Starting phenix.real_space_refine on Thu Feb 22 08:11:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ldi_0874/02_2024/6ldi_0874.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ldi_0874/02_2024/6ldi_0874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ldi_0874/02_2024/6ldi_0874.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ldi_0874/02_2024/6ldi_0874.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ldi_0874/02_2024/6ldi_0874.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ldi_0874/02_2024/6ldi_0874.pdb" } resolution = 3.69 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 723 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Ag 1 8.66 5 Zn 2 6.06 5 P 102 5.49 5 Mg 1 5.21 5 S 138 5.16 5 C 20282 2.51 5 N 5808 2.21 5 O 6536 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 ARG 44": "NH1" <-> "NH2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A GLU 188": "OE1" <-> "OE2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "B ARG 33": "NH1" <-> "NH2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "B ARG 150": "NH1" <-> "NH2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B GLU 165": "OE1" <-> "OE2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "C ARG 10": "NH1" <-> "NH2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 180": "NH1" <-> "NH2" Residue "C ARG 201": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C GLU 286": "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 ARG 407": "NH1" <-> "NH2" Residue "C GLU 415": "OE1" <-> "OE2" Residue "C GLU 441": "OE1" <-> "OE2" Residue "C ARG 454": "NH1" <-> "NH2" Residue "C ARG 465": "NH1" <-> "NH2" Residue "C ARG 478": "NH1" <-> "NH2" Residue "C GLU 504": "OE1" <-> "OE2" Residue "C ARG 528": "NH1" <-> "NH2" Residue "C ARG 540": "NH1" <-> "NH2" Residue "C GLU 625": "OE1" <-> "OE2" Residue "C GLU 626": "OE1" <-> "OE2" Residue "C ARG 637": "NH1" <-> "NH2" Residue "C ARG 687": "NH1" <-> "NH2" Residue "C GLU 778": "OE1" <-> "OE2" Residue "C ARG 779": "NH1" <-> "NH2" Residue "C GLU 876": "OE1" <-> "OE2" Residue "C GLU 898": "OE1" <-> "OE2" Residue "C GLU 899": "OE1" <-> "OE2" Residue "C GLU 908": "OE1" <-> "OE2" Residue "C ARG 936": "NH1" <-> "NH2" Residue "C GLU 940": "OE1" <-> "OE2" Residue "C ARG 944": "NH1" <-> "NH2" Residue "C GLU 1016": "OE1" <-> "OE2" Residue "C ARG 1033": "NH1" <-> "NH2" Residue "C ARG 1142": "NH1" <-> "NH2" Residue "C ARG 1156": "NH1" <-> "NH2" Residue "C ARG 1246": "NH1" <-> "NH2" Residue "C ARG 1269": "NH1" <-> "NH2" Residue "D ARG 47": "NH1" <-> "NH2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ARG 98": "NH1" <-> "NH2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D ARG 220": "NH1" <-> "NH2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D ARG 259": "NH1" <-> "NH2" Residue "D ARG 270": "NH1" <-> "NH2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "D PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 443": "OE1" <-> "OE2" Residue "D ARG 535": "NH1" <-> "NH2" Residue "D ARG 547": "NH1" <-> "NH2" Residue "D GLU 562": "OE1" <-> "OE2" Residue "D ARG 634": "NH1" <-> "NH2" Residue "D GLU 652": "OE1" <-> "OE2" Residue "D GLU 658": "OE1" <-> "OE2" Residue "D ARG 678": "NH1" <-> "NH2" Residue "D ARG 692": "NH1" <-> "NH2" Residue "D ARG 744": "NH1" <-> "NH2" Residue "D GLU 811": "OE1" <-> "OE2" Residue "D ARG 842": "NH1" <-> "NH2" Residue "D ARG 860": "NH1" <-> "NH2" Residue "D GLU 873": "OE1" <-> "OE2" Residue "D ARG 1149": "NH1" <-> "NH2" Residue "D GLU 1152": "OE1" <-> "OE2" Residue "D GLU 1205": "OE1" <-> "OE2" Residue "D ARG 1222": "NH1" <-> "NH2" Residue "D ARG 1258": "NH1" <-> "NH2" Residue "D GLU 1281": "OE1" <-> "OE2" Residue "D ARG 1284": "NH1" <-> "NH2" Residue "D ARG 1290": "NH1" <-> "NH2" Residue "D GLU 1317": "OE1" <-> "OE2" Residue "D ARG 1369": "NH1" <-> "NH2" Residue "E ARG 26": "NH1" <-> "NH2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E ARG 52": "NH1" <-> "NH2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 69": "NH1" <-> "NH2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "F ARG 93": "NH1" <-> "NH2" Residue "F ARG 103": "NH1" <-> "NH2" Residue "F GLU 146": "OE1" <-> "OE2" Residue "F GLU 349": "OE1" <-> "OE2" Residue "F GLU 369": "OE1" <-> "OE2" Residue "F ARG 465": "NH1" <-> "NH2" Residue "F GLU 473": "OE1" <-> "OE2" Residue "F ARG 476": "NH1" <-> "NH2" Residue "F GLU 481": "OE1" <-> "OE2" Residue "F ARG 554": "NH1" <-> "NH2" Residue "F GLU 574": "OE1" <-> "OE2" Residue "F ARG 584": "NH1" <-> "NH2" Residue "F GLU 591": "OE1" <-> "OE2" Residue "F ARG 608": "NH1" <-> "NH2" Residue "G ARG 37": "NH1" <-> "NH2" Residue "G GLU 46": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G ARG 102": "NH1" <-> "NH2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H ARG 54": "NH1" <-> "NH2" Residue "H GLU 62": "OE1" <-> "OE2" Residue "H GLU 65": "OE1" <-> "OE2" Residue "H GLU 96": "OE1" <-> "OE2" Residue "H ARG 102": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 32870 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1784 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 220} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen planarities: 2 Chain: "B" Number of atoms: 1748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1748 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 217} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 10522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1338, 10522 Classifications: {'peptide': 1338} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 1281} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 10290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1331, 10290 Classifications: {'peptide': 1331} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 2, 'PTRANS': 53, 'TRANS': 1275} Chain breaks: 2 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 55 Chain: "E" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 605 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 2, 'TRANS': 73} Chain: "F" Number of atoms: 3748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 465, 3748 Classifications: {'peptide': 465} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 450} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 8, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "1" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1022 Classifications: {'DNA': 50} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 49} Chain: "2" Number of atoms: 1035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1035 Classifications: {'DNA': 50} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 49} Chain: "3" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 102 Classifications: {'RNA': 5} Modifications used: {'5*END': 1, 'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna3p': 4} Chain: "G" Number of atoms: 1009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1009 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "H" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1001 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 11 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: "H" 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 14494 SG CYS D 70 110.196 54.007 70.645 1.00 64.88 S ATOM 14508 SG CYS D 72 111.625 55.549 67.687 1.00 65.53 S ATOM 14616 SG CYS D 85 114.190 56.327 70.243 1.00 71.82 S ATOM 14640 SG CYS D 88 111.024 58.220 70.042 1.00 67.67 S ATOM 20321 SG CYS D 814 83.043 74.289 129.783 1.00 57.49 S ATOM 20882 SG CYS D 888 81.168 74.379 126.238 1.00 46.84 S ATOM 20933 SG CYS D 895 82.231 71.241 128.060 1.00 50.89 S ATOM 20954 SG CYS D 898 78.688 73.940 128.863 1.00 45.25 S ATOM 32766 SG CYS H 112 131.031 58.331 12.225 1.00154.01 S Time building chain proxies: 17.71, per 1000 atoms: 0.54 Number of scatterers: 32870 At special positions: 0 Unit cell: (163.375, 162.068, 168.603, 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 138 16.00 P 102 15.00 Mg 1 11.99 O 6536 8.00 N 5808 7.00 C 20282 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: 13.73 Conformation dependent library (CDL) restraints added in 5.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 70 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 85 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 72 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 898 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 814 " Number of angles added : 12 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7292 Finding SS restraints... Secondary structure from input PDB file: 141 helices and 47 sheets defined 40.2% alpha, 12.3% beta 40 base pairs and 73 stacking pairs defined. Time for finding SS restraints: 11.89 Creating SS restraints... Processing helix chain 'A' and resid 34 through 39 Processing helix chain 'A' and resid 43 through 48 removed outlier: 3.560A pdb=" N LEU A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 87 removed outlier: 4.337A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 161 removed outlier: 3.633A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 228 removed outlier: 3.892A pdb=" N ILE A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ARG A 218 " --> pdb=" O GLU A 214 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 233 removed outlier: 4.269A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 43 removed outlier: 3.820A pdb=" N LEU B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 48 Processing helix chain 'B' and resid 79 through 87 removed outlier: 3.806A pdb=" N LEU B 83 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 162 removed outlier: 3.639A pdb=" N ILE B 159 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 227 removed outlier: 3.649A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 33 Processing helix chain 'C' and resid 35 through 40 removed outlier: 3.550A pdb=" N ILE C 39 " --> pdb=" O PHE C 35 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU C 40 " --> pdb=" O GLN C 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 35 through 40' Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.522A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.690A pdb=" N GLN C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE C 87 " --> pdb=" O GLN C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 201 Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.506A pdb=" N ALA C 212 " --> pdb=" O ILE C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 225 removed outlier: 3.501A pdb=" N PHE C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.726A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 329 Processing helix chain 'C' and resid 345 through 354 removed outlier: 4.291A pdb=" N ARG C 352 " --> pdb=" O SER C 348 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL