Starting phenix.real_space_refine on Fri Mar 22 10:18:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w5w_32322/03_2024/7w5w_32322.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w5w_32322/03_2024/7w5w_32322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w5w_32322/03_2024/7w5w_32322.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w5w_32322/03_2024/7w5w_32322.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w5w_32322/03_2024/7w5w_32322.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w5w_32322/03_2024/7w5w_32322.pdb" } resolution = 4.55 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 125 5.49 5 Mg 1 5.21 5 S 133 5.16 5 C 20317 2.51 5 N 5871 2.21 5 O 6604 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A ASP 118": "OD1" <-> "OD2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 199": "OD1" <-> "OD2" Residue "A GLU 206": "OE1" <-> "OE2" Residue "A GLU 229": "OE1" <-> "OE2" Residue "A PHE 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 233": "OD1" <-> "OD2" Residue "A ASP 588": "OD1" <-> "OD2" Residue "A GLU 590": "OE1" <-> "OE2" Residue "B PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 60": "OE1" <-> "OE2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B GLU 136": "OE1" <-> "OE2" Residue "B GLU 163": "OE1" <-> "OE2" Residue "B ASP 164": "OD1" <-> "OD2" Residue "B GLU 193": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "C ASP 14": "OD1" <-> "OD2" Residue "C ASP 23": "OD1" <-> "OD2" Residue "C ASP 42": "OD1" <-> "OD2" Residue "C GLU 44": "OE1" <-> "OE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C ASP 160": "OD1" <-> "OD2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ASP 303": "OD1" <-> "OD2" Residue "C GLU 308": "OE1" <-> "OE2" Residue "C GLU 316": "OE1" <-> "OE2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C GLU 374": "OE1" <-> "OE2" Residue "C GLU 382": "OE1" <-> "OE2" Residue "C ASP 443": "OD1" <-> "OD2" Residue "C PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 545": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 611": "OE1" <-> "OE2" Residue "C ASP 624": "OD1" <-> "OD2" Residue "C GLU 626": "OE1" <-> "OE2" Residue "C ASP 696": "OD1" <-> "OD2" Residue "C TYR 726": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 728": "OD1" <-> "OD2" Residue "C GLU 740": "OE1" <-> "OE2" Residue "C TYR 751": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 826": "OD1" <-> "OD2" Residue "C ASP 853": "OD1" <-> "OD2" Residue "C ASP 881": "OD1" <-> "OD2" Residue "C GLU 892": "OE1" <-> "OE2" Residue "C GLU 899": "OE1" <-> "OE2" Residue "C GLU 949": "OE1" <-> "OE2" Residue "C GLU 987": "OE1" <-> "OE2" Residue "C ASP 995": "OD1" <-> "OD2" Residue "C GLU 999": "OE1" <-> "OE2" Residue "C ASP 1004": "OD1" <-> "OD2" Residue "C TYR 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1024": "OE1" <-> "OE2" Residue "C GLU 1030": "OE1" <-> "OE2" Residue "C GLU 1083": "OE1" <-> "OE2" Residue "C ASP 1160": "OD1" <-> "OD2" Residue "C ASP 1188": "OD1" <-> "OD2" Residue "C ASP 1214": "OD1" <-> "OD2" Residue "C PHE 1221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1289": "OE1" <-> "OE2" Residue "C ASP 1296": "OD1" <-> "OD2" Residue "C ASP 1341": "OD1" <-> "OD2" Residue "D PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D GLU 142": "OE1" <-> "OE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D ASP 167": "OD1" <-> "OD2" Residue "D ASP 174": "OD1" <-> "OD2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D ASP 267": "OD1" <-> "OD2" Residue "D TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 284": "OD1" <-> "OD2" Residue "D ASP 289": "OD1" <-> "OD2" Residue "D ASP 304": "OD1" <-> "OD2" Residue "D ASP 308": "OD1" <-> "OD2" Residue "D PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 404": "OE1" <-> "OE2" Residue "D ASP 413": "OD1" <-> "OD2" Residue "D GLU 418": "OE1" <-> "OE2" Residue "D PHE 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 534": "OE1" <-> "OE2" Residue "D ASP 558": "OD1" <-> "OD2" Residue "D ASP 571": "OD1" <-> "OD2" Residue "D GLU 648": "OE1" <-> "OE2" Residue "D GLU 656": "OE1" <-> "OE2" Residue "D GLU 666": "OE1" <-> "OE2" Residue "D ASP 691": "OD1" <-> "OD2" Residue "D GLU 713": "OE1" <-> "OE2" Residue "D PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 727": "OD1" <-> "OD2" Residue "D GLU 756": "OE1" <-> "OE2" Residue "D ASP 785": "OD1" <-> "OD2" Residue "D ASP 802": "OD1" <-> "OD2" Residue "D ASP 806": "OD1" <-> "OD2" Residue "D ASP 855": "OD1" <-> "OD2" Residue "D ASP 870": "OD1" <-> "OD2" Residue "D ASP 902": "OD1" <-> "OD2" Residue "D GLU 913": "OE1" <-> "OE2" Residue "D ASP 1042": "OD1" <-> "OD2" Residue "D PHE 1100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1239": "OD1" <-> "OD2" Residue "D PHE 1274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1276": "OE1" <-> "OE2" Residue "D TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 1305": "OD1" <-> "OD2" Residue "D ARG 1355": "NH1" <-> "NH2" Residue "E GLU 42": "OE1" <-> "OE2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E GLU 71": "OE1" <-> "OE2" Residue "E GLU 76": "OE1" <-> "OE2" Residue "F GLU 114": "OE1" <-> "OE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F ASP 125": "OD1" <-> "OD2" Residue "F TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 155": "OE1" <-> "OE2" Residue "F ASP 167": "OD1" <-> "OD2" Residue "F ASP 213": "OD1" <-> "OD2" Residue "F ASP 233": "OD1" <-> "OD2" Residue "F GLU 284": "OE1" <-> "OE2" Residue "F PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 328": "OE1" <-> "OE2" Residue "F ASP 332": "OD1" <-> "OD2" Residue "F GLU 378": "OE1" <-> "OE2" Residue "F TYR 394": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 445": "OD1" <-> "OD2" Residue "F GLU 473": "OE1" <-> "OE2" Residue "F ASP 514": "OD1" <-> "OD2" Residue "F PHE 522": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 524": "OE1" <-> "OE2" Residue "F GLU 538": "OE1" <-> "OE2" Residue "F GLU 555": "OE1" <-> "OE2" Residue "F PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 65": "OE1" <-> "OE2" Residue "J PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 79": "OD1" <-> "OD2" Residue "J PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33053 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2418 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 296} Chain breaks: 1 Chain: "B" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1767 Classifications: {'peptide': 228} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 218} Chain: "C" Number of atoms: 10528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1336, 10528 Classifications: {'peptide': 1336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 1282} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 10344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1335, 10344 Classifications: {'peptide': 1335} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 