, 'ARG:plan': 8, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 48 Chain: "1" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 1188 Classifications: {'DNA': 58} Link IDs: {'rna3p': 57} Chain: "2" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 946 Classifications: {'DNA': 46} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 45} Chain breaks: 1 Chain: "G" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 992 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 987 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 122} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 19 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} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' AG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14883 SG CYS D 70 70.244 43.888 65.111 1.00 68.22 S ATOM 14897 SG CYS D 72 72.300 43.074 61.706 1.00 73.04 S ATOM 20661 SG CYS D 814 84.245 65.453 125.016 1.00 67.56 S ATOM 21218 SG CYS D 888 83.708 66.957 121.680 1.00 58.93 S ATOM 21269 SG CYS D 895 80.688 64.504 122.682 1.00 61.58 S ATOM 21290 SG CYS D 898 81.676 68.279 124.949 1.00 56.03 S ATOM 31964 SG CYS G 112 37.725 60.162 23.976 1.00216.41 S ATOM 32016 SG CYS G 120 37.167 56.837 26.883 1.00241.50 S Time building chain proxies: 17.25, per 1000 atoms: 0.52 Number of scatterers: 33061 At special positions: 0 Unit cell: (158, 149, 169, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ag 1 46.95 Zn 2 29.99 S 137 16.00 P 103 15.00 Mg 1 11.99 O 6576 8.00 N 5838 7.00 C 20403 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.17 Conformation dependent library (CDL) restraints added in 5.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " Number of angles added : 6 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7430 Finding SS restraints... Secondary structure from input PDB file: 139 helices and 40 sheets defined 42.7% alpha, 10.1% beta 40 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 10.89 Creating SS restraints... Processing helix chain 'A' and resid 34 through 49 removed outlier: 3.759A pdb=" N GLY A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER A 49 " --> pdb=" O ARG A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 86 removed outlier: 3.548A pdb=" N ILE A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 161 removed outlier: 3.709A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 159 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N HIS A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 removed outlier: 3.698A pdb=" N ARG A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 261 removed outlier: 3.567A pdb=" N GLU A 261 " --> pdb=" O ASP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 268 Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.570A pdb=" N VAL A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 283' Processing helix chain 'A' and resid 285 through 292 Processing helix chain 'A' and resid 297 through 310 removed outlier: 3.925A pdb=" N THR A 301 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 49 removed outlier: 3.824A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ILE B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 Processing helix chain 'B' and resid 212 through 228 Processing helix chain 'B' and resid 229 through 232 removed outlier: 4.088A pdb=" N VAL B 232 " --> pdb=" O GLU B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'C' and resid 28 through 40 removed outlier: 4.360A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.782A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 206 through 211 Processing helix chain 'C' and resid 212 through 214 No H-bonds generated for 'chain 'C' and resid 212 through 214' Processing helix chain 'C' and resid 216 through 223 Processing helix chain 'C' and resid 270 through 281 removed outlier: 3.627A pdb=" N ILE C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 removed outlier: 4.132A pdb=" N ILE C 292 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 288 through 293' Processing helix chain 'C' and resid 318 through 328 Processing helix chain 'C' and resid 345 through 353 removed outlier: 3.789A pdb=" N VAL C 353 " --> pdb=" O GLU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.618A pdb=" N MET C 369 " --> pdb=" O GLU C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 390 Processing helix chain 'C' and resid 400 through 409 Processing helix chain 'C' and resid 421 through 437 removed outlier: 3.929A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 480 removed outlier: 3.883A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N SER C 480 " --> pdb=" O LYS C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 4.415A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ILE C 493 " --> pdb=" O PRO C 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 488 through 493' Processing helix chain 'C' and resid 494 through 509 removed outlier: 4.617A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE C 506 " --> pdb=" O VAL C 502 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLY C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.657A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 667 removed outlier: 3.631A pdb=" N LEU C 667 " --> pdb=" O VAL C 663 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 688 removed outlier: 3.686A pdb=" N LEU C 680 " --> pdb=" O ALA C 676 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 713 removed outlier: 4.369A pdb=" N ALA C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL C 710 " --> pdb=" O ARG C 706 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLY C 713 " --> pdb=" O ALA C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 942 through 983 removed outlier: 3.847A pdb=" N LEU C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 998 removed outlier: 3.510A pdb=" N ARG C 996 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N TRP C 997 " --> pdb=" O ARG C 994 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU C 998 " --> pdb=" O ASP C 995 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 993 through 998' Processing helix chain 'C' and resid 1005 through 1037 removed outlier: 3.518A pdb=" N GLU C1026 " --> pdb=" O LYS C1022 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N THR C1037 " --> pdb=" O ARG C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1107 removed outlier: 4.722A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG C1106 " --> pdb=" O GLY C1102 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.792A pdb=" N GLN C1134 " --> pdb=" O ALA C1130 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1148 removed outlier: 3.548A pdb=" N GLU C1143 " --> pdb=" O ALA C1139 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN C1146 " --> pdb=" O ARG C1142 " (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 1243 Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1284 through 1291 Processing helix chain 'C' and resid 1297 through 1310 removed outlier: 3.686A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 1322 through 1333 Processing helix chain 'D' and resid 26 through 35 removed outlier: 4.616A pdb=" N PHE D 35 " --> pdb=" O ARG D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.877A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG D 99 " --> pdb=" O LYS D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 117 Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 191 Processing helix chain 'D' and resid 195 through 208 removed outlier: 3.910A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR D 208 " --> pdb=" O GLU D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 230 Processing helix chain 'D' and resid 263 through 285 removed outlier: 3.590A pdb=" N ASP D 267 " --> pdb=" O SER D 263 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU D 285 " --> pdb=" O ARG D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 332 through 336 removed outlier: 3.705A pdb=" N GLN D 335 " --> pdb=" O LYS D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 342 Processing helix chain 'D' and resid 369 through 377 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 405 through 417 removed outlier: 4.149A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) removed outlier: 3.536A 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 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 503 through 514 Processing helix chain 'D' and resid 529 through 539 Processing helix chain 'D' and resid 573 through 583 removed outlier: 3.657A pdb=" N ALA D 577 " --> pdb=" O THR D 573 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 Processing helix chain 'D' and resid 613 through 634 removed outlier: 3.602A pdb=" N THR D 617 " --> pdb=" O GLY D 613 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL D 618 " --> pdb=" O LEU D 614 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 670 Processing helix chain 'D' and resid 674 through 703 removed outlier: 3.628A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 722 through 728 removed outlier: 3.779A pdb=" N SER D 728 " --> pdb=" O MET D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 741 