C 353 " --> pdb=" O GLU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 371 Processing helix chain 'C' and resid 377 through 390 removed outlier: 4.058A pdb=" N SER C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU C 384 " --> pdb=" O ALA C 380 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N PHE C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 4.027A pdb=" N SER C 408 " --> pdb=" O LYS C 404 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU C 409 " --> pdb=" O PHE C 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 409' Processing helix chain 'C' and resid 423 through 438 Processing helix chain 'C' and resid 455 through 479 removed outlier: 3.853A pdb=" N GLU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN C 462 " --> pdb=" O GLU C 458 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL C 466 " --> pdb=" O ASN C 462 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU C 477 " --> pdb=" O ARG C 473 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU C 479 " --> pdb=" O VAL C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 509 removed outlier: 3.923A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS C 503 " --> pdb=" O SER C 499 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY C 507 " --> pdb=" O LYS C 503 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER C 509 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing helix chain 'C' and resid 520 through 525 Processing helix chain 'C' and resid 551 through 555 removed outlier: 4.083A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 614 removed outlier: 3.727A pdb=" N ASN C 613 " --> pdb=" O GLU C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 677 through 685 removed outlier: 3.549A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA C 683 " --> pdb=" O ALA C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 689 removed outlier: 4.029A pdb=" N ALA C 689 " --> pdb=" O GLN C 686 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 686 through 689' Processing helix chain 'C' and resid 704 through 712 removed outlier: 3.619A pdb=" N VAL C 708 " --> pdb=" O MET C 704 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA C 709 " --> pdb=" O GLU C 705 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL C 710 " --> pdb=" O ARG C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 819 through 825 removed outlier: 4.211A pdb=" N VAL C 823 " --> pdb=" O SER C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 943 through 983 removed outlier: 3.693A pdb=" N GLU C 949 " --> pdb=" O ALA C 945 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 966 " --> pdb=" O GLU C 962 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU C 967 " --> pdb=" O GLU C 963 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER C 973 " --> pdb=" O ALA C 969 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL C 978 " --> pdb=" O ARG C 974 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 992 removed outlier: 3.802A pdb=" N LEU C 992 " --> pdb=" O LYS C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1005 through 1038 removed outlier: 3.943A pdb=" N HIS C1023 " --> pdb=" O ASP C1019 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE C1025 " --> pdb=" O LEU C1021 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU C1026 " --> pdb=" O LYS C1022 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN C1038 " --> pdb=" O ARG C1034 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1085 removed outlier: 3.523A pdb=" N ASP C1084 " --> pdb=" O PRO C1081 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N MET C1085 " --> pdb=" O ILE C1082 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1081 through 1085' Processing helix chain 'C' and resid 1099 through 1103 removed outlier: 4.076A pdb=" N GLY C1102 " --> pdb=" O ASN C1099 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL C1103 " --> pdb=" O PRO C1100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1099 through 1103' Processing helix chain 'C' and resid 1109 through 1134 removed outlier: 3.690A pdb=" N LEU C1113 " --> pdb=" O ILE C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1149 removed outlier: 3.840A pdb=" N GLN C1146 " --> pdb=" O ARG C1142 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ARG C1147 " --> pdb=" O GLU C1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 1167 through 1175 Processing helix chain 'C' and resid 1191 through 1200 removed outlier: 3.547A pdb=" N ILE C1195 " --> pdb=" O LYS C1191 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS C1196 " --> pdb=" O GLU C1192 " (cutoff:3.500A) Processing helix chain 'C' and resid 1271 through 1282 removed outlier: 3.654A pdb=" N ALA C1277 " --> pdb=" O MET C1273 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY C1282 " --> pdb=" O LEU C1278 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1290 Processing helix chain 'C' and resid 1300 through 1311 removed outlier: 4.035A pdb=" N LYS C1306 " --> pdb=" O THR C1302 " (cutoff:3.500A) Processing helix chain 'C' and resid 1322 through 1332 removed outlier: 3.634A pdb=" N LEU C1326 " --> pdb=" O SER C1322 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS C1328 " --> pdb=" O ASN C1324 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 33 Processing helix chain 'D' and resid 58 through 63 Processing helix chain 'D' and resid 94 through 100 removed outlier: 3.784A pdb=" N VAL D 97 " --> pdb=" O GLN D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 119 removed outlier: 3.677A pdb=" N SER D 119 " --> pdb=" O TRP D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 removed outlier: 3.666A pdb=" N LEU D 128 " --> pdb=" O ILE D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.915A pdb=" N ARG D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 173 removed outlier: 3.607A pdb=" N ASP D 167 " --> pdb=" O GLU D 163 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 191 removed outlier: 3.607A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 206 removed outlier: 3.708A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 231 removed outlier: 3.531A pdb=" N VAL D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 264 through 283 removed outlier: 3.616A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG D 270 " --> pdb=" O ASN D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.568A pdb=" N ASN D 294 " --> pdb=" O ILE D 290 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG D 297 " --> pdb=" O ARG D 293 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 312 removed outlier: 4.252A pdb=" N ARG D 312 " --> pdb=" O ASN D 309 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 309 through 312' Processing helix chain 'D' and resid 327 through 331 removed outlier: 3.686A pdb=" N ILE D 331 " --> pdb=" O ALA D 328 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 335 removed outlier: 3.818A pdb=" N GLN D 335 " --> pdb=" O LYS D 332 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 332 through 335' Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.622A pdb=" N GLN D 340 " --> pdb=" O GLY D 336 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU D 342 " --> pdb=" O PHE D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 377 removed outlier: 4.226A pdb=" N GLU D 375 " --> pdb=" O LYS D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 388 removed outlier: 3.529A pdb=" N LEU D 387 " --> pdb=" O GLY D 383 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 403 removed outlier: 4.429A pdb=" N LYS D 399 " --> pdb=" O LYS D 395 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N MET D 400 " --> pdb=" O ALA D 396 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL D 401 " --> pdb=" O ALA D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 417 removed outlier: 3.884A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 453 through 458 Processing helix chain 'D' and resid 503 through 514 Processing helix chain 'D' and resid 529 through 532 removed outlier: 3.507A pdb=" N GLU D 532 " --> pdb=" O GLY D 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 529 through 532' Processing helix chain 'D' and resid 533 through 539 removed outlier: 3.570A pdb=" N SER D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 580 removed outlier: 3.713A pdb=" N TRP D 580 " --> pdb=" O ARG D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 592 Processing helix chain 'D' and resid 598 through 613 removed outlier: 3.589A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY D 613 " --> pdb=" O TYR D 609 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 629 removed outlier: 4.075A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N MET D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE D 629 " --> pdb=" O MET D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 634 Processing helix chain 'D' and resid 650 through 670 removed outlier: 3.752A pdb=" N ALA D 662 " --> pdb=" O GLU D 658 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU D 663 " --> pdb=" O ALA D 659 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ILE D 664 " --> pdb=" O GLU D 660 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 702 removed outlier: 3.692A pdb=" N ASN D 680 " --> pdb=" O GLY D 676 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE D 683 " --> pdb=" O TYR D 679 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ALA D 688 " --> pdb=" O ASP D 684 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA D 689 " --> pdb=" O ILE D 685 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL D 693 " --> pdb=" O ALA D 689 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA D 696 " --> pdb=" O ARG D 692 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N MET D 698 " --> pdb=" O SER D 694 " (cutoff:3.500A) Processing helix chain 'D' and resid 723 through 728 Processing helix chain 'D' and resid 769 through 775 Processing helix chain 'D' and resid 775 through 802 removed outlier: 4.187A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR D 786 " --> pdb=" O GLY D 782 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N THR D 797 " --> pdb=" O SER D 793 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG D 798 " --> pdb=" O GLY D 794 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 839 Processing helix chain 'D' and resid 868 through 875 removed outlier: 3.502A pdb=" N LEU D 872 " --> pdb=" O TRP D 868 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 884 through 888 removed outlier: 3.660A pdb=" N CYS D 888 " --> pdb=" O VAL D 885 " (cutoff:3.500A) Processing helix chain 'D' and resid 914 through 925 removed outlier: 4.308A pdb=" N ILE D 918 " --> pdb=" O ALA D 914 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 