1, 'PTRANS': 53, 'TRANS': 1280} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "F" Number of atoms: 3861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3861 Classifications: {'peptide': 481} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 14, 'TRANS': 466} Chain breaks: 3 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 4, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "1" Number of atoms: 1288 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1288 Classifications: {'DNA': 63} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 62} Chain: "2" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 1305 Classifications: {'DNA': 63} Link IDs: {'rna3p': 62} Chain: "J" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 912 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 103} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15317 SG CYS D 88 119.413 89.804 73.674 1.00219.36 S ATOM 21530 SG CYS D 888 85.095 106.273 128.900 1.00 87.42 S ATOM 21581 SG CYS D 895 84.338 103.229 130.693 1.00 90.57 S Time building chain proxies: 16.45, per 1000 atoms: 0.50 Number of scatterers: 33053 At special positions: 0 Unit cell: (177.1, 199.1, 166.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 133 16.00 P 125 15.00 Mg 1 11.99 O 6604 8.00 N 5871 7.00 C 20317 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.87 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D1501 " pdb="ZN ZN D1501 " - pdb=" SG CYS D 88 " pdb=" ZN D1502 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 895 " pdb="ZN ZN D1502 " - pdb=" SG CYS D 888 " 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7210 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 43 sheets defined 39.5% alpha, 10.9% beta 27 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 10.26 Creating SS restraints... Processing helix chain 'A' and resid 35 through 48 removed outlier: 3.559A pdb=" N ARG A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 85 Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 156 through 162 Processing helix chain 'A' and resid 212 through 227 removed outlier: 4.044A pdb=" N ILE A 217 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 583 removed outlier: 3.643A pdb=" N LEU A 583 " --> pdb=" O PRO A 580 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 600 removed outlier: 4.190A pdb=" N LYS A 600 " --> pdb=" O ALA A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 601 through 603 No H-bonds generated for 'chain 'A' and resid 601 through 603' Processing helix chain 'A' and resid 628 through 638 removed outlier: 3.580A pdb=" N VAL A 635 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 636 " --> pdb=" O ILE A 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 removed outlier: 4.172A pdb=" N ARG B 45 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU B 48 " --> pdb=" O ARG B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.696A pdb=" N ILE B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASN B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 85 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 228 removed outlier: 3.668A pdb=" N ILE B 217 " --> pdb=" O PRO B 213 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG B 218 " --> pdb=" O GLU B 214 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 232 removed outlier: 3.697A pdb=" N VAL B 232 " --> pdb=" O GLU B 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 229 through 232' Processing helix chain 'C' and resid 4 through 9 Processing helix chain 'C' and resid 28 through 40 removed outlier: 4.094A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ILE C 39 " --> pdb=" O PHE C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 55 removed outlier: 4.062A pdb=" N ALA C 52 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N PHE C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.607A pdb=" N CYS C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE C 87 " --> pdb=" O GLN C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 213 removed outlier: 3.884A pdb=" N LEU C 210 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 225 removed outlier: 3.672A pdb=" N ASP C 222 " --> pdb=" O GLU C 218 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N LEU C 223 " --> pdb=" O GLN C 219 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE C 224 " --> pdb=" O ILE C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 280 removed outlier: 3.659A pdb=" N ASP C 280 " --> pdb=" O GLN C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.797A pdb=" N ILE C 292 " --> pdb=" O VAL C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 329 removed outlier: 3.608A pdb=" N SER C 326 " --> pdb=" O LEU C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 354 removed outlier: 3.757A pdb=" N VAL C 353 " --> pdb=" O GLU C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 370 removed outlier: 3.604A pdb=" N ALA C 362 " --> pdb=" O ASP C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.653A pdb=" N PHE C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 409 removed outlier: 3.574A pdb=" N LYS C 404 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C 409 " --> pdb=" O PHE C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.532A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ILE C 426 " --> pdb=" O LYS C 422 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN C 437 " --> pdb=" O ILE C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 476 removed outlier: 3.636A pdb=" N GLU C 461 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASN C 462 " --> pdb=" O GLU C 458 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLN C 463 " --> pdb=" O MET C 459 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N PHE C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS C 476 " --> pdb=" O GLU C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 481 removed outlier: 3.707A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 493 removed outlier: 4.119A pdb=" N MET C 492 " --> pdb=" O MET C 488 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ILE C 493 " --> pdb=" O PRO C 489 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 488 through 493' Processing helix chain 'C' and resid 495 through 506 removed outlier: 4.570A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N VAL C 502 " --> pdb=" O ILE C 498 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE C 505 " --> pdb=" O ALA C 501 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE C 506 " --> pdb=" O VAL C 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 525 Processing helix chain 'C' and resid 609 through 614 Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.589A pdb=" N LEU C 667 " --> pdb=" O GLY C 664 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 removed outlier: 3.686A pdb=" N HIS C 673 " --> pdb=" O PHE C 670 " (cutoff:3.500A) Processing helix chain 'C' and resid 675 through 683 removed outlier: 3.998A pdb=" N ALA C 679 " --> pdb=" O ASP C 675 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N MET C 681 " --> pdb=" O ASN C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 710 removed outlier: 3.802A pdb=" N VAL C 710 " --> pdb=" O ARG C 706 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 897 through 907 removed outlier: 3.620A pdb=" N LEU C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE C 906 " --> pdb=" O LEU C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 972 removed outlier: 3.827A pdb=" N LYS C 958 " --> pdb=" O LYS C 954 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASP C 959 " --> pdb=" O GLN C 955 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE C 966 " --> pdb=" O GLU C 962 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU C 967 " --> pdb=" O GLU C 963 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU C 968 " --> pdb=" O LEU C 964 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA C 969 " --> pdb=" O GLN C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.525A pdb=" N ALA C 977 " --> pdb=" O SER C 973 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA C 981 " --> pdb=" O ALA C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 997 removed outlier: 3.609A pdb=" N ARG C 996 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP C 997 " --> pdb=" O ARG C 994 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 993 through 997' Processing helix chain 'C' and resid 1008 through 1038 removed outlier: 3.555A pdb=" N GLU C1016 " --> pdb=" O GLU C1012 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN C1017 " --> pdb=" O GLN C1013 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR C1018 " --> pdb=" O LEU C1014 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP C1019 " --> pdb=" O ALA C1015 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS C1022 " --> pdb=" O TYR C1018 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLU C1026 " --> pdb=" O LYS C1022 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N LYS C1027 " --> pdb=" O HIS C1023 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS C1028 " --> pdb=" O GLU C1024 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS C1032 " --> pdb=" O LYS C1028 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE C1036 " --> pdb=" O LYS C1032 " (cutoff:3.500A) Processing helix chain 'C' and resid 1108 through 1133 removed outlier: 4.177A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS C1116 " --> pdb=" O ILE C1112 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU C1117 " --> pdb=" O LEU C1113 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLY C1118 " --> pdb=" O GLU C1114 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY C1125 " --> pdb=" O ALA C1121 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS C1127 " --> pdb=" O GLY C1123 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE C1128 " --> pdb=" O ILE C1124 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS C1133 " --> pdb=" O ASN C1129 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1150 removed outlier: 3.653A pdb=" N GLU C1143 " --> pdb=" O ALA C1139 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN C1146 " --> pdb=" O ARG C1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1164 removed outlier: 3.832A pdb=" N THR C1163 " --> pdb=" O ASP C1160 " (cutoff:3.500A) Processing helix chain 'C' and resid 1165 through 1173 removed outlier: 3.513A pdb=" N VAL C1169 " --> pdb=" O SER C1165 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.773A pdb=" N LEU C1198 " --> pdb=" O GLU C1194 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS C1200 " --> pdb=" O LYS C1196 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C1201 " --> pdb=" O GLU C1197 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1242 Processing helix chain 'C' and resid 1271 through 1282 removed outlier: 3.742A pdb=" N GLU C1279 " --> pdb=" O VAL C1275 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA C1280 " --> pdb=" O TRP C1276 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR C1281 " --> pdb=" O ALA C1277 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1290 removed outlier: 3.593A pdb=" N LEU C1287 " --> pdb=" O ALA C1283 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLN C1288 " --> pdb=" O ALA C1284 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU C1289 " --> pdb=" O TYR C1285 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N MET C1290 " --> pdb=" O THR C1286 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1283 through 1290' Processing helix chain 'C' and resid 1300 through 1308 removed outlier: 3.642A pdb=" N MET C1304 " --> pdb=" O GLY C1300 " (cutoff:3.500A) Processing helix chain 'C' and resid 1322 through 1332 Processing helix chain 'D' and resid 26 through 34 removed outlier: 3.692A pdb=" N TRP D 33 " --> pdb=" O MET D 29 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER D 34 " --> pdb=" O ILE D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 140 removed outlier: 3.524A pdb=" N ARG D 137 " --> pdb=" O ARG D 133 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL D 138 " --> pdb=" O ASP D 134 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU D 139 " --> pdb=" O ILE D 135 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 172 Processing helix chain 'D' and resid 181 through 192 removed outlier: 3.879A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 206 removed outlier: 3.515A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN D 200 " --> pdb=" O GLN D 196 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASN D 206 " --> pdb=" O ARG D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 231 removed outlier: 3.732A pdb=" N LYS D 216 " --> pdb=" O THR D 212 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG D 220 " --> pdb=" O LYS D 216 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLU D 225 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ALA D 226 " --> pdb=" O LYS D 222 " (cutoff:3.500A) removed outlier: 3.532A 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 284 removed outlier: 3.661A pdb=" N LEU D 268 " --> pdb=" O ASP D 264 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ARG D 270 " --> pdb=" O ASN D 266 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASN D 274 " --> pdb=" O ARG D 270 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 279 " --> pdb=" O ARG D 275 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU D 282 " --> pdb=" O ARG D 278 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 308 removed outlier: 3.751A pdb=" N MET D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU D 299 " --> pdb=" O GLU D 295 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN D 300 " --> pdb=" O LYS D 296 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP D 304 " --> pdb=" O GLN D 300 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 307 " --> pdb=" O VAL D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 336 through 342 removed outlier: 3.789A pdb=" N GLN D 340 " --> pdb=" O GLY D 336 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASN D 341 " --> pdb=" O ARG D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 389 Processing helix chain 'D' and resid 393 through 401 Processing helix chain 'D' and resid 405 through 417 removed outlier: 3.703A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG D 417 " --> pdb=" O ASP D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 434 removed outlier: 4.254A pdb=" N ILE D 434 " --> pdb=" O ARG D 431 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 452 No H-bonds generated for 'chain 'D' and resid 450 through 452' Processing helix chain 'D' and resid 453 through 458 removed outlier: 3.665A pdb=" N TYR D 457 " --> pdb=" O VAL D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 484 removed outlier: 4.187A pdb=" N ARG D 481 " --> pdb=" O GLN D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 489 removed outlier: 3.760A pdb=" N ASN D 489 " --> pdb=" O SER D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 514 Processing helix chain 'D' and resid 529 through 539 removed outlier: 3.565A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) Processing helix chain 'D' and resid 574 through 579 removed outlier: 3.755A pdb=" N ILE D 578 " --> pdb=" O VAL D 574 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU D 579 " --> pdb=" O GLY D 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 574 through 579' Processing helix chain 'D' and resid 580 through 582 No H-bonds generated for 'chain 'D' and resid 580 through 582' Processing helix chain 'D' and resid 588 through 593 removed outlier: 3.942A pdb=" N ILE D 591 " --> pdb=" O PRO D 588 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ASN D 593 " --> pdb=" O SER D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 removed outlier: 3.809A pdb=" N SER D 602 " --> pdb=" O LYS D 598 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS D 603 " --> pdb=" O LYS D 599 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N CYS D 608 " --> pdb=" O MET D 604 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR D 609 " --> pdb=" O LEU D 605 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG D 610 " --> pdb=" O ASN D 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.710A pdb=" N ILE D 619 " --> pdb=" O LYS D 615 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE D 624 " --> pdb=" O PHE D 620 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N MET D 625 " --> pdb=" O ALA D 621 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR D 626 " --> pdb=" O ASP D 622 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR D 627 " --> pdb=" O GLN D 623 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA D 630 " --> pdb=" O TYR D 626 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR D 631 " --> pdb=" O THR D 627 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG D 634 " --> pdb=" O ALA D 630 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 662 removed outlier: 3.708A pdb=" N ALA D 662 " --> pdb=" O GLU D 658 " (cutoff:3.500A) Processing helix chain 'D' and resid 662 through 671 removed outlier: 3.677A pdb=" N GLU D 666 " --> pdb=" O ALA D 662 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN D 669 " --> pdb=" O GLN D 665 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY D 671 " --> pdb=" O GLN D 667 " (cutoff:3.500A) Processing helix chain 'D' and resid 675 through 686 removed outlier: 3.801A pdb=" N ILE D 683 " --> pdb=" O TYR D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 693 Processing helix chain 'D' and resid 693 through 703 removed outlier: 3.641A pdb=" N MET D 697 " --> pdb=" O VAL D 693 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP D 699 " --> pdb=" O LYS D 695 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR D 703 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing helix chain 'D' and resid 722 through 727 Processing helix chain 'D' and resid 768 through 775 Processing helix chain 'D' and resid 776 through 802 removed outlier: 4.055A pdb=" N GLY D 782 " --> pdb=" O GLY D 778 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA D 784 " --> pdb=" O ARG D 780 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP D 785 " --> pdb=" O LYS D 781 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA D 787 " --> pdb=" O LEU D 783 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU D 788 " --> pdb=" O ALA D 784 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP D 802 " --> pdb=" O ARG D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 834 through 840 removed outlier: 3.612A pdb=" N ARG D 838 " --> pdb=" O PRO D 834 " (cutoff:3.500A) Processing helix chain 'D' and resid 865 through 875 removed outlier: 4.263A pdb=" N LEU D 871 " --> pdb=" O GLN D 867 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN D 875 " --> pdb=" O LEU D 871 " (cutoff:3.500A) Processing helix chain 'D' and resid 896 through 900 Processing helix chain 'D' and resid 915 through 925 removed outlier: 3.774A pdb=" N SER D 922 " --> pdb=" O ILE D 918 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY D 924 " --> pdb=" O ALA D 920 " (cutoff:3.500A) Processing helix chain 'D' and resid 926 through 930 Processing helix chain 'D' and resid 1068 through 1072 removed outlier: 3.619A pdb=" N GLY D1071 " --> pdb=" O THR D1068 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS D1072 " --> pdb=" O ALA D1069 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1068 through 1072' Processing helix chain 'D' and resid 1138 through 1147 removed outlier: 4.078A pdb=" N PHE D1145 " --> pdb=" O VAL D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.528A pdb=" N ILE D1220 " --> pdb=" O ALA D1216 " (cutoff:3.500A) Processing helix chain 'D' and resid 1226 through 1244 removed outlier: 3.635A pdb=" N ASN D1235 " --> pdb=" O ARG D1231 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN D1238 " --> pdb=" O VAL D1234 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP D1239 " --> pdb=" O ASN D1235 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR D1241 " --> pdb=" O VAL D1237 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1259 removed outlier: 4.369A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL D1255 " --> pdb=" O LYS D1251 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL D1257 " --> pdb=" O ILE D1253 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1287 removed outlier: 3.743A pdb=" N ARG D1284 " --> pdb=" O VAL D1280 " (cutoff:3.500A) Processing helix chain 'D' and resid 1319 through 1324 Processing helix chain 'D' and resid 1327 through 1337 removed outlier: 4.084A pdb=" N LEU