removed outlier: 3.735A pdb=" N ILE D 737 " --> pdb=" O SER D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 801 removed outlier: 3.871A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) Processing helix chain 'D' and resid 868 through 874 Processing helix chain 'D' and resid 895 through 900 removed outlier: 3.595A pdb=" N TYR D 899 " --> pdb=" O CYS D 895 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 895 through 900' Processing helix chain 'D' and resid 914 through 924 removed outlier: 3.655A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 925 through 929 removed outlier: 4.127A pdb=" N THR D 928 " --> pdb=" O GLU D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 1069 through 1074 Processing helix chain 'D' and resid 1138 through 1147 Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.781A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1245 removed outlier: 3.752A pdb=" N ARG D1231 " --> pdb=" O HIS D1227 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLN D1238 " --> pdb=" O VAL D1234 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ASP D1239 " --> pdb=" O ASN D1235 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY D1245 " --> pdb=" O TYR D1241 " (cutoff:3.500A) Processing helix chain 'D' and resid 1251 through 1261 removed outlier: 4.147A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N VAL D1257 " --> pdb=" O ILE D1253 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU D1261 " --> pdb=" O VAL D1257 " (cutoff:3.500A) Processing helix chain 'D' and resid 1280 through 1291 removed outlier: 3.571A pdb=" N ASN D1289 " --> pdb=" O VAL D1285 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1321 through 1325 removed outlier: 3.811A pdb=" N PHE D1325 " --> pdb=" O ALA D1322 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 removed outlier: 3.512A pdb=" N ALA D1338 " --> pdb=" O GLU D1334 " (cutoff:3.500A) Processing helix chain 'D' and resid 1347 through 1354 removed outlier: 3.707A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1361 through 1370 removed outlier: 3.979A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 Processing helix chain 'E' and resid 16 through 32 removed outlier: 3.540A pdb=" N VAL E 32 " --> pdb=" O ARG E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 Processing helix chain 'E' and resid 60 through 76 Processing helix chain 'F' and resid 96 through 108 removed outlier: 3.535A pdb=" N MET F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL F 108 " --> pdb=" O GLU F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 134 removed outlier: 3.922A pdb=" N VAL F 130 " --> pdb=" O GLY F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 135 through 137 No H-bonds generated for 'chain 'F' and resid 135 through 137' Processing helix chain 'F' and resid 138 through 151 removed outlier: 4.085A pdb=" N THR F 142 " --> pdb=" O PRO F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 154 No H-bonds generated for 'chain 'F' and resid 152 through 154' Processing helix chain 'F' and resid 213 through 220 removed outlier: 3.752A pdb=" N ALA F 217 " --> pdb=" O ASP F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 236 removed outlier: 3.630A pdb=" N ALA F 226 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 254 removed outlier: 3.507A pdb=" N GLN F 246 " --> pdb=" O HIS F 242 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 292 removed outlier: 3.624A pdb=" N ASP F 267 " --> pdb=" O PRO F 263 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N TYR F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LEU F 269 " --> pdb=" O GLN F 265 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL F 270 " --> pdb=" O PHE F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 299 through 307 removed outlier: 3.814A pdb=" N ILE F 303 " --> pdb=" O LYS F 299 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N THR F 304 " --> pdb=" O LYS F 300 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LEU F 305 " --> pdb=" O ASN F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 319 removed outlier: 3.729A pdb=" N ASN F 317 " --> pdb=" O ASP F 313 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA F 319 " --> pdb=" O TRP F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 352 removed outlier: 4.302A pdb=" N GLU F 335 " --> pdb=" O HIS F 331 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N GLU F 336 " --> pdb=" O ASP F 332 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL F 337 " --> pdb=" O VAL F 333 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ARG F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 382 removed outlier: 3.600A pdb=" N VAL F 358 " --> pdb=" O THR F 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 391 removed outlier: 3.718A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 418 removed outlier: 3.918A pdb=" N LEU F 404 " --> pdb=" O GLN F 400 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE F 410 " --> pdb=" O GLN F 406 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASP F 417 " --> pdb=" O MET F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 424 removed outlier: 3.727A pdb=" N ARG F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 446 removed outlier: 3.663A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 475 Processing helix chain 'F' and resid 479 through 487 removed outlier: 3.661A pdb=" N LEU F 483 " --> pdb=" O THR F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 500 removed outlier: 3.565A pdb=" N ILE F 500 " --> pdb=" O LYS F 496 " (cutoff:3.500A) Processing helix chain 'F' and resid 530 through 548 removed outlier: 4.492A pdb=" N THR F 537 " --> pdb=" O ASP F 533 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLU F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG F 541 " --> pdb=" O THR F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 553 through 564 removed outlier: 4.342A pdb=" N LYS F 557 " --> pdb=" O ALA F 553 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N MET F 561 " --> pdb=" O LYS F 557 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N PHE F 563 " --> pdb=" O LEU F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 580 removed outlier: 3.847A pdb=" N GLN F 579 " --> pdb=" O GLU F 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 583 through 599 removed outlier: 3.950A pdb=" N ILE F 587 " --> pdb=" O THR F 583 " (cutoff:3.500A) Processing helix chain 'F' and resid 604 through 609 Processing helix chain 'F' and resid 610 through 612 No H-bonds generated for 'chain 'F' and resid 610 through 612' Processing helix chain 'G' and resid 2 through 11 removed outlier: 3.548A pdb=" N VAL G 6 " --> pdb=" O ASN G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 23 removed outlier: 3.741A pdb=" N ILE G 17 " --> pdb=" O THR G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 57 removed outlier: 3.519A pdb=" N VAL G 56 " --> pdb=" O GLN G 52 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 69 removed outlier: 3.845A pdb=" N LEU G 69 " --> pdb=" O GLU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 78 through 106 Processing helix chain 'G' and resid 122 through 127 Processing helix chain 'H' and resid 4 through 11 Processing helix chain 'H' and resid 13 through 23 removed outlier: 3.664A pdb=" N ILE H 17 " --> pdb=" O THR H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 55 removed outlier: 3.645A pdb=" N GLN H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 71 removed outlier: 4.187A pdb=" N GLU H 65 " --> pdb=" O GLU H 61 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN H 71 " --> pdb=" O VAL H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 78 through 108 Processing helix chain 'H' and resid 121 through 128 Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 17 removed outlier: 4.201A pdb=" N VAL A 14 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 116 removed outlier: 3.870A pdb=" N THR A 101 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU A 58 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N GLY A 149 " --> pdb=" O CYS A 54 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N CYS A 54 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 110 Processing sheet with id=AA4, first strand: chain 'B' and resid 17 through 18 removed outlier: 3.778A pdb=" N ALA B 24 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N MET B 205 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 115 through 116 removed outlier: 3.979A pdb=" N THR B 101 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N MET B 142 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LYS B 104 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 109 through 110 Processing sheet with id=AA7, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.644A pdb=" N ARG C 97 " --> pdb=" O ARG C 74 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG C 74 " --> pdb=" O ARG C 97 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AA9, first strand: chain 'C' and resid 136 through 138 removed outlier: 3.576A pdb=" N VAL C 144 " --> pdb=" O GLN C 513 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN C 513 " --> pdb=" O VAL C 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 451 through 454 removed outlier: 3.526A pdb=" N ARG C 452 " --> pdb=" O HIS C 150 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N SER C 574 " --> pdb=" O CYS C 559 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 154 through 157 removed outlier: 3.564A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 236 through 240 removed outlier: 3.892A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL C 228 " --> pdb=" O THR C 335 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 250 through 251 removed outlier: 3.732A pdb=" N ARG C 267 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.820A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.820A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL C 615 " --> pdb=" O TYR C 652 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N ASP C 654 " --> pdb=" O VAL C 615 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N ALA C 617 " --> pdb=" O ASP C 654 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 634 " --> pdb=" O PHE C 645 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 689 through 690 removed outlier: 3.937A pdb=" N LYS C1234 " --> pdb=" O VAL C 690 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 700 through 701 Processing sheet with id=AB9, first strand: chain 'C' and resid 748 through 752 removed outlier: 3.511A pdb=" N ASP C 749 " --> pdb=" O ILE C 734 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE C 734 " --> pdb=" O ASP C 749 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.530A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC3, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC4, first strand: chain 'C' and resid 1076 through 1079 removed outlier: 8.267A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 830 through 833 removed outlier: 7.238A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 830 through 833 removed outlier: 4.634A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 888 through 889 Processing sheet with id=AC8, first strand: chain 'C' and resid 1269 through 1270 Processing sheet with id=AC9, first strand: chain 'C' and resid 1335 through 1339 Processing sheet with id=AD1, first strand: chain 'D' and resid 158 through 160 removed outlier: 4.290A pdb=" N GLN D 158 " --> pdb=" O VAL D 146 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL D 146 " --> pdb=" O GLN D 158 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS D 179 " --> pdb=" O VAL D 145 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 147 " --> pdb=" O ASP D 177 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 253 through 254 Processing sheet with id=AD3, first strand: chain 'D' and resid 350 through 353 Processing sheet with id=AD4, first strand: chain 'D' and resid 355 through 357 removed outlier: 6.039A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 548 through 556 removed outlier: 3.507A pdb=" N VAL D 550 " --> pdb=" O LYS D 570 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS D 570 " --> pdb=" O VAL D 550 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU D 556 " --> pdb=" O VAL D 564 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.720A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL D 843 " --> pdb=" O ARG D 883 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 949 through 951 removed outlier: 7.649A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL D1017 " --> pdb=" O ILE D 950 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 991 through 994 removed outlier: 3.617A pdb=" N GLU D 993 " --> pdb=" O LEU D 984 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1024 through 1026 removed outlier: 3.604A pdb=" N ILE D1124 " --> pdb=" O MET D1025 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 1077 through 1078 Processing sheet with id=AE2, first strand: chain 'D' and resid 1187 through 1188 removed outlier: 3.902A pdb=" N GLU D1202 " --> pdb=" O VAL D1163 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 1277 through 1279 Processing sheet with id=AE4, first strand: chain 'H' and resid 30 through 31 1240 hydrogen bonds defined for protein. 3543 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 97 hydrogen bonds 186 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 14.45 Time building geometry restraints manager: 14.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9949 1.34 - 1.46: 5255 1.46 - 1.58: 18117 1.58 - 1.70: 204 1.70 - 1.82: 238 Bond restraints: 33763 Sorted by residual: bond pdb=" C ASP C 354 " pdb=" N PRO C 355 " ideal model delta sigma weight residual 1.336 1.391 -0.055 1.20e-02 6.94e+03 2.10e+01 bond pdb=" CD2 TRP D1020 " pdb=" CE2 TRP D1020 " ideal model delta sigma weight residual 1.409 1.484 -0.075 1.70e-02 3.46e+03 1.95e+01 bond pdb=" CD2 TRP F 315 " pdb=" CE2 TRP F 315 " ideal model delta sigma weight residual 1.409 1.484 -0.075 1.70e-02 3.46e+03 1.94e+01 bond pdb=" N PRO C 355 " pdb=" CD PRO C 355 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.85e+01 bond pdb=" N PRO F 504 " pdb=" CD PRO F 504 " ideal model delta sigma weight residual 1.473 1.531 -0.058 1.40e-02 5.10e+03 1.73e+01 ... (remaining 33758 not shown) Histogram of bond angle deviations from ideal: 98.53 - 106.39: 1439 106.39 - 114.26: 19720 114.26 - 122.12: 18276 122.12 - 129.98: 6473 129.98 - 137.85: 161 Bond angle restraints: 46069 Sorted by residual: angle pdb=" N ALA F 501 " pdb=" CA ALA F 501 " pdb=" C ALA F 501 " ideal model delta sigma weight residual 111.36 123.20 -11.84 1.09e+00 8.42e-01 1.18e+02 angle pdb=" CD2 TRP F 315 " pdb=" CE3 TRP F 315 " pdb=" CZ3 TRP F 315 " ideal model delta sigma weight residual 118.60 129.35 -10.75 1.30e+00 5.92e-01 6.84e+01 angle pdb=" CD2 TRP D1020 " pdb=" CE3 TRP D1020 " pdb=" CZ3 TRP D1020 " ideal model delta sigma weight residual 118.60 129.34 -10.74 1.30e+00 5.92e-01 6.82e+01 angle pdb=" N VAL D 839 " pdb=" CA VAL D 839 " pdb=" C VAL D 839 " ideal model delta sigma weight residual 111.91 106.36 5.55 8.90e-01 1.26e+00 3.88e+01 angle pdb=" CE2 TRP D1020 " pdb=" CD2 TRP D1020 " pdb=" CE3 TRP D1020 " ideal model delta sigma weight residual 118.80 124.87 -6.07 1.00e+00 1.00e+00 3.68e+01 ... (remaining 46064 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.14: 19637 33.14 - 66.28: 850 66.28 - 99.41: 37 99.41 - 132.55: 0 132.55 - 165.69: 4 Dihedral angle restraints: 20528 sinusoidal: 9023 harmonic: 11505 Sorted by residual: dihedral pdb=" CA ALA F 321 " pdb=" C ALA F 321 " pdb=" N MET F 322 " pdb=" CA MET F 322 " ideal model delta harmonic sigma weight residual 180.00 -153.26 -26.74 0 5.00e+00 4.00e-02 2.86e+01 dihedral pdb=" CA PHE F 580 " pdb=" C PHE F 580 " pdb=" N ASP F 581 " pdb=" CA ASP F 581 " ideal model delta harmonic sigma weight residual -180.00 -154.39 -25.61 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA GLN F 258 " pdb=" C GLN F 258 " pdb=" N PHE F 259 " pdb=" CA PHE F 259 " ideal model delta harmonic sigma weight residual 180.00 -154.73 -25.27 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 20525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 4786 0.083 - 0.167: 487 0.167 - 0.250: 16 0.250 - 0.333: 3 0.333 - 0.416: 1 Chirality restraints: 5293 Sorted by residual: chirality pdb=" CA ALA F 501 " pdb=" N ALA F 501 " pdb=" C ALA F 501 " pdb=" CB ALA F 501 " both_signs ideal model delta sigma weight residual False 2.48 2.07 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CB ILE H 3 " pdb=" CA ILE H 3 " pdb=" CG1 ILE H 3 " pdb=" CG2 ILE H 3 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CB ILE C1182 " pdb=" CA ILE C1182 " pdb=" CG1 ILE C1182 " pdb=" CG2 ILE C1182 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 5290 not shown) Planarity restraints: 5664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 500 " -0.014 2.00e-02 2.50e+03 2.86e-02 8.20e+00 pdb=" C ILE F 500 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE F 500 " -0.019 2.00e-02 2.50e+03 pdb=" N ALA F 501 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 189 " -0.047 5.00e-02 4.00e+02 7.05e-02 7.94e+00 pdb=" N PRO C 190 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 190 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 190 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 501 " -0.043 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO D 502 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 502 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 502 " -0.036 5.00e-02 4.00e+02 ... (remaining 5661 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.60: 315 2.60 - 3.20: 26860 3.20 - 3.80: 58279 3.80 - 4.40: 77351 4.40 - 5.00: 125211 Nonbonded interactions: 288016 Sorted by model distance: nonbonded pdb=" C2 DA 1 34 " pdb=" O2 DT 2 56 " model vdw 1.995 3.340 nonbonded pdb=" O LEU C 363 " pdb=" CG2 ILE C 366 " model vdw 2.005 3.460 nonbonded pdb=" SG CYS G 120 " pdb="AG AG G 201 " model vdw 2.183 3.140 nonbonded pdb=" OG1 THR C 715 " pdb=" O ALA C 784 " model vdw 2.262 2.440 nonbonded pdb=" CG2 THR D 262 " pdb=" CG PRO F 504 " model vdw 2.265 3.860 ... (remaining 288011 