removed outlier: 3.684A pdb=" N LEU D 930 " --> pdb=" O GLY D 927 " (cutoff:3.500A) Processing helix chain 'D' and resid 1138 through 1146 removed outlier: 3.501A pdb=" N GLU D1146 " --> pdb=" O ALA D1142 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1223 removed outlier: 3.680A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D1221 " --> pdb=" O PRO D1217 " (cutoff:3.500A) Processing helix chain 'D' and resid 1225 through 1228 Processing helix chain 'D' and resid 1229 through 1234 removed outlier: 3.984A pdb=" N VAL D1234 " --> pdb=" O THR D1230 " (cutoff:3.500A) Processing helix chain 'D' and resid 1236 through 1239 Processing helix chain 'D' and resid 1240 through 1245 removed outlier: 3.616A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1261 removed outlier: 3.780A pdb=" N GLU D1254 " --> pdb=" O ASP D1250 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL D1255 " --> pdb=" O LYS D1251 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1281 through 1286 Processing helix chain 'D' and resid 1319 through 1324 removed outlier: 3.530A pdb=" N SER D1324 " --> pdb=" O ILE D1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1335 Processing helix chain 'D' and resid 1348 through 1353 removed outlier: 3.746A pdb=" N ILE D1352 " --> pdb=" O LYS D1348 " (cutoff:3.500A) Processing helix chain 'D' and resid 1360 through 1372 removed outlier: 4.132A pdb=" N ALA D1364 " --> pdb=" O GLY D1360 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR D1365 " --> pdb=" O THR D1361 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN D1367 " --> pdb=" O TYR D1363 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ASP D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG D1369 " --> pdb=" O TYR D1365 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG D1372 " --> pdb=" O ASP D1368 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 14 removed outlier: 3.801A pdb=" N GLU E 11 " --> pdb=" O GLN E 7 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 30 removed outlier: 3.761A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N MET E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 3.742A pdb=" N ALA E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU E 55 " --> pdb=" O LEU E 51 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 77 removed outlier: 3.838A pdb=" N GLU E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU E 71 " --> pdb=" O ARG E 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.560A pdb=" N MET F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 134 removed outlier: 3.922A pdb=" N GLU F 116 " --> pdb=" O THR F 112 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ILE F 117 " --> pdb=" O ARG F 113 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN F 129 " --> pdb=" O ASP F 125 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL F 130 " --> pdb=" O GLY F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 3.573A pdb=" N ILE F 141 " --> pdb=" O TYR F 137 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL F 151 " --> pdb=" O GLN F 147 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ALA F 153 " --> pdb=" O ASP F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 221 removed outlier: 3.580A pdb=" N ALA F 217 " --> pdb=" O ASP F 213 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE F 221 " --> pdb=" O ALA F 217 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 235 removed outlier: 4.108A pdb=" N ALA F 226 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP F 233 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR F 234 " --> pdb=" O VAL F 230 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE F 235 " --> pdb=" O THR F 231 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 255 Processing helix chain 'F' and resid 262 through 294 removed outlier: 4.632A pdb=" N LEU F 269 " --> pdb=" O GLN F 265 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL F 270 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL F 275 " --> pdb=" O ASN F 271 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N MET F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 307 removed outlier: 3.660A pdb=" N THR F 307 " --> pdb=" O ILE F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 319 removed outlier: 4.065A pdb=" N ALA F 319 " --> pdb=" O TRP F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 322 No H-bonds generated for 'chain 'F' and resid 320 through 322' Processing helix chain 'F' and resid 333 through 352 removed outlier: 4.634A pdb=" N VAL F 337 " --> pdb=" O VAL F 333 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N HIS F 338 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ARG F 339 " --> pdb=" O GLU F 335 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LYS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 383 removed outlier: 3.664A pdb=" N LYS F 359 " --> pdb=" O ILE F 355 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ASP F 360 " --> pdb=" O GLU F 356 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ILE F 361 " --> pdb=" O GLN F 357 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN F 362 " --> pdb=" O VAL F 358 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET F 379 " --> pdb=" O ALA F 375 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN F 383 " --> pdb=" O MET F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 391 removed outlier: 4.043A pdb=" N VAL F 387 " --> pdb=" O ASN F 383 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE F 388 " --> pdb=" O LEU F 384 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 419 removed outlier: 3.811A pdb=" N LEU F 404 " --> pdb=" O GLN F 400 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE F 405 " --> pdb=" O PHE F 401 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE F 410 " --> pdb=" O GLN F 406 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP F 417 " --> pdb=" O MET F 413 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LYS F 418 " --> pdb=" O LYS F 414 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 446 removed outlier: 3.814A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N THR F 432 " --> pdb=" O SER F 428 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA F 438 " --> pdb=" O TRP F 434 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA F 444 " --> pdb=" O THR F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 475 removed outlier: 3.635A pdb=" N ILE F 457 " --> pdb=" O PRO F 453 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU F 458 " --> pdb=" O VAL F 454 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR F 459 " --> pdb=" O HIS F 455 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU F 471 " --> pdb=" O SER F 467 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN F 472 " --> pdb=" O ARG F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 488 removed outlier: 3.757A pdb=" N GLU F 485 " --> pdb=" O GLU F 481 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG F 486 " --> pdb=" O GLU F 482 " (cutoff:3.500A) Processing helix chain 'F' and resid 490 through 501 removed outlier: 3.927A pdb=" N LYS F 499 " --> pdb=" O ARG F 495 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ILE F 500 " --> pdb=" O LYS F 496 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ALA F 501 " --> pdb=" O VAL F 497 " (cutoff:3.500A) Processing helix chain 'F' and resid 518 through 522 removed outlier: 3.580A pdb=" N ASP F 521 " --> pdb=" O HIS F 518 " (cutoff:3.500A) Processing helix chain 'F' and resid 535 through 548 removed outlier: 3.671A pdb=" N ARG F 541 " --> pdb=" O THR F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 554 through 563 removed outlier: 3.588A pdb=" N PHE F 563 " --> pdb=" O LEU F 559 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 581 removed outlier: 3.878A pdb=" N GLN F 579 " --> pdb=" O GLU F 575 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE F 580 " --> pdb=" O VAL F 576 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP F 581 " --> pdb=" O GLY F 577 " (cutoff:3.500A) Processing helix chain 'F' and resid 584 through 600 removed outlier: 3.603A pdb=" N ARG F 588 " --> pdb=" O ARG F 584 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N HIS F 600 " --> pdb=" O ARG F 596 " (cutoff:3.500A) Processing helix chain 'F' and resid 605 through 609 removed outlier: 3.527A pdb=" N ARG F 608 " --> pdb=" O GLU F 605 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER F 609 " --> pdb=" O VAL F 606 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 605 through 609' Processing helix chain 'G' and resid 5 through 10 removed outlier: 3.526A pdb=" N THR G 10 " --> pdb=" O VAL G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 23 removed outlier: 3.864A pdb=" N ARG G 18 " --> pdb=" O SER G 14 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 57 removed outlier: 3.695A pdb=" N GLN G 52 " --> pdb=" O THR G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 72 removed outlier: 4.242A pdb=" N ASN G 68 " --> pdb=" O GLY G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 107 removed outlier: 3.656A pdb=" N GLU G 97 " --> pdb=" O ARG G 93 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA G 107 " --> pdb=" O ASP G 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 11 Processing helix chain 'H' and resid 13 through 24 removed outlier: 3.712A pdb=" N GLY H 24 " --> pdb=" O TYR H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 56 removed outlier: 4.164A pdb=" N THR H 48 " --> pdb=" O LEU H 44 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL H 56 " --> pdb=" O GLN H 52 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 71 removed outlier: 3.974A pdb=" N LEU H 66 " --> pdb=" O GLU H 62 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL H 67 " --> pdb=" O SER H 63 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN H 71 " --> pdb=" O VAL H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 77 through 110 removed outlier: 4.400A pdb=" N LYS H 81 " --> pdb=" O SER H 77 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG H 82 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ARG H 83 " --> pdb=" O ASP H 79 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS H 87 " --> pdb=" O ARG H 83 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU H 108 " --> pdb=" O GLN H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 128 removed outlier: 3.638A pdb=" N GLU H 124 " --> pdb=" O CYS H 120 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY H 128 " --> pdb=" O GLU H 124 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18 removed outlier: 5.592A pdb=" N LEU A 13 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N GLU A 29 " --> pdb=" O LEU A 13 