D1332 " --> pdb=" O THR D1328 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU D1334 " --> pdb=" O ARG D1330 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA D1335 " --> pdb=" O VAL D1331 " (cutoff:3.500A) Processing helix chain 'D' and resid 1348 through 1353 removed outlier: 3.525A pdb=" N VAL D1353 " --> pdb=" O GLU D1349 " (cutoff:3.500A) Processing helix chain 'D' and resid 1362 through 1373 removed outlier: 3.844A pdb=" N GLN D1367 " --> pdb=" O TYR D1363 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ASP D1368 " --> pdb=" O ALA D1364 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG D1369 " --> pdb=" O TYR D1365 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG D1371 " --> pdb=" O GLN D1367 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 14 removed outlier: 3.961A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 30 removed outlier: 3.541A pdb=" N VAL E 20 " --> pdb=" O ARG E 16 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ALA E 23 " --> pdb=" O LEU E 19 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 56 removed outlier: 4.308A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG E 52 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU E 53 " --> pdb=" O ILE E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 80 removed outlier: 4.193A pdb=" N ASP E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLU E 68 " --> pdb=" O LEU E 64 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU E 74 " --> pdb=" O GLN E 70 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA E 77 " --> pdb=" O GLN E 73 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLU E 79 " --> pdb=" O GLN E 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 106 removed outlier: 3.698A pdb=" N MET F 100 " --> pdb=" O ASP F 96 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N MET F 102 " --> pdb=" O VAL F 98 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU F 104 " --> pdb=" O MET F 100 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY F 106 " --> pdb=" O MET F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 135 removed outlier: 3.946A pdb=" N GLY F 126 " --> pdb=" O ARG F 122 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE F 127 " --> pdb=" O ILE F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 142 removed outlier: 4.269A pdb=" N THR F 142 " --> pdb=" O PRO F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 152 removed outlier: 3.695A pdb=" N TYR F 148 " --> pdb=" O LEU F 144 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 155 No H-bonds generated for 'chain 'F' and resid 153 through 155' Processing helix chain 'F' and resid 213 through 218 removed outlier: 3.642A pdb=" N ALA F 217 " --> pdb=" O ASP F 213 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG F 218 " --> pdb=" O PRO F 214 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 213 through 218' Processing helix chain 'F' and resid 219 through 237 removed outlier: 3.650A pdb=" N GLU F 223 " --> pdb=" O GLU F 219 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU F 224 " --> pdb=" O LYS F 220 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG F 225 " --> pdb=" O PHE F 221 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA F 226 " --> pdb=" O ALA F 222 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL F 230 " --> pdb=" O ALA F 226 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR F 231 " --> pdb=" O GLN F 227 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA F 237 " --> pdb=" O ASP F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 242 through 257 removed outlier: 3.649A pdb=" N ILE F 249 " --> pdb=" O ALA F 245 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 291 removed outlier: 3.555A pdb=" N VAL F 270 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL F 275 " --> pdb=" O ASN F 271 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N MET F 276 " --> pdb=" O SER F 272 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG F 281 " --> pdb=" O MET F 277 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE F 287 " --> pdb=" O GLN F 283 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS F 289 " --> pdb=" O ARG F 285 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU F 290 " --> pdb=" O LEU F 286 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N CYS F 291 " --> pdb=" O ILE F 287 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 307 removed outlier: 3.868A pdb=" N THR F 307 " --> pdb=" O ILE F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 319 Processing helix chain 'F' and resid 325 through 329 removed outlier: 3.967A pdb=" N GLU F 328 " --> pdb=" O PRO F 325 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LYS F 329 " --> pdb=" O TRP F 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 325 through 329' Processing helix chain 'F' and resid 334 through 352 removed outlier: 3.607A pdb=" N HIS F 338 " --> pdb=" O SER F 334 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LYS F 343 " --> pdb=" O ARG F 339 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU F 344 " --> pdb=" O ALA F 340 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ILE F 347 " --> pdb=" O LYS F 343 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU F 348 " --> pdb=" O LEU F 344 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLU F 349 " --> pdb=" O GLN F 345 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU F 350 " --> pdb=" O GLN F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 383 removed outlier: 4.007A pdb=" N LYS F 359 " --> pdb=" O ILE F 355 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASP F 360 " --> pdb=" O GLU F 356 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N ILE F 361 " --> pdb=" O GLN F 357 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER F 366 " --> pdb=" O ASN F 362 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY F 368 " --> pdb=" O ARG F 364 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA F 370 " --> pdb=" O SER F 366 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA F 375 " --> pdb=" O LYS F 371 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS F 376 " --> pdb=" O ALA F 372 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS F 377 " --> pdb=" O ARG F 373 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU F 378 " --> pdb=" O ARG F 374 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN F 383 " --> pdb=" O MET F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 394 removed outlier: 3.570A pdb=" N ILE F 388 " --> pdb=" O LEU F 384 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS F 393 " --> pdb=" O SER F 389 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 418 removed outlier: 4.029A pdb=" N LEU F 404 " --> pdb=" O GLN F 400 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY F 408 " --> pdb=" O LEU F 404 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASN F 409 " --> pdb=" O ILE F 405 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ILE F 410 " --> pdb=" O GLN F 406 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY F 411 " --> pdb=" O GLU F 407 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASP F 417 " --> pdb=" O MET F 413 " (cutoff:3.500A) Processing helix chain 'F' and resid 420 through 424 removed outlier: 3.594A pdb=" N ARG F 423 " --> pdb=" O GLU F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 443 removed outlier: 4.226A pdb=" N TYR F 430 " --> pdb=" O LYS F 426 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR F 432 " --> pdb=" O SER F 428 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TRP F 433 " --> pdb=" O THR F 429 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N TRP F 434 " --> pdb=" O TYR F 430 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE F 435 " --> pdb=" O ALA F 431 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER F 442 " --> pdb=" O ALA F 438 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 474 removed outlier: 3.702A pdb=" N ILE F 457 " --> pdb=" O PRO F 453 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU F 458 " --> pdb=" O VAL F 454 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR F 459 " --> pdb=" O HIS F 455 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE F 466 " --> pdb=" O LYS F 462 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG F 468 " --> pdb=" O ASN F 464 " (cutoff:3.500A) Processing helix chain 'F' and resid 479 through 487 Processing helix chain 'F' and resid 490 through 498 removed outlier: 3.618A pdb=" N ILE F 494 " --> pdb=" O PRO F 490 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU F 498 " --> pdb=" O ILE F 494 " (cutoff:3.500A) Processing helix chain 'F' and resid 499 through 501 No H-bonds generated for 'chain 'F' and resid 499 through 501' Processing helix chain 'F' and resid 518 through 522 Processing helix chain 'F' and resid 530 through 550 removed outlier: 3.842A pdb=" N SER F 534 " --> pdb=" O LEU F 530 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA F 535 " --> pdb=" O PRO F 531 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU F 538 " --> pdb=" O SER F 534 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER F 539 " --> pdb=" O ALA F 535 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG F 541 " --> pdb=" O THR F 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 554 through 556 No H-bonds generated for 'chain 'F' and resid 554 through 556' Processing helix chain 'F' and resid 557 through 564 removed outlier: 3.684A pdb=" N MET F 561 " --> pdb=" O LYS F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 577 removed outlier: 3.567A pdb=" N VAL F 576 " --> pdb=" O THR F 572 " (cutoff:3.500A) Processing helix chain 'F' and resid 590 through 600 removed outlier: 3.797A pdb=" N ALA F 594 " --> pdb=" O ILE F 590 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU F 598 " --> pdb=" O ALA F 594 " (cutoff:3.500A) Processing helix chain 'F' and resid 603 through 607 removed outlier: 3.706A pdb=" N VAL F 606 " --> pdb=" O ARG F 603 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 613 removed outlier: 3.806A pdb=" N ASP F 612 " --> pdb=" O SER F 609 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP F 613 " --> pdb=" O PHE F 610 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 17 removed outlier: 3.656A pdb=" N ILE J 6 " --> pdb=" O SER J 2 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ALA J 12 " --> pdb=" O GLN J 8 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N TRP J 13 " --> pdb=" O ASP J 9 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE J 14 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ASP J 15 " --> pdb=" O ILE J 11 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS J 17 " --> pdb=" O TRP J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 23 through 32 removed outlier: 3.682A pdb=" N VAL J 27 " --> pdb=" O ASN J 23 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS J 30 " --> pdb=" O VAL J 26 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 42 Processing helix chain 'J' and resid 42 through 47 Processing helix chain 'J' and resid 52 through 69 removed outlier: 3.813A pdb=" N ARG J 58 " --> pdb=" O ILE J 54 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL J 64 " --> pdb=" O LEU J 60 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU J 66 " --> pdb=" O ALA J 62 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG J 67 " --> pdb=" O ALA J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 84 through 96 removed outlier: 4.236A pdb=" N ARG J 94 " --> pdb=" O ARG J 90 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLN J 95 " --> pdb=" O VAL J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 106 removed outlier: 3.534A pdb=" N ARG J 104 " --> pdb=" O PRO J 100 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 3.526A pdb=" N GLU A 29 " --> pdb=" O ARG A 12 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL A 14 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N THR A 27 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N ILE A 16 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N LYS A 25 " --> pdb=" O ILE A 16 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N GLN A 18 " --> pdb=" O HIS A 23 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N HIS A 23 " --> pdb=" O GLN A 18 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ASP A 199 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 184 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 97 through 99 Processing sheet with id=AA3, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.828A pdb=" N GLN A 147 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL A 56 " --> pdb=" O GLN A 147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA5, first strand: chain 'A' and resid 108 through 109 Processing sheet with id=AA6, first strand: chain 'B' and resid 12 through 18 removed outlier: 6.089A pdb=" N LEU B 13 " --> pdb=" O GLU B 29 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLU B 29 " --> pdb=" O LEU B 13 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASP B 15 " --> pdb=" O THR B 27 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS B 25 " --> pdb=" O GLU B 17 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B 24 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET B 205 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU B 198 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL B 202 " --> pdb=" O ASN B 186 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 115 through 116 removed outlier: 4.269A pdb=" N THR B 101 " --> pdb=" O THR B 116 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL B 98 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL B 146 " --> pdb=" O VAL B 98 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 