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'G' and (resid 1 through 80 or (resid 81 and (name N or name CA or name C \ or name O or name CB )) or resid 82 or (resid 83 and (name N or name CA or name \ C or name O or name CB )) or resid 84 through 114 or (resid 115 through 119 and \ (name N or name CA or name C or name O or name CB )) or resid 120 through 127)) \ selection = (chain 'H' and (resid 1 through 5 or (resid 6 through 7 and (name N or name CA o \ r name C or name O or name CB )) or resid 8 through 43 or (resid 44 and (name N \ or name CA or name C or name O or name CB )) or resid 45 through 46 or (resid 47 \ and (name N or name CA or name C or name O or name CB )) or resid 48 or (resid \ 49 and (name N or name CA or name C or name O or name CB )) or resid 50 through \ 127)) } 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=0.30 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 7.610 Check model and map are aligned: 0.500 Set scattering table: 0.320 Process input model: 98.710 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.130 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.092 33763 Z= 0.215 Angle : 0.730 15.771 46069 Z= 0.414 Chirality : 0.048 0.416 5293 Planarity : 0.005 0.070 5664 Dihedral : 16.452 165.691 13098 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.21 % Allowed : 6.79 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: -4.63 (0.10), residues: 3971 helix: -3.12 (0.08), residues: 1516 sheet: -3.06 (0.24), residues: 308 loop : -3.09 (0.11), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 315 HIS 0.017 0.001 HIS F 338 PHE 0.025 0.001 PHE F 259 TYR 0.017 0.001 TYR F 421 ARG 0.006 0.000 ARG C1246 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1003 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 996 time to evaluate : 3.738 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: 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 199 ASP cc_start: 0.5691 (m-30) cc_final: 0.4983 (m-30) REVERT: A 206 GLU cc_start: 0.6109 (tp30) cc_final: 0.5219 (tp30) REVERT: B 46 ILE cc_start: 0.8597 (pt) cc_final: 0.8276 (tt) REVERT: C 136 PHE cc_start: 0.8368 (m-80) cc_final: 0.7602 (m-10) REVERT: C 171 LEU cc_start: 0.6511 (mp) cc_final: 0.6248 (pp) REVERT: C 367 TYR cc_start: 0.8078 (t80) cc_final: 0.7576 (t80) REVERT: C 555 TYR cc_start: 0.7965 (t80) cc_final: 0.7710 (t80) REVERT: C 616 ILE cc_start: 0.7941 (mm) cc_final: 0.6794 (mm) REVERT: C 662 SER cc_start: 0.8479 (m) cc_final: 0.8278 (p) REVERT: C 739 ASP cc_start: 0.7192 (p0) cc_final: 0.6024 (t0) REVERT: C 742 TYR cc_start: 0.6748 (m-80) cc_final: 0.6490 (m-10) REVERT: C 829 THR cc_start: 0.7853 (p) cc_final: 0.7650 (p) REVERT: C 882 ILE cc_start: 0.7535 (mt) cc_final: 0.6647 (mt) REVERT: C 1064 ASP cc_start: 0.7891 (t0) cc_final: 0.7551 (t0) REVERT: C 1187 PHE cc_start: 0.7644 (m-80) cc_final: 0.7433 (m-80) REVERT: C 1240 ASP cc_start: 0.7145 (m-30) cc_final: 0.6877 (t0) REVERT: C 1242 LYS cc_start: 0.8775 (mmtp) cc_final: 0.8389 (mmtp) REVERT: C 1257 GLN cc_start: 0.6820 (tt0) cc_final: 0.6584 (mt0) REVERT: C 1281 TYR cc_start: 0.7774 (m-80) cc_final: 0.7349 (m-80) REVERT: D 24 LEU cc_start: 0.7188 (mt) cc_final: 0.6684 (mt) REVERT: D 117 LEU cc_start: 0.8736 (tp) cc_final: 0.8473 (tp) REVERT: D 298 MET cc_start: 0.7177 (mtp) cc_final: 0.4672 (mtp) REVERT: D 300 GLN cc_start: 0.8472 (tm-30) cc_final: 0.7482 (tm-30) REVERT: D 341 ASN cc_start: 0.7576 (m110) cc_final: 0.7160 (m110) REVERT: D 355 ILE cc_start: 0.9233 (pt) cc_final: 0.8875 (mm) REVERT: D 443 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7416 (tp30) REVERT: D 450 HIS cc_start: 0.8628 (t-90) cc_final: 0.8030 (t70) REVERT: D 464 ASP cc_start: 0.8120 (m-30) cc_final: 0.7185 (m-30) REVERT: D 681 LYS cc_start: 0.8823 (mmtt) cc_final: 0.8619 (mmtp) REVERT: D 903 LEU cc_start: 0.8497 (tp) cc_final: 0.8247 (tp) REVERT: D 925 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7242 (tm-30) REVERT: D 958 ILE cc_start: 0.7660 (mm) cc_final: 0.7431 (mp) REVERT: D 1037 PHE cc_start: 0.2816 (m-10) cc_final: 0.2063 (m-80) REVERT: D 1250 ASP cc_start: 0.7076 (p0) cc_final: 0.6414 (p0) REVERT: D 1350 ASN cc_start: 0.7938 (m-40) cc_final: 0.7546 (t0) REVERT: F 100 MET cc_start: 0.8088 (ptp) cc_final: 0.6466 (ptp) REVERT: F 150 ARG cc_start: 0.5947 (mtt90) cc_final: 0.5351 (tmm160) REVERT: F 277 MET cc_start: 0.7255 (tpt) cc_final: 0.7028 (tpp) REVERT: F 297 MET cc_start: 0.3685 (ptt) cc_final: 0.3168 (ptm) REVERT: F 322 MET cc_start: 0.1819 (pmm) cc_final: 0.0728 (tmm) REVERT: F 393 LYS cc_start: 0.4187 (mttp) cc_final: 0.3650 (tptt) REVERT: F 418 LYS cc_start: 0.8747 (mmmt) cc_final: 0.8361 (tptt) REVERT: F 430 TYR cc_start: 0.6251 (t80) cc_final: 0.5196 (t80) REVERT: F 578 LYS cc_start: 0.8499 (mttt) cc_final: 0.8261 (ttpt) REVERT: G 1 MET cc_start: 0.4992 (mpp) cc_final: 0.4293 (ttp) REVERT: G 50 LEU cc_start: 0.7288 (tp) cc_final: 0.6967 (tp) REVERT: H 58 PHE cc_start: 0.7468 (m-10) cc_final: 0.7251 (m-80) REVERT: H 91 ILE cc_start: 0.7438 (pt) cc_final: 0.7200 (pt) outliers start: 7 outliers final: 3 residues processed: 1002 average time/residue: 0.5379 time to fit residues: 814.7328 Evaluate side-chains 576 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 573 time to evaluate : 3.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 341 optimal weight: 7.9990 chunk 306 optimal weight: 4.9990 chunk 169 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 206 optimal weight: 5.9990 chunk 163 optimal weight: 0.9980 chunk 316 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 chunk 366 optimal weight: 0.8980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 ASN B 160 HIS B 208 ASN B 227 GLN C 447 HIS C 510 GLN C 554 HIS C 618 GLN ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN C 932 GLN ** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1116 HIS C1264 GLN C1299 ASN ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 762 ASN ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 817 HIS D 897 HIS D 929 GLN D1197 ASN D1244 GLN E 15 ASN F 129 GLN F 210 ASN F 246 GLN F 265 GLN F 357 GLN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 446 GLN ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 33763 Z= 0.277 Angle : 0.650 11.744 46069 Z= 0.342 Chirality : 0.043 0.190 5293 Planarity : 0.005 0.076 5664 Dihedral : 15.685 167.014 5475 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.23 % Rotamer: Outliers : 0.33 % Allowed : 5.55 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.12), residues: 3971 helix: -1.23 (0.12), residues: 1582 sheet: -2.51 (0.25), residues: 311 loop : -2.57 (0.12), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 115 HIS 0.013 0.001 HIS C 551 PHE 0.027 0.002 PHE D 719 TYR 0.021 0.002 TYR G 20 ARG 0.014 0.001 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 711 time to evaluate : 3.615 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.7473 (tp30) cc_final: 0.7243 (tp30) REVERT: A 75 GLN cc_start: 0.7459 (tt0) cc_final: 0.7192 (tm-30) REVERT: A 206 GLU cc_start: 0.6689 (tp30) cc_final: 0.5647 (tp30) REVERT: C 367 TYR cc_start: 0.8448 (t80) cc_final: 0.7103 (t80) REVERT: C 458 GLU cc_start: 0.7875 (tt0) cc_final: 0.7546 (tt0) REVERT: C 503 LYS cc_start: 0.8242 (mtmm) cc_final: 0.7677 (mttt) REVERT: C 516 ASP cc_start: 0.8176 (p0) cc_final: 0.7173 (p0) REVERT: C 686 GLN cc_start: 0.7801 (mt0) cc_final: 0.7542 (tt0) REVERT: C 688 GLN cc_start: 0.8204 (mt0) cc_final: 0.7793 (mt0) REVERT: C 739 ASP cc_start: 0.7488 (p0) cc_final: 0.6610 (t0) REVERT: C 800 MET cc_start: 0.9033 (pmm) cc_final: 0.8595 (pmm) REVERT: C 816 ILE cc_start: 0.9433 (mm) cc_final: 0.8889 (mm) REVERT: C 829 THR cc_start: 0.8849 (p) cc_final: 0.8617 (p) REVERT: C 898 GLU cc_start: 0.9468 (mp0) cc_final: 0.9161 (mp0) REVERT: C 1209 GLN cc_start: 0.7889 (pt0) cc_final: 0.7596 (pt0) REVERT: C 1220 GLN cc_start: 0.7069 (pp30) cc_final: 0.6763 (pp30) REVERT: C 1240 ASP cc_start: 0.8056 (m-30) cc_final: 0.7721 (m-30) REVERT: C 1242 LYS cc_start: 0.9001 (mmtp) cc_final: 0.8601 (mmtp) REVERT: C 1257 GLN cc_start: 0.7194 (tt0) cc_final: 0.6965 (mt0) REVERT: C 1276 TRP cc_start: 0.8417 (m-10) cc_final: 0.7945 (m-10) REVERT: C 1328 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8395 (mmtm) REVERT: D 24 LEU cc_start: 0.7811 (mt) cc_final: 0.6966 (mt) REVERT: D 47 ARG cc_start: 0.6881 (mtm110) cc_final: 0.6661 (ptt180) REVERT: D 246 PRO cc_start: 0.9050 (Cg_exo) cc_final: 0.8829 (Cg_endo) REVERT: D 289 ASP cc_start: 0.7606 (p0) cc_final: 0.7133 (p0) REVERT: D 293 ARG cc_start: 0.8369 (ptp-110) cc_final: 0.7532 (ptp-170) REVERT: D 299 LEU cc_start: 0.9322 (tp) cc_final: 0.9060 (tt) REVERT: D 341 ASN cc_start: 0.7935 (m110) cc_final: 0.7518 (m-40) REVERT: D 450 HIS cc_start: 0.8699 (t-90) cc_final: 0.8440 (t70) REVERT: D 625 MET cc_start: 0.8562 (ttp) cc_final: 0.8234 (ttp) REVERT: D 631 TYR cc_start: 0.6287 (m-80) cc_final: 0.5920 (m-10) REVERT: D 646 ILE cc_start: 0.7546 (mm) cc_final: 0.7336 (mm) REVERT: D 743 MET cc_start: 0.7406 (ppp) cc_final: 0.6965 (ppp) REVERT: D 925 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7379 (tm-30) REVERT: D 958 ILE cc_start: 0.8119 (mm) cc_final: 0.7689 (mp) REVERT: D 1037 PHE cc_start: 0.3257 (m-10) cc_final: 0.2476 (m-80) REVERT: D 1256 ILE cc_start: 0.9143 (mm) cc_final: 0.8730 (mm) REVERT: D 1350 ASN cc_start: 0.8601 (m-40) cc_final: 0.8331 (t0) REVERT: E 17 PHE cc_start: 0.7308 (m-10) cc_final: 0.6544 (m-10) REVERT: E 70 GLN cc_start: 0.8359 (OUTLIER) cc_final: 0.7823 (mp10) REVERT: F 100 MET cc_start: 0.8070 (ptp) cc_final: 0.7633 (ptp) REVERT: F 150 ARG cc_start: 0.6125 (mtt90) cc_final: 0.5515 (tmm160) REVERT: F 297 MET cc_start: 0.3948 (ptt) cc_final: 0.3108 (ptm) REVERT: F 378 GLU cc_start: 0.8922 (pt0) cc_final: 0.8449 (pt0) REVERT: F 393 LYS cc_start: 0.5178 (mttp) cc_final: 0.4426 (tptt) REVERT: F 578 LYS cc_start: 0.8597 (mttt) cc_final: 0.8356 (ttmt) REVERT: G 1 MET cc_start: 0.5425 (mpp) cc_final: 0.4688 (ttm) REVERT: H 87 LYS cc_start: 0.7018 (tptm) cc_final: 0.6611 (pttp) outliers start: 11 outliers final: 4 residues processed: 719 average time/residue: 0.4716 time to fit residues: 536.9160 Evaluate side-chains 515 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 510 time to evaluate : 3.