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU A 17 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 6.585A 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: 4.694A pdb=" N THR A 101 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 111 removed outlier: 3.564A pdb=" N VAL A 110 " --> pdb=" O CYS A 131 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS A 131 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 152 through 153 removed outlier: 3.522A pdb=" N ALA A 175 " --> pdb=" O VAL A 153 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 17 through 18 removed outlier: 6.448A pdb=" N ASP B 199 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ARG B 182 " --> pdb=" O GLU B 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 98 through 104 removed outlier: 3.702A pdb=" N MET B 142 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU B 58 " --> pdb=" O LYS B 145 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLN B 147 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N VAL B 56 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLY B 149 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N CYS B 54 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 90 through 91 Processing sheet with id=AA8, first strand: chain 'B' and resid 152 through 153 removed outlier: 3.806A pdb=" N VAL B 153 " --> pdb=" O ALA B 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.518A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.618A pdb=" N ILE C 59 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLU C 67 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 4.901A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA C 94 " --> pdb=" O GLU C 126 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLU C 126 " --> pdb=" O ALA C 94 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N LEU C 96 " --> pdb=" O MET C 124 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASP C 116 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB3, first strand: chain 'C' and resid 451 through 453 removed outlier: 3.515A pdb=" N HIS C 150 " --> pdb=" O ARG C 452 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER C 531 " --> pdb=" O SER C 147 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 159 removed outlier: 3.715A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 284 through 286 removed outlier: 3.807A pdb=" N ARG C 233 " --> pdb=" O LYS C 236 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ILE C 229 " --> pdb=" O GLU C 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 250 through 251 removed outlier: 3.762A pdb=" N ARG C 267 " --> pdb=" O ALA C 251 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 295 through 296 removed outlier: 4.699A pdb=" N LYS C 295 " --> pdb=" O LEU C 317 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.636A pdb=" N LYS C 593 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AC1, first strand: chain 'C' and resid 616 through 617 Processing sheet with id=AC2, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.511A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.969A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.840A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC6, first strand: chain 'C' and resid 1066 through 1067 removed outlier: 4.922A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET C 800 " --> pdb=" O MET C1230 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU C 817 " --> pdb=" O VAL C1097 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N ILE C 816 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ILE C1079 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL C 818 " --> pdb=" O ILE C1079 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 1066 through 1067 Processing sheet with id=AC8, first strand: chain 'C' and resid 830 through 832 Processing sheet with id=AC9, first strand: chain 'C' and resid 835 through 841 removed outlier: 3.810A pdb=" N LYS C1048 " --> pdb=" O SER C 840 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 849 through 850 Processing sheet with id=AD2, first strand: chain 'C' and resid 882 through 884 removed outlier: 7.170A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 3.661A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 7.765A pdb=" N ILE D 447 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 1269 through 1270 removed outlier: 3.645A pdb=" N LYS D 345 " --> pdb=" O PHE C1270 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 1335 through 1339 removed outlier: 3.540A pdb=" N LYS D 21 " --> pdb=" O GLU C1338 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 34 through 37 removed outlier: 7.508A pdb=" N HIS D 104 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU D 37 " --> pdb=" O HIS D 104 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N GLU D 106 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 10.271A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 9.974A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 159 through 160 removed outlier: 7.386A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 252 through 254 removed outlier: 7.047A pdb=" N PHE D 260 " --> pdb=" O ILE F 505 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 548 through 556 removed outlier: 3.551A pdb=" N SER D 568 " --> pdb=" O ILE D 552 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 704 through 706 Processing sheet with id=AE3, first strand: chain 'D' and resid 949 through 951 removed outlier: 6.959A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 957 through 959 Processing sheet with id=AE5, first strand: chain 'D' and resid 965 through 967 removed outlier: 3.817A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1024 through 1026 Processing sheet with id=AE7, first strand: chain 'D' and resid 1033 through 1034 Processing sheet with id=AE8, first strand: chain 'D' and resid 1077 through 1078 Processing sheet with id=AE9, first strand: chain 'D' and resid 1089 through 1090 removed outlier: 5.824A pdb=" N MET D1095 " --> pdb=" O ILE D1090 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 1187 through 1189 removed outlier: 3.725A pdb=" N LEU D1175 " --> pdb=" O GLU D1188 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER D1164 " --> pdb=" O VAL D1176 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLY D1161 " --> pdb=" O VAL D1204 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 1277 through 1279 1040 hydrogen bonds defined for protein. 2934 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 204 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 73 stacking parallelities Total time for adding SS restraints: 15.64 Time building geometry restraints manager: 14.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6620 1.33 - 1.45: 7640 1.45 - 1.57: 18871 1.57 - 1.69: 204 1.69 - 1.82: 241 Bond restraints: 33576 Sorted by residual: bond pdb=" CD2 TRP D1020 " pdb=" CE2 TRP D1020 " ideal model delta sigma weight residual 1.409 1.483 -0.074 1.70e-02 3.46e+03 1.88e+01 bond pdb=" CD2 TRP F 315 " pdb=" CE2 TRP F 315 " ideal model delta sigma weight residual 1.409 1.483 -0.074 1.70e-02 3.46e+03 1.87e+01 bond pdb=" O3' DG 2 10 " pdb=" P DA 2 11 " ideal model delta sigma weight residual 1.607 1.667 -0.060 1.50e-02 4.44e+03 1.58e+01 bond pdb=" CD2 TRP D1020 " pdb=" CE3 TRP D1020 " ideal model delta sigma weight residual 1.398 1.457 -0.059 1.60e-02 3.91e+03 1.34e+01 bond pdb=" CD2 TRP F 315 " pdb=" CE3 TRP F 315 " ideal model delta sigma weight residual 1.398 1.456 -0.058 1.60e-02 3.91e+03 1.30e+01 ... (remaining 33571 not shown) Histogram of bond angle deviations from ideal: 97.68 - 105.02: 979 105.02 - 112.36: 16963 112.36 - 119.69: 12196 119.69 - 127.03: 15146 127.03 - 134.37: 500 Bond angle restraints: 45784 Sorted by residual: angle pdb=" CD2 TRP D1020 " pdb=" CE3 TRP D1020 " pdb=" CZ3 TRP D1020 " ideal model delta sigma weight residual 118.60 129.39 -10.79 1.30e+00 5.92e-01 6.89e+01 angle pdb=" CD2 TRP F 315 " pdb=" CE3 TRP F 315 " pdb=" CZ3 TRP F 315 " ideal model delta sigma weight residual 118.60 129.37 -10.77 1.30e+00 5.92e-01 6.86e+01 angle pdb=" N ILE C1109 " pdb=" CA ILE C1109 " pdb=" C ILE C1109 " ideal model delta sigma weight residual 112.29 105.83 6.46 9.40e-01 1.13e+00 4.73e+01 angle pdb=" CE2 TRP F 315 " pdb=" CD2 TRP F 315 " pdb=" CE3 TRP F 315 " ideal model delta sigma weight residual 118.80 124.87 -6.07 1.00e+00 1.00e+00 3.68e+01 angle pdb=" CE2 TRP D1020 " pdb=" CD2 TRP D1020 " pdb=" CE3 TRP D1020 " ideal model delta sigma weight residual 118.80 124.79 -5.99 1.00e+00 1.00e+00 3.59e+01 ... (remaining 45779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.74: 18992 25.74 - 51.48: 1258 51.48 - 77.23: 180 77.23 - 102.97: 14 102.97 - 128.71: 1 Dihedral angle restraints: 20445 sinusoidal: 9148 harmonic: 11297 Sorted by residual: dihedral pdb=" CA VAL F 582 " pdb=" C VAL F 582 " pdb=" N THR F 583 " pdb=" CA THR F 583 " ideal model delta harmonic sigma weight residual -180.00 -144.08 -35.92 0 5.00e+00 4.00e-02 5.16e+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 -145.20 -34.80 0 5.00e+00 4.00e-02 4.85e+01 dihedral pdb=" CA LYS D 76 " pdb=" C LYS D 76 " pdb=" N ARG D 77 " pdb=" CA ARG D 77 " ideal model delta harmonic sigma weight residual 180.00 146.25 33.75 0 5.00e+00 4.00e-02 4.56e+01 ... (remaining 20442 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4347 0.066 - 0.132: 791 0.132 - 0.198: 82 0.198 - 0.264: 8 0.264 - 0.330: 3 Chirality restraints: 5231 Sorted by residual: 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 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CB VAL D1027 " pdb=" CA VAL D1027 " pdb=" CG1 VAL D1027 " pdb=" CG2 VAL D1027 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CB VAL F 333 " pdb=" CA VAL F 333 " pdb=" CG1 VAL F 333 " pdb=" CG2 VAL F 333 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 5228 not shown) Planarity restraints: 5614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 189 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.76e+00 pdb=" N PRO C 190 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 190 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 190 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 615 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.64e+00 pdb=" N PRO D 616 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO D 616 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 616 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C1061 " -0.043 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO C1062 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO C1062 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO C1062 " -0.036 5.00e-02 4.00e+02 ... (remaining 5611 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.63: 385 2.63 - 3.22: 28157 3.22 - 3.82: 54942 3.82 - 4.41: 68202 4.41 - 5.00: 117313 Nonbonded interactions: 268999 Sorted by model distance: nonbonded pdb=" O3' A 3 5 " pdb="MG MG D1503 " model vdw 2.039 2.170 nonbonded pdb=" OD1 ASP D 460 " pdb="MG MG D1503 " model vdw 2.114 2.170 nonbonded pdb=" OG1 THR F 583 " pdb=" OP2 DT 1 40 " model vdw 2.143 2.440 nonbonded pdb=" OD1 ASP D 464 " pdb="MG MG D1503 " model vdw 2.145 2.170 nonbonded pdb=" OD1 ASP D 462 " pdb="MG MG D1503 " model vdw 2.227 2.170 ... (remaining 268994 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 6 through 43 or (resid 44 through 45 and (name N or name C \ A or name C or name O or name CB or name CG or name CD or name NE or name CZ )) \ or resid 46 through 70 or (resid 71 and (name N or name CA or name C or name O o \ r name CB )) or resid 72 through 106 or (resid 107 and (name N or name CA or nam \ e C or name O or name CB )) or resid 108 through 232)) selection = (chain 'B' and (resid 6 through 67 or (resid 68 and (name N or name CA or name C \ or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name CE2 \ or name CZ )) or resid 69 through 151 or (resid 152 and (name N or name CA or n \ ame C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or nam \ e CE2 or name CZ )) or resid 153 through 232)) } ncs_group { reference = (chain 'G' and (resid 1 through 50 or (resid 51 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ )) or resid 52 \ 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 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: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.030 Extract box with map and model: 7.430 Check model and map are aligned: 0.510 Set scattering table: 0.350 Process input model: 101.210 Find NCS groups from input model: 1.270 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 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 : 0.006 0.074 33576 Z= 0.375 Angle : 0.797 10.789 45784 Z= 0.455 Chirality : 0.052 0.330 5231 Planarity : 0.006 0.070 5614 Dihedral : 16.285 128.708 13153 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.33 % Allowed : 6.58 % Favored : 93.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.65 % Twisted General : 0.13 % 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: -4.72 (0.10), residues: 3900 helix: -3.62 (0.08), residues: 1468 sheet: -2.29 (0.25), residues: 356 loop : -2.94 (0.11), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 115 HIS 0.008 0.001 HIS F 338 PHE 0.024 0.002 PHE C 514 TYR 0.017 0.002 TYR C 123 ARG 0.008 0.000 ARG C 180 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 473 time to evaluate : 3.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.8968 (tttt) cc_final: 0.8744 (tttp) REVERT: A 194 GLN cc_start: 0.7751 (mt0) cc_final: 0.7428 (pm20) REVERT: A 204 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7734 (tm-30) REVERT: C 107 ARG cc_start: 0.7498 (ttm-80) cc_final: 0.6987 (ttm-80) REVERT: C 117 ILE cc_start: 0.8218 (mm) cc_final: 0.7990 (tt) REVERT: C 562 GLU cc_start: 0.8206 (tp30) cc_final: 0.7851 (tp30) REVERT: C 1028 LYS cc_start: 0.8786 (mtpt) cc_final: 0.8499 (mtpp) REVERT: C 1188 ASP cc_start: 0.8109 (t0) cc_final: 0.7702 (t0) REVERT: C 1241 ASP cc_start: 0.7787 (m-30) cc_final: 0.7489 (t0) REVERT: D 29 MET cc_start: 0.7909 (tpp) cc_final: 0.7632 (mmt) REVERT: D 625 MET cc_start: 0.8834 (ttp) cc_final: 0.8127 (tmm) REVERT: D 725 MET cc_start: 0.9061 (mtt) cc_final: 0.8817 (mtt) REVERT: D 806 ASP cc_start: 0.8805 (p0) cc_final: 0.8572 (p0) REVERT: D 867 GLN cc_start: 0.7350 (tm-30) cc_final: 0.6903 (tm-30) REVERT: D 1143 ASP cc_start: 0.7442 (t0) cc_final: 0.7159 (t0) REVERT: D 1256 ILE cc_start: 0.8695 (pt) cc_final: 0.8469 (pt) REVERT: F 137 TYR cc_start: 0.6952 (t80) cc_final: 0.6282 (t80) REVERT: F 276 MET cc_start: 0.7814 (mtp) cc_final: 0.7420 (mtp) REVERT: F 291 CYS cc_start: 0.3526 (p) cc_final: 0.3083 (p) REVERT: F 430 TYR cc_start: 0.9288 (t80) cc_final: 0.8537 (t80) REVERT: F 489 MET cc_start: 0.7877 (mmm) cc_final: 0.7421 (mmm) REVERT: F 538 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7591 (tm-30) REVERT: G 59 ASN cc_start: 0.7514 (p0) cc_final: 0.7131 (p0) REVERT: G 122 ILE cc_start: 0.7589 (mt) cc_final: 0.7106 (pt) REVERT: H 15 LYS cc_start: 0.8206 (tptt) cc_final: 0.7974 (tppt) REVERT: H 19 PHE cc_start: 0.8670 (t80) cc_final: 0.8349 (t80) REVERT: H 52 GLN cc_start: 0.8786 (mm110) cc_final: 0.8345 (mp10) outliers start: 11 outliers final: 6 residues processed: 483 average time/residue: 0.5382 time to fit residues: 393.7569 Evaluate side-chains 344 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 338 time to evaluate : 3.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 1036 ARG Chi-restraints excluded: chain D residue 1261 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 336 optimal weight: 20.0000 chunk 301 optimal weight: 6.9990 chunk 167 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 203 optimal weight: 1.9990 chunk 161 optimal weight: 0.6980 chunk 311 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 361 optimal weight: 5.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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** C 273 HIS C 314 ASN C 673 HIS C 932 GLN C1136 GLN D 294 ASN D 341 ASN D 419 HIS D 488 ASN D 489 ASN D 665 GLN D 700 ASN D 875 ASN D 962 ASN D1197 ASN D1235 ASN D1249 ASN D1367 GLN E 43 ASN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 ASN F 461 ASN G 68 ASN G 104 GLN H 55 GLN H 110 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 33576 Z= 0.258 Angle : 0.570 13.980 45784 Z= 0.308 Chirality : 0.042 0.161 5231 Planarity : 0.004 0.054 5614 Dihedral : 15.101 129.507 5441 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.92 % Allowed : 11.43 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -3.36 (0.12), residues: 3900 helix: -2.05 (0.11), residues: 1473 sheet: -1.87 (0.24), residues: 393 loop : -2.46 (0.12), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 236 HIS 0.005 0.001 HIS D 430 PHE 0.013 0.001 PHE C1221 TYR 0.012 0.001 TYR C 47 ARG 0.010 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 350 time to evaluate : 3.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 LYS cc_start: 0.8899 (tttt) cc_final: 0.8697 (tttp) REVERT: A 131 CYS cc_start: 0.8393 (m) cc_final: 0.7722 (m) REVERT: A 194 GLN cc_start: 0.7768 (mt0) cc_final: 0.7483 (pm20) REVERT: B 93 GLN cc_start: 0.7925 (mm110) cc_final: 0.7616 (mm110) REVERT: C 107 ARG cc_start: 0.7466 (ttm-80) cc_final: 0.6984 (ttm-80) REVERT: C 124 MET cc_start: 0.8625 (ptp) cc_final: 0.8409 (ptm) REVERT: C 314 ASN cc_start: 0.8916 (OUTLIER) cc_final: 0.8660 (t0) REVERT: C 562 GLU cc_start: 0.8363 (tp30) cc_final: 0.8105 (tp30) REVERT: C 1003 THR cc_start: 0.5904 (OUTLIER) cc_final: 0.5545 (m) REVERT: C 1028 LYS cc_start: 0.8771 (mtpt) cc_final: 0.8545 (mtpp) REVERT: C 1188 ASP cc_start: 0.7930 (t0) cc_final: 0.7447 (t0) REVERT: C 1241 ASP cc_start: 0.7859 (m-30) cc_final: 0.7541 (t0) REVERT: D 29 MET cc_start: 0.7963 (tpp) cc_final: 0.7640 (mmt) REVERT: D 77 ARG cc_start: 0.7902 (ttp-170) cc_final: 0.7643 (ttp-170) REVERT: D 581 MET cc_start: 0.8513 (mtp) cc_final: 0.8275 (mtp) REVERT: D 725 MET cc_start: 0.8960 (mtt) cc_final: 0.8516 (mtt) REVERT: D 806 ASP cc_start: 0.8676 (p0) cc_final: 0.8428 (p0) REVERT: D 1025 MET cc_start: 0.8089 (ttm) cc_final: 0.7883 (ttp) REVERT: D 1143 ASP cc_start: 0.7612 (t0) cc_final: 0.7363 (t0) REVERT: D 1256 ILE cc_start: 0.8592 (pt) cc_final: 0.8383 (mt) REVERT: E 74 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7580 (mt-10) REVERT: F 276 MET cc_start: 0.7790 (mtp) cc_final: 0.7338 (mtp) REVERT: F 489 MET cc_start: 0.7603 (mmm) cc_final: 0.6874 (mmm) REVERT: F 538 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7611 (tm-30) REVERT: G 59 ASN cc_start: 0.7293 (p0) cc_final: 0.7059 (p0) REVERT: G 102 ARG cc_start: 0.8487 (ttt180) cc_final: 0.8096 (ptm160) REVERT: H 19 PHE cc_start: 0.8631 (t80) cc_final: 0.8343 (t80) REVERT: H 31 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7720 (tpp80) REVERT: H 42 GLN cc_start: 0.7471 (tt0) cc_final: 0.7266 (tt0) outliers start: 64 outliers final: 43 residues processed: 392 average time/residue: 0.4824 time to fit residues: 298.1568 Evaluate side-chains 369 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 323 time to evaluate : 3.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1133 LYS Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1036 ARG Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain F residue 148 TYR Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 94 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 200 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 300 optimal weight: 0.8980 chunk 246 optimal weight: 6.9990 chunk 99 optimal weight: 4.9990 chunk 362 optimal weight: 2.9990 chunk 391 optimal weight: 10.0000 chunk 322 optimal weight: 5.9990 chunk 359 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 290 optimal weight: 6.9990 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** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN C 273 HIS C1313 HIS D 232 ASN D1108 GLN D1197 ASN F 338 HIS G 99 GLN H 55 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 33576 Z= 0.350 Angle : 0.599 13.619 45784 Z= 0.318 Chirality : 0.043 0.159 5231 Planarity : 0.004 0.050 5614 Dihedral : 15.102 128.686 5441 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.60 % Allowed : 13.94 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.12), residues: 3900 helix: -1.28 (0.13), residues: 1469 sheet: -1.67 (0.25), residues: 393 loop : -2.25 (0.13), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 236 HIS 0.005 0.001 HIS D 430 PHE 0.019 0.001 PHE H 70 TYR 0.015 0.001 TYR F 137 ARG 0.006 0.000 ARG D1123 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 330 time to evaluate : 3.668 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.8329 (OUTLIER) cc_final: 0.7749 (m-80) REVERT: A 71 LYS cc_start: 0.8957 (tttt) cc_final: 0.8752 (tttp) REVERT: A 194 GLN cc_start: 0.7642 (mt0) cc_final: 0.7415 (pm20) REVERT: B 93 GLN cc_start: 0.7939 (mm110) cc_final: 0.7646 (mm110) REVERT: C 107 ARG cc_start: 0.7545 (ttm-80) cc_final: 0.7140 (ttm-80) REVERT: C 247 ARG cc_start: 0.7866 (mtt180) cc_final: 0.7612 (mtt-85) REVERT: C 272 ARG cc_start: 0.7048 (tmm160) cc_final: 0.5956 (ttp80) REVERT: C 562 GLU cc_start: 0.8405 (tp30) cc_final: 0.8102 (tp30) REVERT: C 1003 THR cc_start: 0.6055 (OUTLIER) cc_final: 0.5731 (m) REVERT: C 1188 ASP cc_start: 0.8036 (t0) cc_final: 0.7662 (t0) REVERT: C 1241 ASP cc_start: 0.7901 (m-30) cc_final: 0.7553 (t0) REVERT: C 1264 GLN cc_start: 0.8387 (tp-100) cc_final: 0.8136 (tp-100) REVERT: D 29 MET cc_start: 0.7956 (tpp) cc_final: 0.7633 (mmt) REVERT: D 77 ARG cc_start: 0.7791 (ttp-170) cc_final: 0.7057 (tmm-80) REVERT: D 301 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7543 (tm-30) REVERT: D 644 MET cc_start: 0.8151 (mtt) cc_final: 0.7939 (mtm) REVERT: D 725 MET cc_start: 0.8993 (mtt) cc_final: 0.8552 (mtt) REVERT: D 806 ASP cc_start: 0.8659 (p0) cc_final: 0.8456 (p0) REVERT: D 1143 ASP cc_start: 0.7681 (t0) cc_final: 0.7478 (t0) REVERT: F 276 MET cc_start: 0.7819 (mtp) cc_final: 0.7463 (mtp) REVERT: F 277 MET cc_start: 0.7551 (tpt) cc_final: 0.7342 (tpp) REVERT: F 291 CYS cc_start: 0.4211 (p) cc_final: 0.3863 (p) REVERT: F 489 MET cc_start: 0.7575 (mmm) cc_final: 0.7113 (mmm) REVERT: F 538 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7640 (tm-30) REVERT: G 59 ASN cc_start: 0.7178 (p0) cc_final: 0.6956 (p0) REVERT: H 1 MET cc_start: 0.3898 (tpt) cc_final: 0.3677 (tpt) REVERT: H 19 PHE cc_start: 0.8623 (t80) cc_final: 0.8333 (t80) REVERT: H 31 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7660 (tpp80) REVERT: H 52 GLN cc_start: 0.8810 (mm110) cc_final: 0.8222 (mp10) outliers start: 87 outliers final: 69 residues processed: 384 average time/residue: 0.4825 time to fit residues: 293.3668 Evaluate side-chains 384 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 312 time to evaluate : 3.