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 203 optimal weight: 9.9990 chunk 113 optimal weight: 10.0000 chunk 305 optimal weight: 3.9990 chunk 249 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 367 optimal weight: 8.9990 chunk 397 optimal weight: 3.9990 chunk 327 optimal weight: 1.9990 chunk 364 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 294 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 HIS A 75 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN ** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 HIS ** D 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 897 HIS D 929 GLN ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 265 GLN ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 ASN F 400 GLN ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 33763 Z= 0.316 Angle : 0.673 15.479 46069 Z= 0.350 Chirality : 0.043 0.217 5293 Planarity : 0.005 0.066 5664 Dihedral : 15.774 163.258 5475 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 19.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.80 % Favored : 93.18 % Rotamer: Outliers : 0.12 % Allowed : 5.40 % Favored : 94.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: -2.41 (0.12), residues: 3971 helix: -0.62 (0.12), residues: 1589 sheet: -2.31 (0.25), residues: 317 loop : -2.31 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 236 HIS 0.014 0.001 HIS C 604 PHE 0.021 0.002 PHE D 719 TYR 0.031 0.002 TYR D 140 ARG 0.012 0.001 ARG D 515 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 661 time to evaluate : 3.586 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 277 TYR cc_start: 0.4866 (m-10) cc_final: 0.4494 (m-10) REVERT: C 136 PHE cc_start: 0.8518 (m-80) cc_final: 0.7971 (m-10) REVERT: C 409 LEU cc_start: 0.8652 (mp) cc_final: 0.8357 (mt) REVERT: C 458 GLU cc_start: 0.7653 (tt0) cc_final: 0.7208 (tt0) REVERT: C 515 MET cc_start: 0.8750 (ppp) cc_final: 0.8301 (ppp) REVERT: C 549 ASP cc_start: 0.6407 (t0) cc_final: 0.6164 (t0) REVERT: C 739 ASP cc_start: 0.7667 (p0) cc_final: 0.7004 (t0) REVERT: C 741 MET cc_start: 0.8374 (mtt) cc_final: 0.7956 (mtt) REVERT: C 800 MET cc_start: 0.9127 (pmm) cc_final: 0.8888 (pmm) REVERT: C 816 ILE cc_start: 0.9566 (mm) cc_final: 0.9100 (mm) REVERT: C 898 GLU cc_start: 0.9438 (mp0) cc_final: 0.9202 (mp0) REVERT: C 1085 MET cc_start: 0.9240 (mmm) cc_final: 0.9032 (mmm) REVERT: C 1220 GLN cc_start: 0.7303 (pp30) cc_final: 0.7054 (pp30) REVERT: C 1240 ASP cc_start: 0.8319 (m-30) cc_final: 0.7759 (m-30) REVERT: C 1262 LYS cc_start: 0.7258 (ttmm) cc_final: 0.6903 (ttmm) REVERT: C 1276 TRP cc_start: 0.8584 (m-10) cc_final: 0.8001 (m-10) REVERT: C 1279 GLU cc_start: 0.8472 (tt0) cc_final: 0.8162 (tt0) REVERT: C 1286 THR cc_start: 0.8544 (p) cc_final: 0.8196 (p) REVERT: C 1319 MET cc_start: 0.7619 (tpt) cc_final: 0.7412 (tpt) REVERT: C 1328 LYS cc_start: 0.8953 (mmtt) cc_final: 0.8699 (mmtm) REVERT: D 341 ASN cc_start: 0.8009 (m110) cc_final: 0.7784 (m-40) REVERT: D 355 ILE cc_start: 0.9445 (pt) cc_final: 0.9008 (mt) REVERT: D 435 GLN cc_start: 0.8547 (pm20) cc_final: 0.8316 (pm20) REVERT: D 644 MET cc_start: 0.5994 (ttm) cc_final: 0.5523 (mtp) REVERT: D 743 MET cc_start: 0.7556 (ppp) cc_final: 0.7110 (ppp) REVERT: D 805 GLN cc_start: 0.6505 (pt0) cc_final: 0.6243 (pp30) REVERT: D 925 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7476 (tm-30) REVERT: D 958 ILE cc_start: 0.8149 (mm) cc_final: 0.7683 (mp) REVERT: D 983 LYS cc_start: 0.7946 (pttm) cc_final: 0.7656 (ptpp) REVERT: D 1037 PHE cc_start: 0.3497 (m-10) cc_final: 0.2764 (m-80) REVERT: D 1095 MET cc_start: 0.6839 (tmm) cc_final: 0.6626 (tmm) REVERT: D 1256 ILE cc_start: 0.9253 (mm) cc_final: 0.9028 (mm) REVERT: D 1329 THR cc_start: 0.8633 (p) cc_final: 0.8240 (p) REVERT: E 72 GLN cc_start: 0.6290 (pm20) cc_final: 0.5767 (pp30) REVERT: F 150 ARG cc_start: 0.5864 (mtt90) cc_final: 0.5419 (ttp80) REVERT: F 297 MET cc_start: 0.3877 (ptt) cc_final: 0.2908 (ptm) REVERT: G 1 MET cc_start: 0.5705 (mpp) cc_final: 0.4598 (ttp) REVERT: H 94 HIS cc_start: 0.8174 (m90) cc_final: 0.7913 (m-70) outliers start: 4 outliers final: 3 residues processed: 664 average time/residue: 0.4528 time to fit residues: 482.3424 Evaluate side-chains 476 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 473 time to evaluate : 3.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 363 optimal weight: 5.9990 chunk 276 optimal weight: 0.7980 chunk 190 optimal weight: 8.9990 chunk 40 optimal weight: 20.0000 chunk 175 optimal weight: 0.6980 chunk 246 optimal weight: 4.9990 chunk 368 optimal weight: 2.9990 chunk 390 optimal weight: 20.0000 chunk 192 optimal weight: 0.8980 chunk 349 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 622 ASN ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN C1038 GLN ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 768 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 771 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 929 GLN ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 ASN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 ASN ** F 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 GLN ** F 568 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33763 Z= 0.206 Angle : 0.592 12.794 46069 Z= 0.308 Chirality : 0.042 0.247 5293 Planarity : 0.004 0.076 5664 Dihedral : 15.671 164.728 5475 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.06 % Allowed : 3.59 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % 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: -2.06 (0.13), residues: 3971 helix: -0.30 (0.13), residues: 1610 sheet: -2.24 (0.26), residues: 312 loop : -2.14 (0.13), residues: 2049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 580 HIS 0.008 0.001 HIS D 777 PHE 0.015 0.002 PHE C1187 TYR 0.034 0.002 TYR G 20 ARG 0.010 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 657 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 655 time to evaluate : 4.019 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: A 171 LEU cc_start: 0.8689 (mt) cc_final: 0.8489 (mt) REVERT: B 186 ASN cc_start: 0.7978 (p0) cc_final: 0.7122 (p0) REVERT: C 136 PHE cc_start: 0.8418 (m-80) cc_final: 0.7792 (m-10) REVERT: C 182 SER cc_start: 0.8317 (p) cc_final: 0.8105 (p) REVERT: C 349 GLU cc_start: 0.8263 (tt0) cc_final: 0.8028 (tt0) REVERT: C 367 TYR cc_start: 0.8352 (t80) cc_final: 0.7940 (t80) REVERT: C 409 LEU cc_start: 0.8591 (mp) cc_final: 0.8294 (mt) REVERT: C 473 ARG cc_start: 0.7731 (ttp-110) cc_final: 0.7481 (ttp-110) REVERT: C 549 ASP cc_start: 0.6428 (t0) cc_final: 0.6155 (t0) REVERT: C 662 SER cc_start: 0.8675 (p) cc_final: 0.8428 (p) REVERT: C 739 ASP cc_start: 0.7724 (p0) cc_final: 0.7052 (t0) REVERT: C 816 ILE cc_start: 0.9433 (mm) cc_final: 0.8975 (mm) REVERT: C 898 GLU cc_start: 0.9388 (mp0) cc_final: 0.9175 (mp0) REVERT: C 1038 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.6673 (pp30) REVERT: C 1064 ASP cc_start: 0.8476 (t0) cc_final: 0.8133 (t0) REVERT: C 1242 LYS cc_start: 0.9176 (mmtp) cc_final: 0.8894 (mmmm) REVERT: C 1276 TRP cc_start: 0.8458 (m-10) cc_final: 0.8013 (m-10) REVERT: C 1279 GLU cc_start: 0.8348 (tt0) cc_final: 0.8140 (tt0) REVERT: C 1328 LYS cc_start: 0.8910 (mmtt) cc_final: 0.8681 (mmtm) REVERT: D 30 ILE cc_start: 0.9017 (mt) cc_final: 0.8704 (mm) REVERT: D 114 ILE cc_start: 0.9318 (tp) cc_final: 0.9057 (tp) REVERT: D 341 ASN cc_start: 0.7889 (m110) cc_final: 0.7370 (m-40) REVERT: D 355 ILE cc_start: 0.9356 (pt) cc_final: 0.8880 (mt) REVERT: D 484 MET cc_start: 0.6727 (ttp) cc_final: 0.5928 (ptm) REVERT: D 644 MET cc_start: 0.5405 (ttm) cc_final: 0.5109 (mtp) REVERT: D 719 PHE cc_start: 0.6190 (m-80) cc_final: 0.5978 (m-80) REVERT: D 743 MET cc_start: 0.7621 (ppp) cc_final: 0.7170 (ppp) REVERT: D 958 ILE cc_start: 0.8043 (mm) cc_final: 0.7547 (mp) REVERT: D 983 LYS cc_start: 0.7956 (pttm) cc_final: 0.7663 (ptpp) REVERT: D 1037 PHE cc_start: 0.3353 (m-10) cc_final: 0.2527 (m-80) REVERT: D 1227 HIS cc_start: 0.7384 (m-70) cc_final: 0.6658 (m-70) REVERT: D 1313 SER cc_start: 0.9316 (m) cc_final: 0.8816 (t) REVERT: D 1329 THR cc_start: 0.8528 (p) cc_final: 0.8220 (p) REVERT: D 1357 ILE cc_start: 0.9105 (mp) cc_final: 0.8868 (mp) REVERT: E 19 LEU cc_start: 0.7490 (tt) cc_final: 0.7287 (tp) REVERT: F 150 ARG cc_start: 0.5790 (mtt90) cc_final: 0.5407 (ttp80) REVERT: F 320 ILE cc_start: 0.4841 (mm) cc_final: 0.4509 (mm) REVERT: F 430 TYR cc_start: 0.6501 (t80) cc_final: 0.6082 (t80) REVERT: G 1 MET cc_start: 0.5668 (mpp) cc_final: 0.4627 (ttp) REVERT: H 87 LYS cc_start: 0.7040 (tptm) cc_final: 0.6603 (pttp) REVERT: H 94 HIS cc_start: 0.8154 (m90) cc_final: 0.7946 (m-70) outliers start: 2 outliers final: 1 residues processed: 657 average time/residue: 0.4542 time to fit residues: 486.6927 Evaluate side-chains 490 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 488 time to evaluate : 3.