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 273 HIS Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 839 VAL Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1133 LYS Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain C residue 1324 ASN Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 774 ILE Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1036 ARG Chi-restraints excluded: chain D residue 1197 ASN Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1248 ILE Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain F residue 148 TYR Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 505 ILE Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 80 VAL Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 94 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 357 optimal weight: 4.9990 chunk 272 optimal weight: 10.0000 chunk 187 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 172 optimal weight: 0.5980 chunk 243 optimal weight: 0.8980 chunk 363 optimal weight: 6.9990 chunk 384 optimal weight: 10.0000 chunk 189 optimal weight: 0.7980 chunk 344 optimal weight: 2.9990 chunk 103 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 314 ASN D 157 GLN D1197 ASN H 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 33576 Z= 0.158 Angle : 0.503 14.590 45784 Z= 0.270 Chirality : 0.040 0.150 5231 Planarity : 0.004 0.049 5614 Dihedral : 14.868 126.973 5441 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.24 % Allowed : 15.53 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.18 (0.13), residues: 3900 helix: -0.74 (0.13), residues: 1480 sheet: -1.47 (0.25), residues: 395 loop : -1.99 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 580 HIS 0.031 0.001 HIS C 273 PHE 0.017 0.001 PHE C1025 TYR 0.012 0.001 TYR F 137 ARG 0.012 0.000 ARG C 272 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 345 time to evaluate : 4.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 LYS cc_start: 0.8994 (mtpp) cc_final: 0.8760 (mttm) REVERT: A 84 ASN cc_start: 0.8688 (m110) cc_final: 0.8309 (m110) REVERT: C 107 ARG cc_start: 0.7506 (ttm-80) cc_final: 0.7139 (ttm-80) REVERT: C 314 ASN cc_start: 0.8796 (OUTLIER) cc_final: 0.8552 (t0) REVERT: C 562 GLU cc_start: 0.8356 (tp30) cc_final: 0.8083 (tp30) REVERT: C 800 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.8040 (mtm) REVERT: C 1003 THR cc_start: 0.5980 (OUTLIER) cc_final: 0.5670 (m) REVERT: C 1188 ASP cc_start: 0.7946 (t0) cc_final: 0.7627 (t0) REVERT: C 1241 ASP cc_start: 0.7848 (m-30) cc_final: 0.7517 (t0) REVERT: C 1315 MET cc_start: 0.7738 (tpp) cc_final: 0.7388 (tpp) REVERT: D 77 ARG cc_start: 0.7720 (ttp-170) cc_final: 0.7049 (tmm-80) REVERT: D 295 GLU cc_start: 0.8639 (tp30) cc_final: 0.8427 (tp30) REVERT: D 301 GLU cc_start: 0.7817 (tm-30) cc_final: 0.7429 (tm-30) REVERT: D 725 MET cc_start: 0.8925 (mtt) cc_final: 0.8471 (mtt) REVERT: D 806 ASP cc_start: 0.8640 (p0) cc_final: 0.8436 (p0) REVERT: D 1108 GLN cc_start: 0.2272 (OUTLIER) cc_final: 0.2057 (mt0) REVERT: D 1143 ASP cc_start: 0.7644 (t0) cc_final: 0.7436 (t0) REVERT: E 74 GLU cc_start: 0.8234 (tm-30) cc_final: 0.7546 (mt-10) REVERT: E 75 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8349 (tm-30) REVERT: F 276 MET cc_start: 0.7749 (mtp) cc_final: 0.7492 (mtp) REVERT: F 470 MET cc_start: 0.8548 (mmm) cc_final: 0.8315 (mmm) REVERT: F 489 MET cc_start: 0.7495 (mmm) cc_final: 0.7008 (mmm) REVERT: F 538 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7672 (tm-30) REVERT: G 102 ARG cc_start: 0.8321 (ttt180) cc_final: 0.7994 (ptm-80) REVERT: H 19 PHE cc_start: 0.8616 (t80) cc_final: 0.8051 (t80) REVERT: H 31 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7733 (tpp80) REVERT: H 52 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8308 (mp10) outliers start: 75 outliers final: 48 residues processed: 396 average time/residue: 0.5083 time to fit residues: 319.8523 Evaluate side-chains 373 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 320 time to evaluate : 3.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 314 ASN Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1133 LYS Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1324 ASN Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1108 GLN Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain F residue 148 TYR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 505 ILE Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain H residue 31 ARG Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 94 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 320 optimal weight: 0.7980 chunk 218 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 286 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 chunk 328 optimal weight: 10.0000 chunk 265 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 196 optimal weight: 6.9990 chunk 345 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN G 99 GLN H 55 GLN H 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 33576 Z= 0.316 Angle : 0.564 13.961 45784 Z= 0.298 Chirality : 0.042 0.148 5231 Planarity : 0.004 0.047 5614 Dihedral : 14.916 127.739 5437 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.05 % Allowed : 16.25 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.13), residues: 3900 helix: -0.53 (0.14), residues: 1479 sheet: -1.47 (0.25), residues: 409 loop : -1.92 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 236 HIS 0.005 0.001 HIS D 430 PHE 0.023 0.001 PHE H 70 TYR 0.016 0.001 TYR H 20 ARG 0.008 0.000 ARG C 332 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 309 time to evaluate : 3.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8713 (m110) cc_final: 0.8386 (m110) REVERT: B 18 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7707 (tp40) REVERT: C 107 ARG cc_start: 0.7559 (ttm-80) cc_final: 0.7188 (ttm-80) REVERT: C 562 GLU cc_start: 0.8385 (tp30) cc_final: 0.8101 (tp30) REVERT: C 1003 THR cc_start: 0.5931 (OUTLIER) cc_final: 0.5640 (m) REVERT: C 1188 ASP cc_start: 0.8011 (t0) cc_final: 0.7682 (t0) REVERT: C 1241 ASP cc_start: 0.7810 (m-30) cc_final: 0.7487 (t0) REVERT: D 77 ARG cc_start: 0.7769 (ttp-170) cc_final: 0.7178 (tmm-80) REVERT: D 301 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7533 (tm-30) REVERT: D 725 MET cc_start: 0.8988 (mtt) cc_final: 0.8568 (mtt) REVERT: F 276 MET cc_start: 0.7775 (mtp) cc_final: 0.7395 (mtp) REVERT: F 450 ILE cc_start: 0.9516 (OUTLIER) cc_final: 0.9254 (mm) REVERT: F 489 MET cc_start: 0.7551 (mmm) cc_final: 0.7057 (mmm) REVERT: F 538 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7689 (tm-30) REVERT: H 1 MET cc_start: 0.3781 (tpt) cc_final: 0.3555 (tpt) REVERT: H 19 PHE cc_start: 0.8824 (t80) cc_final: 0.8263 (t80) REVERT: H 31 ARG cc_start: 0.7905 (mtt90) cc_final: 0.7652 (tpp80) REVERT: H 52 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8269 (mp10) outliers start: 102 outliers final: 81 residues processed: 382 average time/residue: 0.4864 time to fit residues: 294.4402 Evaluate side-chains 388 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 304 time to evaluate : 3.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 356 THR Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 445 ILE Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 734 ILE Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 851 THR Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1133 LYS Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain C residue 1324 ASN Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 560 ASN Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1039 ASP Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 20 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 148 TYR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 505 ILE Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 94 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 129 optimal weight: 0.4980 chunk 346 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 225 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 385 optimal weight: 0.0770 chunk 319 optimal weight: 3.9990 chunk 178 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 202 optimal weight: 2.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1209 GLN H 55 GLN H 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 33576 Z= 0.147 Angle : 0.492 14.404 45784 Z= 0.262 Chirality : 0.039 0.146 5231 Planarity : 0.003 0.048 5614 Dihedral : 14.745 126.367 5437 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 2.54 % Allowed : 17.24 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.63 (0.13), residues: 3900 helix: -0.21 (0.14), residues: 1484 sheet: -1.12 (0.25), residues: 399 loop : -1.77 (0.13), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 580 HIS 0.002 0.000 HIS D 430 PHE 0.026 0.001 PHE H 70 TYR 0.015 0.001 TYR H 20 ARG 0.005 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 328 time to evaluate : 3.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8662 (m110) cc_final: 0.8327 (m110) REVERT: A 185 TYR cc_start: 0.9014 (p90) cc_final: 0.8683 (p90) REVERT: B 18 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7644 (tp40) REVERT: C 107 ARG cc_start: 0.7488 (ttm-80) cc_final: 0.7115 (ttm-80) REVERT: C 562 GLU cc_start: 0.8371 (tp30) cc_final: 0.8125 (tp30) REVERT: C 800 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.7981 (mtm) REVERT: C 1003 THR cc_start: 0.5966 (OUTLIER) cc_final: 0.5689 (m) REVERT: C 1188 ASP cc_start: 0.7918 (t0) cc_final: 0.7600 (t0) REVERT: C 1241 ASP cc_start: 0.7821 (m-30) cc_final: 0.7515 (t0) REVERT: C 1264 GLN cc_start: 0.8237 (tp-100) cc_final: 0.7886 (tp-100) REVERT: C 1315 MET cc_start: 0.7896 (tpp) cc_final: 0.7537 (mmm) REVERT: D 77 ARG cc_start: 0.7667 (ttp-170) cc_final: 0.7164 (tmm-80) REVERT: D 295 GLU cc_start: 0.8625 (tp30) cc_final: 0.8379 (tp30) REVERT: D 301 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7404 (tm-30) REVERT: D 698 MET cc_start: 0.8319 (tpp) cc_final: 0.8061 (mmt) REVERT: D 725 MET cc_start: 0.8921 (mtt) cc_final: 0.8484 (mtt) REVERT: D 812 ASP cc_start: 0.8133 (t0) cc_final: 0.7907 (t0) REVERT: D 1108 GLN cc_start: 0.2281 (OUTLIER) cc_final: 0.2008 (mt0) REVERT: D 1149 ARG cc_start: 0.8100 (ttm-80) cc_final: 0.7800 (mtp180) REVERT: E 55 GLU cc_start: 0.8073 (pp20) cc_final: 0.6806 (pp20) REVERT: E 56 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.8007 (mp0) REVERT: F 137 TYR cc_start: 0.6009 (t80) cc_final: 0.5766 (t80) REVERT: F 288 MET cc_start: 0.4243 (mtt) cc_final: 0.3765 (mtm) REVERT: F 450 ILE cc_start: 0.9479 (OUTLIER) cc_final: 0.9234 (mm) REVERT: F 489 MET cc_start: 0.7428 (mmm) cc_final: 0.6843 (mmm) REVERT: F 538 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7719 (tm-30) REVERT: G 102 ARG cc_start: 0.8381 (tmm-80) cc_final: 0.8107 (ptm-80) REVERT: H 19 PHE cc_start: 0.8748 (t80) cc_final: 0.8363 (t80) REVERT: H 31 ARG cc_start: 0.7946 (mtt90) cc_final: 0.7680 (tpp80) REVERT: H 52 GLN cc_start: 0.8998 (mm-40) cc_final: 0.8316 (mp10) REVERT: H 83 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7475 (mtm-85) REVERT: H 102 ARG cc_start: 0.7799 (ttp80) cc_final: 0.7372 (tmt-80) outliers start: 85 outliers final: 59 residues processed: 385 average time/residue: 0.4745 time to fit residues: 290.0808 Evaluate side-chains 380 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 315 time to evaluate : 3.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1133 LYS Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain C residue 1324 ASN Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1108 GLN Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 56 GLU Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 148 TYR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 94 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 371 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 219 optimal weight: 3.9990 chunk 281 optimal weight: 0.0970 chunk 217 optimal weight: 3.9990 chunk 324 optimal weight: 0.6980 chunk 215 optimal weight: 3.9990 chunk 383 optimal weight: 2.9990 chunk 240 optimal weight: 0.0170 chunk 233 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- 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** ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 273 HIS ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 33576 Z= 0.159 Angle : 0.491 12.930 45784 Z= 0.261 Chirality : 0.039 0.180 5231 Planarity : 0.004 0.092 5614 Dihedral : 14.694 128.039 5437 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.63 % Allowed : 17.62 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.41 (0.13), residues: 3900 helix: 0.02 (0.14), residues: 1485 sheet: -1.03 (0.26), residues: 409 loop : -1.67 (0.13), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 868 HIS 0.002 0.000 HIS D 430 PHE 0.027 0.001 PHE H 70 TYR 0.018 0.001 TYR H 20 ARG 0.009 0.000 ARG C 247 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 328 time to evaluate : 3.778 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8715 (m110) cc_final: 0.8422 (m-40) REVERT: A 185 TYR cc_start: 0.9019 (p90) cc_final: 0.8765 (p90) REVERT: B 18 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7580 (tp40) REVERT: C 107 ARG cc_start: 0.7445 (ttm-80) cc_final: 0.7113 (ttm-80) REVERT: C 315 MET cc_start: 0.7829 (tpt) cc_final: 0.7554 (tpt) REVERT: C 332 ARG cc_start: 0.7636 (mmm160) cc_final: 0.7305 (tpp80) REVERT: C 562 GLU cc_start: 0.8396 (tp30) cc_final: 0.8140 (tp30) REVERT: C 800 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8015 (mtm) REVERT: C 1003 THR cc_start: 0.6042 (OUTLIER) cc_final: 0.5774 (m) REVERT: C 1188 ASP cc_start: 0.7997 (t0) cc_final: 0.7669 (t0) REVERT: C 1241 ASP cc_start: 0.7753 (m-30) cc_final: 0.7438 (t0) REVERT: C 1264 GLN cc_start: 0.8229 (tp-100) cc_final: 0.7917 (tp-100) REVERT: C 1315 MET cc_start: 0.7848 (tpp) cc_final: 0.7585 (mmm) REVERT: C 1319 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7787 (ttt) REVERT: D 77 ARG cc_start: 0.7610 (ttp-170) cc_final: 0.7148 (tmm-80) REVERT: D 248 ASP cc_start: 0.8356 (m-30) cc_final: 0.8136 (t0) REVERT: D 298 MET cc_start: 0.8632 (mtm) cc_final: 0.8304 (mtm) REVERT: D 301 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7383 (tm-30) REVERT: D 725 MET cc_start: 0.8926 (mtt) cc_final: 0.8492 (mtt) REVERT: D 1123 ARG cc_start: 0.6353 (pmt170) cc_final: 0.6023 (mmt180) REVERT: D 1149 ARG cc_start: 0.8080 (ttm-80) cc_final: 0.7790 (mtp180) REVERT: E 55 GLU cc_start: 0.8089 (pp20) cc_final: 0.6816 (pp20) REVERT: F 450 ILE cc_start: 0.9455 (OUTLIER) cc_final: 0.9184 (mm) REVERT: F 489 MET cc_start: 0.7430 (mmm) cc_final: 0.6839 (mmm) REVERT: F 538 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7723 (tm-30) REVERT: G 102 ARG cc_start: 0.8442 (tmm-80) cc_final: 0.8004 (ptm-80) REVERT: H 19 PHE cc_start: 0.8756 (t80) cc_final: 0.8304 (t80) REVERT: H 31 ARG cc_start: 0.7885 (mtt90) cc_final: 0.7574 (tpp80) REVERT: H 52 GLN cc_start: 0.8923 (mm-40) cc_final: 0.8312 (mp10) REVERT: H 83 ARG cc_start: 0.7805 (mtm-85) cc_final: 0.7342 (mtm-85) REVERT: H 94 HIS cc_start: 0.8502 (OUTLIER) cc_final: 0.8084 (t-90) outliers start: 88 outliers final: 65 residues processed: 389 average time/residue: 0.4772 time to fit residues: 296.8968 Evaluate side-chains 386 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 315 time to evaluate : 3.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 18 GLN Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1133 LYS Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain C residue 1319 MET Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1120 THR Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1347 LEU Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain F residue 105 MET Chi-restraints excluded: chain F residue 148 TYR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 94 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 237 optimal weight: 3.9990 chunk 153 optimal weight: 0.3980 chunk 229 optimal weight: 0.4980 chunk 115 optimal weight: 0.4980 chunk 75 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 243 optimal weight: 9.9990 chunk 261 optimal weight: 0.3980 chunk 189 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 301 optimal weight: 7.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1017 GLN C1324 ASN D 153 ASN G 99 GLN H 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 33576 Z= 0.141 Angle : 0.493 14.123 45784 Z= 0.260 Chirality : 0.039 0.150 5231 Planarity : 0.003 0.046 5614 Dihedral : 14.642 128.607 5437 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.51 % Allowed : 18.25 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.13), residues: 3900 helix: 0.23 (0.14), residues: 1489 sheet: -0.85 (0.26), residues: 414 loop : -1.54 (0.14), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 868 HIS 0.002 0.000 HIS D 430 PHE 0.024 0.001 PHE H 70 TYR 0.020 0.001 TYR H 20 ARG 0.009 0.000 ARG H 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 332 time to evaluate : 3.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASN cc_start: 0.9457 (t0) cc_final: 0.9233 (t0) REVERT: A 84 ASN cc_start: 0.8709 (m110) cc_final: 0.8412 (m-40) REVERT: A 185 TYR cc_start: 0.8996 (p90) cc_final: 0.8796 (p90) REVERT: C 239 MET cc_start: 0.7844 (ptp) cc_final: 0.7622 (ptm) REVERT: C 276 GLN cc_start: 0.8484 (OUTLIER) cc_final: 0.8123 (tp-100) REVERT: C 315 MET cc_start: 0.7888 (tpt) cc_final: 0.7644 (tpt) REVERT: C 332 ARG cc_start: 0.7737 (mmm160) cc_final: 0.7406 (tpp80) REVERT: C 562 GLU cc_start: 0.8372 (tp30) cc_final: 0.8123 (tp30) REVERT: C 800 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8024 (mtm) REVERT: C 1003 THR cc_start: 0.6026 (OUTLIER) cc_final: 0.5768 (m) REVERT: C 1131 MET cc_start: 0.8418 (mtp) cc_final: 0.8216 (mtm) REVERT: C 1188 ASP cc_start: 0.7971 (t0) cc_final: 0.7629 (t0) REVERT: C 1241 ASP cc_start: 0.7721 (m-30) cc_final: 0.7429 (t0) REVERT: C 1264 GLN cc_start: 0.8207 (tp-100) cc_final: 0.7880 (tp-100) REVERT: C 1315 MET cc_start: 0.7708 (tpp) cc_final: 0.7452 (mmm) REVERT: D 77 ARG cc_start: 0.7559 (ttp-170) cc_final: 0.7103 (tmm-80) REVERT: D 295 GLU cc_start: 0.8614 (tp30) cc_final: 0.8340 (tp30) REVERT: D 301 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7337 (tm-30) REVERT: D 625 MET cc_start: 0.8899 (ttp) cc_final: 0.8278 (tmm) REVERT: D 725 MET cc_start: 0.8900 (mtt) cc_final: 0.8462 (mtt) REVERT: D 1123 ARG cc_start: 0.6273 (pmt170) cc_final: 0.6011 (mmm-85) REVERT: D 1149 ARG cc_start: 0.8056 (ttm-80) cc_final: 0.7782 (mtp180) REVERT: E 55 GLU cc_start: 0.7954 (pp20) cc_final: 0.7494 (pp20) REVERT: F 450 ILE cc_start: 0.9441 (OUTLIER) cc_final: 0.9193 (mm) REVERT: F 489 MET cc_start: 0.7393 (mmm) cc_final: 0.6807 (mmm) REVERT: F 538 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7711 (tm-30) REVERT: G 102 ARG cc_start: 0.8468 (tmm-80) cc_final: 0.8266 (ptm-80) REVERT: H 19 PHE cc_start: 0.8723 (t80) cc_final: 0.8273 (t80) REVERT: H 31 ARG cc_start: 0.7872 (mtt90) cc_final: 0.7533 (tpp80) REVERT: H 52 GLN cc_start: 0.8968 (mm-40) cc_final: 0.8337 (mp10) REVERT: H 75 ARG cc_start: 0.5116 (ptp90) cc_final: 0.4907 (ptp90) REVERT: H 82 ARG cc_start: 0.7289 (ptt90) cc_final: 0.6871 (ptt180) REVERT: H 93 ARG cc_start: 0.8478 (mtm180) cc_final: 0.8278 (mtm-85) REVERT: H 94 HIS cc_start: 0.8788 (OUTLIER) cc_final: 0.8371 (t-90) outliers start: 84 outliers final: 64 residues processed: 391 average time/residue: 0.4822 time to fit residues: 301.4376 Evaluate side-chains 385 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 316 time to evaluate : 4.