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 325 optimal weight: 6.9990 chunk 221 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 290 optimal weight: 0.0370 chunk 161 optimal weight: 2.9990 chunk 333 optimal weight: 9.9990 chunk 269 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 199 optimal weight: 0.0970 chunk 350 optimal weight: 0.6980 chunk 98 optimal weight: 8.9990 overall best weight: 0.9660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 37 HIS ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 910 ASN D 929 GLN ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 568 ASN H 43 HIS ** H 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.4526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33763 Z= 0.195 Angle : 0.589 12.954 46069 Z= 0.306 Chirality : 0.042 0.237 5293 Planarity : 0.004 0.054 5664 Dihedral : 15.614 164.446 5475 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 0.03 % Allowed : 2.38 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.13), residues: 3971 helix: -0.10 (0.13), residues: 1604 sheet: -2.15 (0.26), residues: 313 loop : -2.02 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 115 HIS 0.011 0.001 HIS D 450 PHE 0.017 0.001 PHE C1187 TYR 0.031 0.001 TYR D 140 ARG 0.011 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 645 time to evaluate : 3.691 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: A 206 GLU cc_start: 0.6406 (tp30) cc_final: 0.5463 (tp30) REVERT: B 85 LEU cc_start: 0.9209 (mt) cc_final: 0.8905 (tt) REVERT: C 136 PHE cc_start: 0.8343 (m-80) cc_final: 0.7835 (m-10) REVERT: C 182 SER cc_start: 0.8290 (p) cc_final: 0.8042 (p) REVERT: C 367 TYR cc_start: 0.8359 (t80) cc_final: 0.7908 (t80) REVERT: C 458 GLU cc_start: 0.7652 (tt0) cc_final: 0.7429 (tt0) REVERT: C 473 ARG cc_start: 0.7637 (ttp-110) cc_final: 0.7395 (ttp80) REVERT: C 516 ASP cc_start: 0.8439 (p0) cc_final: 0.7985 (p0) REVERT: C 549 ASP cc_start: 0.6467 (t0) cc_final: 0.6246 (t0) REVERT: C 739 ASP cc_start: 0.7561 (p0) cc_final: 0.6902 (t0) REVERT: C 898 GLU cc_start: 0.9374 (mp0) cc_final: 0.9173 (mp0) REVERT: C 1064 ASP cc_start: 0.8350 (t0) cc_final: 0.7997 (t0) REVERT: C 1225 VAL cc_start: 0.9225 (t) cc_final: 0.9024 (p) REVERT: C 1230 MET cc_start: 0.7626 (tpt) cc_final: 0.7359 (tpt) REVERT: C 1242 LYS cc_start: 0.9042 (mmtp) cc_final: 0.8647 (mmmm) REVERT: C 1276 TRP cc_start: 0.8463 (m-10) cc_final: 0.8067 (m-10) REVERT: C 1339 LEU cc_start: 0.7395 (mt) cc_final: 0.7157 (mt) REVERT: D 30 ILE cc_start: 0.9029 (mt) cc_final: 0.8741 (mm) REVERT: D 268 LEU cc_start: 0.9163 (mp) cc_final: 0.8882 (mp) REVERT: D 355 ILE cc_start: 0.9373 (pt) cc_final: 0.8844 (mt) REVERT: D 380 PHE cc_start: 0.8367 (m-80) cc_final: 0.8022 (m-80) REVERT: D 644 MET cc_start: 0.5443 (ttm) cc_final: 0.5199 (mtp) REVERT: D 719 PHE cc_start: 0.6305 (m-80) cc_final: 0.6067 (m-80) REVERT: D 743 MET cc_start: 0.7695 (ppp) cc_final: 0.7255 (ppp) REVERT: D 796 LEU cc_start: 0.9201 (tp) cc_final: 0.8955 (tt) REVERT: D 958 ILE cc_start: 0.8006 (mm) cc_final: 0.7512 (mp) REVERT: D 1037 PHE cc_start: 0.3351 (m-10) cc_final: 0.2534 (m-80) REVERT: D 1313 SER cc_start: 0.9328 (m) cc_final: 0.8762 (t) REVERT: D 1357 ILE cc_start: 0.8749 (mp) cc_final: 0.8466 (mt) REVERT: E 17 PHE cc_start: 0.7338 (m-10) cc_final: 0.7127 (m-80) REVERT: F 150 ARG cc_start: 0.5652 (mtt90) cc_final: 0.5338 (ttp80) REVERT: F 320 ILE cc_start: 0.4744 (mm) cc_final: 0.4391 (mm) REVERT: F 430 TYR cc_start: 0.6628 (t80) cc_final: 0.6198 (t80) REVERT: G 1 MET cc_start: 0.5594 (mpp) cc_final: 0.4991 (ttp) REVERT: G 17 ILE cc_start: 0.8638 (pt) cc_final: 0.8325 (pt) REVERT: H 1 MET cc_start: 0.1818 (ptm) cc_final: 0.1434 (ptt) REVERT: H 87 LYS cc_start: 0.7012 (tptm) cc_final: 0.6437 (pttp) outliers start: 1 outliers final: 1 residues processed: 645 average time/residue: 0.4245 time to fit residues: 447.5969 Evaluate side-chains 493 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 492 time to evaluate : 3.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 131 optimal weight: 0.1980 chunk 351 optimal weight: 2.9990 chunk 77 optimal weight: 0.0270 chunk 229 optimal weight: 0.9980 chunk 96 optimal weight: 9.9990 chunk 390 optimal weight: 0.7980 chunk 324 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 129 optimal weight: 2.9990 chunk 205 optimal weight: 2.9990 overall best weight: 0.6040 ------------------------------------------------------------------------------- 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 75 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 HIS ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1257 GLN ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 341 ASN ** D 419 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 458 ASN ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 929 GLN ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1227 HIS ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 HIS ** H 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.4583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33763 Z= 0.177 Angle : 0.585 12.762 46069 Z= 0.301 Chirality : 0.041 0.183 5293 Planarity : 0.004 0.052 5664 Dihedral : 15.541 164.500 5475 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 0.09 % Allowed : 2.60 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.13), residues: 3971 helix: -0.03 (0.13), residues: 1602 sheet: -1.98 (0.28), residues: 288 loop : -1.95 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 236 HIS 0.021 0.001 HIS C 551 PHE 0.025 0.001 PHE H 58 TYR 0.025 0.001 TYR G 20 ARG 0.012 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 649 time to evaluate : 3.529 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: A 171 LEU cc_start: 0.8642 (mt) cc_final: 0.8413 (mt) REVERT: A 199 ASP cc_start: 0.6847 (m-30) cc_final: 0.6613 (m-30) REVERT: A 226 GLU cc_start: 0.7388 (pp20) cc_final: 0.7157 (pp20) REVERT: B 85 LEU cc_start: 0.9164 (mt) cc_final: 0.8877 (tt) REVERT: C 136 PHE cc_start: 0.8357 (m-80) cc_final: 0.7788 (m-10) REVERT: C 182 SER cc_start: 0.8191 (p) cc_final: 0.7924 (p) REVERT: C 367 TYR cc_start: 0.8380 (t80) cc_final: 0.8068 (t80) REVERT: C 409 LEU cc_start: 0.8611 (mp) cc_final: 0.8350 (mt) REVERT: C 458 GLU cc_start: 0.7576 (tt0) cc_final: 0.7342 (tt0) REVERT: C 516 ASP cc_start: 0.8427 (p0) cc_final: 0.7841 (p0) REVERT: C 688 GLN cc_start: 0.8380 (tt0) cc_final: 0.8000 (tt0) REVERT: C 739 ASP cc_start: 0.7496 (p0) cc_final: 0.6846 (t0) REVERT: C 741 MET cc_start: 0.8439 (mtt) cc_final: 0.7720 (mtt) REVERT: C 1107 MET cc_start: 0.7659 (mmt) cc_final: 0.7173 (mmt) REVERT: C 1232 MET cc_start: 0.6950 (ptp) cc_final: 0.6645 (ptp) REVERT: C 1276 TRP cc_start: 0.8563 (m-10) cc_final: 0.8084 (m-10) REVERT: C 1286 THR cc_start: 0.8456 (p) cc_final: 0.8102 (p) REVERT: C 1329 GLU cc_start: 0.7632 (tt0) cc_final: 0.6460 (tt0) REVERT: C 1339 LEU cc_start: 0.7339 (mt) cc_final: 0.7079 (mt) REVERT: D 114 ILE cc_start: 0.9256 (tp) cc_final: 0.9054 (tp) REVERT: D 719 PHE cc_start: 0.6253 (m-80) cc_final: 0.5987 (m-80) REVERT: D 760 THR cc_start: 0.8543 (p) cc_final: 0.8325 (p) REVERT: D 958 ILE cc_start: 0.7931 (mm) cc_final: 0.7457 (mp) REVERT: D 1037 PHE cc_start: 0.3202 (m-10) cc_final: 0.2421 (m-80) REVERT: D 1313 SER cc_start: 0.9318 (m) cc_final: 0.8809 (t) REVERT: E 72 GLN cc_start: 0.6938 (OUTLIER) cc_final: 0.6053 (pp30) REVERT: F 150 ARG cc_start: 0.5582 (mtt90) cc_final: 0.5222 (tmm160) REVERT: F 320 ILE cc_start: 0.4668 (mm) cc_final: 0.4270 (mm) REVERT: F 322 MET cc_start: 0.2000 (mpp) cc_final: 0.1471 (tmm) REVERT: F 430 TYR cc_start: 0.6650 (t80) cc_final: 0.6262 (t80) REVERT: F 487 MET cc_start: 0.6487 (tpp) cc_final: 0.5991 (tpp) REVERT: G 1 MET cc_start: 0.6105 (mpp) cc_final: 0.5105 (ttp) REVERT: G 88 VAL cc_start: 0.7034 (m) cc_final: 0.6736 (p) REVERT: H 87 LYS cc_start: 0.7035 (tptm) cc_final: 0.6542 (pttp) REVERT: H 91 ILE cc_start: 0.7774 (pt) cc_final: 0.7482 (pt) REVERT: H 94 HIS cc_start: 0.8220 (m-70) cc_final: 0.7991 (m-70) outliers start: 3 outliers final: 2 residues processed: 651 average time/residue: 0.4445 time to fit residues: 472.3676 Evaluate side-chains 488 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 485 time to evaluate : 3.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 376 optimal weight: 10.0000 chunk 44 optimal weight: 1.9990 chunk 222 optimal weight: 0.3980 chunk 285 optimal weight: 0.9980 chunk 221 optimal weight: 0.8980 chunk 329 optimal weight: 8.9990 chunk 218 optimal weight: 5.9990 chunk 389 optimal weight: 20.0000 chunk 243 optimal weight: 6.9990 chunk 237 optimal weight: 0.6980 chunk 179 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN C1061 GLN ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 419 HIS D 458 ASN D 477 GLN ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 929 GLN ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 HIS ** H 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 94 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33763 Z= 0.183 Angle : 0.599 13.438 46069 Z= 0.309 Chirality : 0.042 0.170 5293 Planarity : 0.004 0.060 5664 Dihedral : 15.521 167.843 5475 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % Rotamer: Outliers : 0.03 % Allowed : 1.63 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.13), residues: 3971 helix: 0.01 (0.13), residues: 1605 sheet: -1.90 (0.28), residues: 293 loop : -1.89 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP D 236 HIS 0.015 0.001 HIS C 551 PHE 0.025 0.002 PHE H 58 TYR 0.022 0.001 TYR D 269 ARG 0.013 0.000 ARG F 486 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 625 time to evaluate : 3.584 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: A 171 LEU cc_start: 0.8622 (mt) cc_final: 0.8406 (mt) REVERT: A 199 ASP cc_start: 0.6796 (m-30) cc_final: 0.6564 (m-30) REVERT: A 226 GLU cc_start: 0.7157 (pp20) cc_final: 0.6696 (tm-30) REVERT: B 85 LEU cc_start: 0.9162 (mt) cc_final: 0.8859 (tt) REVERT: C 136 PHE cc_start: 0.8328 (m-80) cc_final: 0.7786 (m-10) REVERT: C 182 SER cc_start: 0.8166 (p) cc_final: 0.7919 (p) REVERT: C 204 LEU cc_start: 0.7767 (tt) cc_final: 0.7426 (tt) REVERT: C 367 TYR cc_start: 0.8318 (t80) cc_final: 0.7957 (t80) REVERT: C 458 GLU cc_start: 0.7594 (tt0) cc_final: 0.7324 (tt0) REVERT: C 473 ARG cc_start: 0.8075 (ttp80) cc_final: 0.7807 (ttp80) REVERT: C 688 GLN cc_start: 0.8458 (tt0) cc_final: 0.8017 (tt0) REVERT: C 739 ASP cc_start: 0.7497 (p0) cc_final: 0.6849 (t0) REVERT: C 741 MET cc_start: 0.8445 (mtt) cc_final: 0.7773 (mtt) REVERT: C 1220 GLN cc_start: 0.7330 (pp30) cc_final: 0.7077 (pp30) REVERT: C 1276 TRP cc_start: 0.8566 (m-10) cc_final: 0.7655 (m100) REVERT: C 1329 GLU cc_start: 0.7555 (tt0) cc_final: 0.7346 (tt0) REVERT: C 1339 LEU cc_start: 0.7393 (mt) cc_final: 0.7106 (mt) REVERT: D 29 MET cc_start: 0.6876 (ptp) cc_final: 0.5731 (ptp) REVERT: D 133 ARG cc_start: 0.8271 (ttp80) cc_final: 0.7968 (ptm-80) REVERT: D 466 MET cc_start: 0.8001 (tpp) cc_final: 0.7722 (mtt) REVERT: D 619 ILE cc_start: 0.8781 (mt) cc_final: 0.8579 (tp) REVERT: D 719 PHE cc_start: 0.6403 (m-80) cc_final: 0.6084 (m-80) REVERT: D 958 ILE cc_start: 0.8020 (mm) cc_final: 0.7526 (mp) REVERT: D 983 LYS cc_start: 0.7418 (ptpp) cc_final: 0.6945 (pttm) REVERT: D 1037 PHE cc_start: 0.3213 (m-10) cc_final: 0.2428 (m-80) REVERT: D 1313 SER cc_start: 0.9191 (m) cc_final: 0.8706 (t) REVERT: F 150 ARG cc_start: 0.5539 (mtt90) cc_final: 0.5189 (tmm160) REVERT: F 320 ILE cc_start: 0.4710 (mm) cc_final: 0.4309 (mm) REVERT: F 322 MET cc_start: 0.2012 (mpp) cc_final: 0.1433 (tmm) REVERT: F 378 GLU cc_start: 0.8453 (mt-10) cc_final: 0.8242 (mt-10) REVERT: F 430 TYR cc_start: 0.6732 (t80) cc_final: 0.6363 (t80) REVERT: F 487 MET cc_start: 0.6169 (tpp) cc_final: 0.5843 (tpp) REVERT: G 1 MET cc_start: 0.5978 (mpp) cc_final: 0.5298 (ttm) REVERT: G 17 ILE cc_start: 0.8633 (pt) cc_final: 0.8347 (pt) REVERT: H 1 MET cc_start: 0.1255 (ptm) cc_final: 0.0772 (ptm) REVERT: H 87 LYS cc_start: 0.7054 (tptm) cc_final: 0.6508 (pttp) REVERT: H 94 HIS cc_start: 0.8180 (m90) cc_final: 0.7945 (m-70) outliers start: 1 outliers final: 1 residues processed: 626 average time/residue: 0.4261 time to fit residues: 438.3144 Evaluate side-chains 482 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 481 time to evaluate : 3.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 240 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 chunk 117 optimal weight: 0.0570 chunk 76 optimal weight: 20.0000 chunk 75 optimal weight: 4.9990 chunk 247 optimal weight: 4.9990 chunk 265 optimal weight: 10.0000 chunk 192 optimal weight: 6.9990 chunk 36 optimal weight: 5.9990 chunk 306 optimal weight: 0.9980 overall best weight: 2.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1288 GLN ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 157 GLN ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 777 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 929 GLN D1108 GLN ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 ASN ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 125 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.5409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 33763 Z= 0.319 Angle : 0.703 12.360 46069 Z= 0.363 Chirality : 0.045 0.263 5293 Planarity : 0.005 0.055 5664 Dihedral : 15.753 167.232 5475 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 23.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.71 % Favored : 92.27 % Rotamer: Outliers : 0.03 % Allowed : 1.33 % Favored : 98.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.13), residues: 3971 helix: -0.11 (0.13), residues: 1607 sheet: -1.91 (0.27), residues: 312 loop : -1.94 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP D 236 HIS 0.022 0.002 HIS C 551 PHE 0.020 0.002 PHE C 812 TYR 0.028 0.002 TYR C1281 ARG 0.013 0.001 ARG F 486 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 581 time to evaluate : 3.450 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 206 GLU cc_start: 0.6651 (tp30) cc_final: 0.6187 (tp30) REVERT: A 226 GLU cc_start: 0.7434 (pp20) cc_final: 0.7040 (tm-30) REVERT: A 229 GLU cc_start: 0.7411 (tm-30) cc_final: 0.6572 (tm-30) REVERT: B 85 LEU cc_start: 0.9181 (mt) cc_final: 0.8892 (tt) REVERT: C 130 MET cc_start: 0.8693 (tpt) cc_final: 0.8264 (mmm) REVERT: C 136 PHE cc_start: 0.8505 (m-80) cc_final: 0.7663 (m-10) REVERT: C 189 ASP cc_start: 0.6417 (m-30) cc_final: 0.6039 (m-30) REVERT: C 369 MET cc_start: 0.8015 (mmp) cc_final: 0.7282 (ttm) REVERT: C 458 GLU cc_start: 0.7591 (tt0) cc_final: 0.7326 (tt0) REVERT: C 739 ASP cc_start: 0.7630 (p0) cc_final: 0.7022 (t0) REVERT: C 898 GLU cc_start: 0.9395 (mp0) cc_final: 0.9130 (mp0) REVERT: C 1064 ASP cc_start: 0.8219 (t0) cc_final: 0.7885 (t0) REVERT: C 1103 VAL cc_start: 0.8905 (t) cc_final: 0.8645 (t) REVERT: C 1107 MET cc_start: 0.7931 (mmt) cc_final: 0.7016 (mmm) REVERT: C 1244 HIS cc_start: 0.8073 (t-170) cc_final: 0.7839 (t-170) REVERT: C 1276 TRP cc_start: 0.8676 (m-10) cc_final: 0.8135 (m-10) REVERT: D 47 ARG cc_start: 0.7495 (ptt180) cc_final: 0.7280 (ptt180) REVERT: D 269 TYR cc_start: 0.9048 (m-80) cc_final: 0.8791 (m-80) REVERT: D 466 MET cc_start: 0.8046 (tpp) cc_final: 0.7825 (mtt) REVERT: D 796 LEU cc_start: 0.9339 (tp) cc_final: 0.8984 (tt) REVERT: D 925 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7722 (tm-30) REVERT: D 983 LYS cc_start: 0.7464 (ptpp) cc_final: 0.6637 (pttm) REVERT: D 1037 PHE cc_start: 0.3659 (m-10) cc_final: 0.2728 (m-80) REVERT: D 1313 SER cc_start: 0.9298 (m) cc_final: 0.8973 (t) REVERT: E 36 ASP cc_start: 0.7327 (m-30) cc_final: 0.7062 (m-30) REVERT: E 71 GLU cc_start: 0.8647 (mp0) cc_final: 0.8205 (mp0) REVERT: F 100 MET cc_start: 0.7198 (ptt) cc_final: 0.6988 (ptt) REVERT: F 150 ARG cc_start: 0.5595 (mtt90) cc_final: 0.5327 (ttp80) REVERT: F 430 TYR cc_start: 0.6880 (t80) cc_final: 0.6499 (t80) REVERT: H 1 MET cc_start: 0.1777 (ppp) cc_final: 0.1009 (ptm) REVERT: H 91 ILE cc_start: 0.7790 (pt) cc_final: 0.7383 (pt) REVERT: H 94 HIS cc_start: 0.8251 (m90) cc_final: 0.8014 (m90) outliers start: 1 outliers final: 1 residues processed: 582 average time/residue: 0.4375 time to fit residues: 418.8544 Evaluate side-chains 454 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 453 time to evaluate : 3.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 354 optimal weight: 5.9990 chunk 373 optimal weight: 8.9990 chunk 340 optimal weight: 10.0000 chunk 362 optimal weight: 0.8980 chunk 372 optimal weight: 10.0000 chunk 218 optimal weight: 1.9990 chunk 158 optimal weight: 0.0980 chunk 284 optimal weight: 8.9990 chunk 111 optimal weight: 20.0000 chunk 327 optimal weight: 0.9980 chunk 343 optimal weight: 20.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 686 GLN C 688 GLN ** C1038 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1237 HIS ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1288 GLN ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 ASN ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33763 Z= 0.259 Angle : 0.666 11.543 46069 Z= 0.344 Chirality : 0.044 0.239 5293 Planarity : 0.004 0.059 5664 Dihedral : 15.668 167.409 5475 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 22.