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 276 GLN Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1133 LYS Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1347 LEU Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 19 LEU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain F residue 148 TYR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 94 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 348 optimal weight: 0.8980 chunk 367 optimal weight: 4.9990 chunk 335 optimal weight: 5.9990 chunk 357 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 155 optimal weight: 0.6980 chunk 280 optimal weight: 20.0000 chunk 109 optimal weight: 0.6980 chunk 323 optimal weight: 10.0000 chunk 338 optimal weight: 8.9990 chunk 356 optimal weight: 0.9980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33576 Z= 0.227 Angle : 0.521 13.412 45784 Z= 0.273 Chirality : 0.040 0.144 5231 Planarity : 0.003 0.046 5614 Dihedral : 14.701 129.782 5437 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.42 % Allowed : 18.37 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.11 (0.13), residues: 3900 helix: 0.26 (0.14), residues: 1492 sheet: -0.77 (0.26), residues: 402 loop : -1.52 (0.14), residues: 2006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 236 HIS 0.003 0.001 HIS D 430 PHE 0.012 0.001 PHE C 506 TYR 0.018 0.001 TYR H 20 ARG 0.007 0.000 ARG E 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 318 time to evaluate : 3.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 ASN cc_start: 0.8691 (m110) cc_final: 0.8406 (m-40) REVERT: A 185 TYR cc_start: 0.9024 (p90) cc_final: 0.8788 (p90) REVERT: C 239 MET cc_start: 0.7868 (ptp) cc_final: 0.7159 (tmm) REVERT: C 247 ARG cc_start: 0.7784 (mpt-90) cc_final: 0.7493 (mpt-90) REVERT: C 332 ARG cc_start: 0.7627 (mmm160) cc_final: 0.7283 (tpp80) REVERT: C 562 GLU cc_start: 0.8428 (tp30) cc_final: 0.8169 (tp30) REVERT: C 1003 THR cc_start: 0.6080 (OUTLIER) cc_final: 0.5815 (m) REVERT: C 1188 ASP cc_start: 0.7932 (t0) cc_final: 0.7608 (t0) REVERT: C 1241 ASP cc_start: 0.7752 (m-30) cc_final: 0.7453 (t0) REVERT: C 1264 GLN cc_start: 0.8248 (tp-100) cc_final: 0.7901 (tp-100) REVERT: C 1315 MET cc_start: 0.7999 (tpp) cc_final: 0.7759 (mmm) REVERT: D 77 ARG cc_start: 0.7608 (ttp-170) cc_final: 0.7058 (tmm-80) REVERT: D 301 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7443 (tm-30) REVERT: D 625 MET cc_start: 0.8882 (ttp) cc_final: 0.8269 (tmm) REVERT: D 725 MET cc_start: 0.8955 (mtt) cc_final: 0.8518 (mtt) REVERT: D 1149 ARG cc_start: 0.8037 (ttm-80) cc_final: 0.7757 (mtp180) REVERT: E 55 GLU cc_start: 0.7985 (pp20) cc_final: 0.7613 (pp20) REVERT: F 137 TYR cc_start: 0.6588 (t80) cc_final: 0.6200 (t80) REVERT: F 273 MET cc_start: 0.7727 (mmm) cc_final: 0.7426 (tmm) REVERT: F 288 MET cc_start: 0.4512 (mtt) cc_final: 0.4017 (mtm) REVERT: F 450 ILE cc_start: 0.9460 (OUTLIER) cc_final: 0.9182 (mm) REVERT: F 489 MET cc_start: 0.7447 (mmm) cc_final: 0.6976 (mmm) REVERT: F 538 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7739 (tm-30) REVERT: H 19 PHE cc_start: 0.8754 (t80) cc_final: 0.8312 (t80) REVERT: H 31 ARG cc_start: 0.7934 (mtt90) cc_final: 0.7602 (tpp80) REVERT: H 52 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8338 (mp10) REVERT: H 82 ARG cc_start: 0.7337 (ptt90) cc_final: 0.6967 (ptt180) REVERT: H 83 ARG cc_start: 0.7713 (mtm-85) cc_final: 0.7285 (mtm-85) REVERT: H 94 HIS cc_start: 0.8785 (OUTLIER) cc_final: 0.8397 (t-90) outliers start: 81 outliers final: 69 residues processed: 378 average time/residue: 0.4780 time to fit residues: 288.8112 Evaluate side-chains 389 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 317 time to evaluate : 3.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1133 LYS Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1347 LEU Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 55 GLN Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 94 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 234 optimal weight: 0.0870 chunk 378 optimal weight: 5.9990 chunk 230 optimal weight: 4.9990 chunk 179 optimal weight: 0.9980 chunk 262 optimal weight: 3.9990 chunk 396 optimal weight: 3.9990 chunk 364 optimal weight: 6.9990 chunk 315 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 243 optimal weight: 9.9990 chunk 193 optimal weight: 7.9990 overall best weight: 1.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1209 GLN D 153 ASN H 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 33576 Z= 0.323 Angle : 0.576 13.963 45784 Z= 0.301 Chirality : 0.042 0.155 5231 Planarity : 0.004 0.045 5614 Dihedral : 14.835 129.703 5437 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.33 % Allowed : 18.52 % Favored : 79.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.13), residues: 3900 helix: 0.17 (0.14), residues: 1483 sheet: -0.94 (0.26), residues: 418 loop : -1.52 (0.14), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 236 HIS 0.005 0.001 HIS D 430 PHE 0.014 0.001 PHE C 506 TYR 0.017 0.001 TYR H 20 ARG 0.007 0.000 ARG H 93 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7800 Ramachandran restraints generated. 3900 Oldfield, 0 Emsley, 3900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 313 time to evaluate : 3.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 185 TYR cc_start: 0.9022 (p90) cc_final: 0.8714 (p90) REVERT: C 315 MET cc_start: 0.7990 (tpt) cc_final: 0.7790 (tpt) REVERT: C 562 GLU cc_start: 0.8454 (tp30) cc_final: 0.8178 (tp30) REVERT: C 1003 THR cc_start: 0.6157 (OUTLIER) cc_final: 0.5879 (m) REVERT: C 1188 ASP cc_start: 0.8015 (t0) cc_final: 0.7708 (t0) REVERT: C 1241 ASP cc_start: 0.7781 (m-30) cc_final: 0.7483 (t0) REVERT: C 1264 GLN cc_start: 0.8429 (tp-100) cc_final: 0.8168 (tp-100) REVERT: D 77 ARG cc_start: 0.7722 (ttp-170) cc_final: 0.7118 (tmm-80) REVERT: D 301 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7560 (tm-30) REVERT: D 625 MET cc_start: 0.9012 (ttp) cc_final: 0.8358 (tmm) REVERT: D 725 MET cc_start: 0.8996 (mtt) cc_final: 0.8593 (mtt) REVERT: D 1123 ARG cc_start: 0.6401 (pmt170) cc_final: 0.5975 (mmm160) REVERT: D 1149 ARG cc_start: 0.8023 (ttm-80) cc_final: 0.7746 (mtp180) REVERT: D 1274 PHE cc_start: 0.7600 (t80) cc_final: 0.7393 (t80) REVERT: E 55 GLU cc_start: 0.8005 (pp20) cc_final: 0.7615 (pp20) REVERT: F 273 MET cc_start: 0.7700 (mmm) cc_final: 0.7423 (tmm) REVERT: F 288 MET cc_start: 0.4526 (mtt) cc_final: 0.4030 (mtm) REVERT: F 450 ILE cc_start: 0.9480 (OUTLIER) cc_final: 0.9195 (mm) REVERT: F 489 MET cc_start: 0.7537 (mmm) cc_final: 0.7064 (mmm) REVERT: F 538 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7745 (tm-30) REVERT: H 1 MET cc_start: 0.4390 (tpt) cc_final: 0.4156 (tpt) REVERT: H 19 PHE cc_start: 0.8758 (t80) cc_final: 0.8317 (t80) REVERT: H 31 ARG cc_start: 0.7815 (mtt90) cc_final: 0.7370 (tpp80) REVERT: H 52 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8296 (mp10) REVERT: H 82 ARG cc_start: 0.7453 (ptt90) cc_final: 0.7009 (ptt180) REVERT: H 94 HIS cc_start: 0.8929 (OUTLIER) cc_final: 0.8525 (t-90) outliers start: 78 outliers final: 70 residues processed: 370 average time/residue: 0.4846 time to fit residues: 286.1535 Evaluate side-chains 381 residues out of total 3366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 308 time to evaluate : 3.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 118 ASP Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 54 CYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain C residue 412 GLU Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain C residue 494 ASN Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 800 MET Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 888 THR Chi-restraints excluded: chain C residue 978 VAL Chi-restraints excluded: chain C residue 1003 THR Chi-restraints excluded: chain C residue 1133 LYS Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1159 VAL Chi-restraints excluded: chain C residue 1255 THR Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 180 MET Chi-restraints excluded: chain D residue 320 ASN Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 501 VAL Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 569 LEU Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 710 ASP Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 849 LEU Chi-restraints excluded: chain D residue 870 ASP Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 928 THR Chi-restraints excluded: chain D residue 985 ILE Chi-restraints excluded: chain D residue 1196 LEU Chi-restraints excluded: chain D residue 1209 VAL Chi-restraints excluded: chain D residue 1255 VAL Chi-restraints excluded: chain D residue 1261 LEU Chi-restraints excluded: chain D residue 1365 TYR Chi-restraints excluded: chain D residue 1366 HIS Chi-restraints excluded: chain E residue 8 ASP Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 36 ASP Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 53 GLU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain F residue 344 LEU Chi-restraints excluded: chain F residue 450 ILE Chi-restraints excluded: chain F residue 487 MET Chi-restraints excluded: chain F residue 524 GLU Chi-restraints excluded: chain F residue 547 VAL Chi-restraints excluded: chain F residue 591 GLU Chi-restraints excluded: chain G residue 13 THR Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 100 SER Chi-restraints excluded: chain H residue 23 LYS Chi-restraints excluded: chain H residue 94 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 398 random chunks: chunk 250 optimal weight: 0.9990 chunk 336 optimal weight: 20.0000 chunk 96 optimal weight: 0.6980 chunk 291 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 316 optimal weight: 0.3980 chunk 132 optimal weight: 5.9990 chunk 324 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1209 GLN H 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.110485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.081962 restraints weight = 63384.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.081627 restraints weight = 47149.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.082187 restraints weight = 38552.819| |-----------------------------------------------------------------------------| r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3022 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3022 r_free = 0.3022 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3022 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33576 Z= 0.167 Angle : 0.520 13.470 45784 Z= 0.271 Chirality : 0.040 0.143 5231 Planarity : 0.003 0.046 5614 Dihedral : 14.709 128.945 5437 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 2.24 % Allowed : 18.76 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -1.01 (0.14), residues: 3900 helix: 0.32 (0.14), residues: 1491 sheet: -0.69 (0.26), residues: 401 loop : -1.45 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 868 HIS 0.002 0.000 HIS D 430 PHE 0.012 0.001 PHE C1221 TYR 0.047 0.001 TYR F 137 ARG 0.006 0.000 ARG E 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6438.54 seconds wall clock time: 117 minutes 30.43 seconds (7050.43 seconds total)