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 0.03 % Allowed : 0.88 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.13), residues: 3971 helix: -0.13 (0.13), residues: 1610 sheet: -2.10 (0.26), residues: 337 loop : -1.91 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 236 HIS 0.025 0.001 HIS C 551 PHE 0.027 0.002 PHE C 812 TYR 0.036 0.002 TYR C1281 ARG 0.012 0.000 ARG F 486 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 589 time to evaluate : 3.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 GLU cc_start: 0.6535 (tp30) cc_final: 0.6232 (tp30) REVERT: A 226 GLU cc_start: 0.7417 (pp20) cc_final: 0.6995 (tm-30) REVERT: A 229 GLU cc_start: 0.7406 (tm-30) cc_final: 0.6582 (tm-30) REVERT: C 53 PHE cc_start: 0.7546 (m-10) cc_final: 0.7242 (m-10) REVERT: C 130 MET cc_start: 0.8644 (tpt) cc_final: 0.8352 (mmm) REVERT: C 136 PHE cc_start: 0.8498 (m-80) cc_final: 0.7759 (m-10) REVERT: C 458 GLU cc_start: 0.7594 (tt0) cc_final: 0.7346 (tt0) REVERT: C 473 ARG cc_start: 0.8123 (ttp80) cc_final: 0.7848 (ttp80) REVERT: C 516 ASP cc_start: 0.8125 (p0) cc_final: 0.7653 (p0) REVERT: C 549 ASP cc_start: 0.6597 (t0) cc_final: 0.6364 (t0) REVERT: C 739 ASP cc_start: 0.7599 (p0) cc_final: 0.7064 (t0) REVERT: C 741 MET cc_start: 0.8697 (mtt) cc_final: 0.8057 (mtt) REVERT: C 1076 ILE cc_start: 0.9501 (mm) cc_final: 0.9249 (mm) REVERT: C 1188 ASP cc_start: 0.6511 (m-30) cc_final: 0.6141 (m-30) REVERT: C 1244 HIS cc_start: 0.8026 (t-170) cc_final: 0.7653 (t-170) REVERT: C 1262 LYS cc_start: 0.7223 (ttpt) cc_final: 0.6739 (mmmt) REVERT: C 1276 TRP cc_start: 0.8640 (m-10) cc_final: 0.8036 (m-10) REVERT: C 1290 MET cc_start: 0.8012 (mmp) cc_final: 0.7777 (mmp) REVERT: D 29 MET cc_start: 0.6999 (ptp) cc_final: 0.5962 (ptp) REVERT: D 269 TYR cc_start: 0.9027 (m-80) cc_final: 0.8739 (m-80) REVERT: D 283 LEU cc_start: 0.8499 (mt) cc_final: 0.7953 (tt) REVERT: D 760 THR cc_start: 0.8660 (p) cc_final: 0.8449 (p) REVERT: D 821 MET cc_start: 0.7105 (tpp) cc_final: 0.6618 (tpp) REVERT: D 822 MET cc_start: 0.8433 (tpp) cc_final: 0.8214 (tpp) REVERT: D 983 LYS cc_start: 0.7428 (ptpp) cc_final: 0.6706 (pttm) REVERT: D 1037 PHE cc_start: 0.3638 (m-10) cc_final: 0.2758 (m-80) REVERT: D 1313 SER cc_start: 0.9269 (m) cc_final: 0.8931 (t) REVERT: E 71 GLU cc_start: 0.8499 (mp0) cc_final: 0.8208 (mp0) REVERT: F 150 ARG cc_start: 0.5634 (mtt90) cc_final: 0.5242 (ttp80) REVERT: F 430 TYR cc_start: 0.7032 (t80) cc_final: 0.6651 (t80) REVERT: G 17 ILE cc_start: 0.8721 (pt) cc_final: 0.8364 (pt) REVERT: G 30 MET cc_start: 0.4362 (mmm) cc_final: 0.3640 (tpt) REVERT: G 88 VAL cc_start: 0.7561 (p) cc_final: 0.7037 (m) REVERT: H 1 MET cc_start: 0.1389 (ppp) cc_final: 0.0601 (ptm) REVERT: H 91 ILE cc_start: 0.7765 (pt) cc_final: 0.7443 (pt) REVERT: H 94 HIS cc_start: 0.8240 (m90) cc_final: 0.8022 (m-70) outliers start: 1 outliers final: 1 residues processed: 589 average time/residue: 0.4303 time to fit residues: 419.0108 Evaluate side-chains 457 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 456 time to evaluate : 3.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 361 optimal weight: 0.6980 chunk 238 optimal weight: 2.9990 chunk 383 optimal weight: 0.0670 chunk 234 optimal weight: 0.6980 chunk 182 optimal weight: 0.9980 chunk 266 optimal weight: 4.9990 chunk 402 optimal weight: 20.0000 chunk 370 optimal weight: 1.9990 chunk 320 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 247 optimal weight: 3.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 620 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 GLN ** C1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 929 GLN ** D1195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 HIS H 71 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33763 Z= 0.195 Angle : 0.644 12.271 46069 Z= 0.331 Chirality : 0.043 0.223 5293 Planarity : 0.004 0.066 5664 Dihedral : 15.526 166.705 5475 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 19.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 0.03 % Allowed : 0.51 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.13), residues: 3971 helix: -0.06 (0.13), residues: 1615 sheet: -2.04 (0.27), residues: 328 loop : -1.84 (0.14), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRP D 236 HIS 0.023 0.001 HIS C 551 PHE 0.027 0.002 PHE C 812 TYR 0.025 0.001 TYR C1281 ARG 0.011 0.000 ARG F 486 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7942 Ramachandran restraints generated. 3971 Oldfield, 0 Emsley, 3971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 611 time to evaluate : 4.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 LEU cc_start: 0.8720 (mt) cc_final: 0.8489 (mt) REVERT: A 226 GLU cc_start: 0.7410 (pp20) cc_final: 0.6893 (tm-30) REVERT: A 229 GLU cc_start: 0.7355 (tm-30) cc_final: 0.6520 (tm-30) REVERT: B 85 LEU cc_start: 0.9179 (mt) cc_final: 0.8861 (tt) REVERT: C 53 PHE cc_start: 0.7553 (m-10) cc_final: 0.7338 (m-10) REVERT: C 130 MET cc_start: 0.8616 (tpt) cc_final: 0.8295 (mmm) REVERT: C 136 PHE cc_start: 0.8442 (m-80) cc_final: 0.7750 (m-10) REVERT: C 189 ASP cc_start: 0.6321 (m-30) cc_final: 0.5943 (m-30) REVERT: C 367 TYR cc_start: 0.8341 (t80) cc_final: 0.7838 (t80) REVERT: C 369 MET cc_start: 0.7677 (mmp) cc_final: 0.6947 (ttm) REVERT: C 458 GLU cc_start: 0.7588 (tt0) cc_final: 0.7332 (tt0) REVERT: C 473 ARG cc_start: 0.8105 (ttp80) cc_final: 0.7686 (ttp80) REVERT: C 516 ASP cc_start: 0.8063 (p0) cc_final: 0.7831 (p0) REVERT: C 739 ASP cc_start: 0.7574 (p0) cc_final: 0.7007 (t0) REVERT: C 741 MET cc_start: 0.8659 (mtt) cc_final: 0.7989 (mtt) REVERT: C 761 GLN cc_start: 0.8205 (mp10) cc_final: 0.7902 (mp10) REVERT: C 898 GLU cc_start: 0.9253 (mp0) cc_final: 0.8729 (mm-30) REVERT: C 1103 VAL cc_start: 0.8984 (t) cc_final: 0.8681 (t) REVERT: C 1107 MET cc_start: 0.7438 (mmt) cc_final: 0.6177 (mmm) REVERT: C 1187 PHE cc_start: 0.7351 (m-80) cc_final: 0.6277 (m-10) REVERT: C 1188 ASP cc_start: 0.6203 (m-30) cc_final: 0.5038 (m-30) REVERT: C 1240 ASP cc_start: 0.8014 (m-30) cc_final: 0.7628 (t0) REVERT: C 1244 HIS cc_start: 0.7861 (t-170) cc_final: 0.7587 (t-170) REVERT: C 1276 TRP cc_start: 0.8642 (m-10) cc_final: 0.8053 (m-10) REVERT: D 29 MET cc_start: 0.7025 (ptp) cc_final: 0.6503 (ptp) REVERT: D 114 ILE cc_start: 0.9373 (tp) cc_final: 0.9135 (tp) REVERT: D 133 ARG cc_start: 0.8319 (ttp80) cc_final: 0.8099 (mpt-90) REVERT: D 342 LEU cc_start: 0.8936 (mm) cc_final: 0.8667 (mm) REVERT: D 355 ILE cc_start: 0.9400 (pt) cc_final: 0.9147 (tt) REVERT: D 466 MET cc_start: 0.7821 (tpp) cc_final: 0.7519 (mtt) REVERT: D 625 MET cc_start: 0.7993 (ttp) cc_final: 0.7733 (ttp) REVERT: D 760 THR cc_start: 0.8649 (p) cc_final: 0.8443 (p) REVERT: D 821 MET cc_start: 0.7087 (tpp) cc_final: 0.6582 (tpp) REVERT: D 983 LYS cc_start: 0.7404 (ptpp) cc_final: 0.6939 (pttm) REVERT: D 1037 PHE cc_start: 0.3412 (m-10) cc_final: 0.2709 (m-80) REVERT: F 297 MET cc_start: 0.1313 (ptm) cc_final: -0.0037 (ptm) REVERT: F 430 TYR cc_start: 0.7045 (t80) cc_final: 0.6697 (t80) REVERT: F 487 MET cc_start: 0.6634 (tpt) cc_final: 0.6311 (tpp) REVERT: G 88 VAL cc_start: 0.7613 (p) cc_final: 0.7235 (m) REVERT: H 1 MET cc_start: 0.1027 (ppp) cc_final: 0.0225 (ptm) REVERT: H 91 ILE cc_start: 0.7711 (pt) cc_final: 0.7349 (pt) outliers start: 1 outliers final: 1 residues processed: 611 average time/residue: 0.4207 time to fit residues: 425.1364 Evaluate side-chains 473 residues out of total 3431 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 472 time to evaluate : 3.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 196 optimal weight: 0.9990 chunk 254 optimal weight: 8.9990 chunk 341 optimal weight: 0.0970 chunk 98 optimal weight: 0.9990 chunk 295 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 321 optimal weight: 0.0870 chunk 134 optimal weight: 4.9990 chunk 329 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 193 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 620 ASN ** C 686 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1264 GLN ** C1313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 929 GLN D1195 GLN D1218 HIS ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 406 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 43 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.116219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.097874 restraints weight = 105380.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.099027 restraints weight = 67789.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.099489 restraints weight = 46631.510| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33763 Z= 0.189 Angle : 0.647 13.579 46069 Z= 0.330 Chirality : 0.043 0.269 5293 Planarity : 0.004 0.062 5664 Dihedral : 15.471 166.448 5475 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 0.03 % Allowed : 0.63 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.13), residues: 3971 helix: -0.01 (0.13), residues: 1612 sheet: -1.98 (0.27), residues: 341 loop : -1.82 (0.14), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP D 236 HIS 0.023 0.001 HIS C 551 PHE 0.021 0.001 PHE C 670 TYR 0.022 0.001 TYR G 20 ARG 0.010 0.000 ARG F 486 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8434.72 seconds wall clock time: 151 minutes 51.45 seconds (9111.45 seconds total)