102 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N MET B 142 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS B 104 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N SER B 141 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ILE B 61 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ARG B 143 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL B 59 " --> pdb=" O ARG B 143 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL B 59 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AA9, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.610A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 66 through 75 removed outlier: 4.642A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA C 94 " --> pdb=" O ILE C 127 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU C 100 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N GLU C 121 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 137 removed outlier: 3.679A pdb=" N VAL C 144 " --> pdb=" O GLN C 513 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 147 through 148 removed outlier: 6.425A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 150 through 151 Processing sheet with id=AB5, first strand: chain 'C' and resid 154 through 158 removed outlier: 3.688A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 285 through 286 Processing sheet with id=AB7, first strand: chain 'C' and resid 296 through 297 removed outlier: 3.837A pdb=" N MET C 315 " --> pdb=" O VAL C 297 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.659A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR C 600 " --> pdb=" O LYS C 593 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.659A pdb=" N GLN C 580 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLU C 588 " --> pdb=" O GLN C 580 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 616 " --> pdb=" O ARG C 637 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL C 634 " --> pdb=" O PHE C 645 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE C 645 " --> pdb=" O VAL C 634 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.744A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 748 through 752 removed outlier: 6.911A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN C 725 " --> pdb=" O VAL C 733 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 798 through 802 removed outlier: 3.697A pdb=" N LEU C1233 " --> pdb=" O ALA C1067 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA C1067 " --> pdb=" O LEU C1233 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 830 through 841 removed outlier: 7.208A pdb=" N THR C 830 " --> pdb=" O LYS C1057 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LYS C1057 " --> pdb=" O THR C 830 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N HIS C 832 " --> pdb=" O ALA C1055 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ALA C1055 " --> pdb=" O HIS C 832 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N GLN C 834 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N TYR C1053 " --> pdb=" O GLN C 834 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU C 836 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N LYS C1051 " --> pdb=" O LEU C 836 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N CYS C 838 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ILE C1049 " --> pdb=" O CYS C 838 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N SER C 840 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N LEU C1047 " --> pdb=" O THR C 935 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N THR C 935 " --> pdb=" O LEU C1047 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE C1049 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL C 933 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE C 929 " --> pdb=" O TYR C1053 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 849 through 850 removed outlier: 3.855A pdb=" N GLU C 849 " --> pdb=" O VAL C 887 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL C 887 " --> pdb=" O GLU C 849 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 882 through 884 removed outlier: 3.593A pdb=" N LEU C 883 " --> pdb=" O LEU C 918 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'C' and resid 1209 through 1210 Processing sheet with id=AC8, first strand: chain 'C' and resid 1244 through 1246 removed outlier: 4.215A pdb=" N GLY D 351 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER D 353 " --> pdb=" O MET D 466 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET D 466 " --> pdb=" O SER D 353 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLN D 435 " --> pdb=" O LEU D 423 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 1268 through 1270 removed outlier: 3.989A pdb=" N GLN C1268 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1335 through 1338 removed outlier: 3.743A pdb=" N ILE D 20 " --> pdb=" O ASP D1342 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 103 through 112 removed outlier: 3.530A pdb=" N LEU D 242 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU D 107 " --> pdb=" O THR D 240 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N THR D 240 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 11.137A pdb=" N SER D 109 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 10.837A pdb=" N ILE D 238 " --> pdb=" O SER D 109 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 159 through 160 removed outlier: 3.520A pdb=" N LEU D 160 " --> pdb=" O TYR D 144 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N ASP D 177 " --> pdb=" O ILE D 147 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 252 through 254 removed outlier: 3.635A pdb=" N VAL D 253 " --> pdb=" O ALA D 261 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 355 through 357 Processing sheet with id=AD6, first strand: chain 'D' and resid 550 through 556 removed outlier: 3.653A pdb=" N VAL D 550 " --> pdb=" O LYS D 570 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS D 570 " --> pdb=" O VAL D 550 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU D 556 " --> pdb=" O VAL D 564 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 809 through 811 removed outlier: 7.702A pdb=" N VAL D 894 " --> pdb=" O THR D 810 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.507A pdb=" N ILE D 820 " --> pdb=" O VAL D 882 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 901 through 902 removed outlier: 3.773A pdb=" N HIS D 907 " --> pdb=" O ASP D 902 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 949 through 952 removed outlier: 6.987A pdb=" N ILE D 950 " --> pdb=" O VAL D1017 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLU D1015 " --> pdb=" O VAL D 952 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 991 through 993 removed outlier: 4.191A pdb=" N GLY D 956 " --> pdb=" O VAL D1011 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL D1011 " --> pdb=" O GLY D 956 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 965 through 967 removed outlier: 3.955A pdb=" N VAL D 966 " --> pdb=" O VAL D 974 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL D 974 " --> pdb=" O VAL D 966 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ALA D1001 " --> pdb=" O ILE D 975 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1034 through 1036 removed outlier: 3.621A pdb=" N ARG D1036 " --> pdb=" O LYS D1079 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LYS D1079 " --> pdb=" O ARG D1036 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU D1078 " --> pdb=" O TYR D1099 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR D1099 " --> pdb=" O LEU D1078 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 1161 through 1162 removed outlier: 3.872A pdb=" N VAL D1204 " --> pdb=" O GLY D1161 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1173 through 1174 Processing sheet with id=AE7, first strand: chain 'D' and resid 1264 through 1265 850 hydrogen bonds defined for protein. 2376 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 62 hydrogen bonds 116 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 14.44 Time building geometry restraints manager: 13.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9583 1.33 - 1.45: 6205 1.45 - 1.58: 17538 1.58 - 1.70: 248 1.70 - 1.82: 235 Bond restraints: 33809 Sorted by residual: bond pdb=" C ASP D1184 " pdb=" N PRO D1185 " ideal model delta sigma weight residual 1.335 1.403 -0.068 1.36e-02 5.41e+03 2.49e+01 bond pdb=" C VAL C 550 " pdb=" N HIS C 551 " ideal model delta sigma weight residual 1.331 1.232 0.099 2.83e-02 1.25e+03 1.23e+01 bond pdb=" C LEU D 449 " pdb=" N HIS D 450 " ideal model delta sigma weight residual 1.331 1.259 0.072 2.07e-02 2.33e+03 1.20e+01 bond pdb=" C ARG J 71 " pdb=" N PRO J 72 " ideal model delta sigma weight residual 1.332 1.371 -0.039 1.26e-02 6.30e+03 9.68e+00 bond pdb=" C GLN C1256 " pdb=" N GLN C1257 " ideal model delta sigma weight residual 1.327 1.284 0.042 1.39e-02 5.18e+03 9.26e+00 ... (remaining 33804 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.18: 1078 105.18 - 112.45: 17166 112.45 - 119.72: 12397 119.72 - 126.98: 14977 126.98 - 134.25: 574 Bond angle restraints: 46192 Sorted by residual: angle pdb=" N VAL F 166 " pdb=" CA VAL F 166 " pdb=" C VAL F 166 " ideal model delta sigma weight residual 110.62 119.73 -9.11 1.02e+00 9.61e-01 7.98e+01 angle pdb=" C GLN C 41 " pdb=" N ASP C 42 " pdb=" CA ASP C 42 " ideal model delta sigma weight residual 121.74 132.65 -10.91 1.32e+00 5.74e-01 6.83e+01 angle pdb=" N ILE D 500 " pdb=" CA ILE D 500 " pdb=" C ILE D 500 " ideal model delta sigma weight residual 111.91 106.29 5.62 8.90e-01 1.26e+00 3.99e+01 angle pdb=" N THR F 163 " pdb=" CA THR F 163 " pdb=" C THR F 163 " ideal model delta sigma weight residual 111.28 104.66 6.62 1.09e+00 8.42e-01 3.69e+01 angle pdb=" C LYS F 502 " pdb=" N GLU F 503 " pdb=" CA GLU F 503 " ideal model delta sigma weight residual 122.48 132.21 -9.73 1.62e+00 3.81e-01 3.60e+01 ... (remaining 46187 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.20: 19515 34.20 - 68.40: 921 68.40 - 102.60: 50 102.60 - 136.81: 2 136.81 - 171.01: 4 Dihedral angle restraints: 20492 sinusoidal: 9321 harmonic: 11171 Sorted by residual: dihedral pdb=" CA GLY C 45 " pdb=" C GLY C 45 " pdb=" N GLN C 46 " pdb=" CA GLN C 46 " ideal model delta harmonic sigma weight residual -180.00 -152.04 -27.96 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA ASP B 199 " pdb=" C ASP B 199 " pdb=" N LYS B 200 " pdb=" CA LYS B 200 " ideal model delta harmonic sigma weight residual 180.00 153.13 26.87 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA TYR D 457 " pdb=" C TYR D 457 " pdb=" N ASN D 458 " pdb=" CA ASN D 458 " ideal model delta harmonic sigma weight residual -180.00 -153.43 -26.57 0 5.00e+00 4.00e-02 2.82e+01 ... (remaining 20489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 3801 0.056 - 0.111: 1175 0.111 - 0.167: 235 0.167 - 0.223: 37 0.223 - 0.279: 11 Chirality restraints: 5259 Sorted by residual: chirality pdb=" CB ILE F 212 " pdb=" CA ILE F 212 " pdb=" CG1 ILE F 212 " pdb=" CG2 ILE F 212 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CG LEU A 618 " pdb=" CB LEU A 618 " pdb=" CD1 LEU A 618 " pdb=" CD2 LEU A 618 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CB VAL E 6 " pdb=" CA VAL E 6 " pdb=" CG1 VAL E 6 " pdb=" CG2 VAL E 6 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 5256 not shown) Planarity restraints: 5591 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D1138 " 0.059 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO D1139 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO D1139 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO D1139 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS C 551 " -0.048 5.00e-02 4.00e+02 7.29e-02 8.50e+00 pdb=" N PRO C 552 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO C 552 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 552 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C1204 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.73e+00 pdb=" N PRO C1205 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C1205 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO C1205 " -0.038 5.00e-02 4.00e+02 ... (remaining 5588 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 326 2.55 - 3.14: 24218 3.14 - 3.73: 51742 3.73 - 4.31: 67602 4.31 - 4.90: 104836 Nonbonded interactions: 248724 Sorted by model distance: nonbonded pdb=" N GLU B 193 " pdb=" OE1 GLU B 193 " model vdw 1.968 2.520 nonbonded pdb=" N7 DG 1 73 " pdb=" N1 DA 1 74 " model vdw 1.978 3.200 nonbonded pdb=" N GLU C 374 " pdb=" OE1 GLU C 374 " model vdw 1.985 2.520 nonbonded pdb=" O4 DT 1 86 " pdb=" O6 DG 1 87 " model vdw 2.039 3.040 nonbonded pdb=" O6 DG 1 84 " pdb=" N6 DA 1 85 " model vdw 2.092 2.520 ... (remaining 248719 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.260 Check model and map are aligned: 0.530 Set scattering table: 0.300 Process input model: 96.160 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.110 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 107.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 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 : 0.007 0.099 33809 Z= 0.427 Angle : 0.996 10.911 46192 Z= 0.580 Chirality : 0.056 0.279 5259 Planarity : 0.007 0.088 5591 Dihedral : 18.253 171.007 13282 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.63 % Favored : 93.24 % Rotamer: Outliers : 0.91 % Allowed : 11.30 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.65 (0.10), residues: 3845 helix: -4.08 (0.08), residues: 1217 sheet: -2.34 (0.24), residues: 356 loop : -2.70 (0.11), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP D 580 HIS 0.008 0.002 HIS D 364 PHE 0.025 0.002 PHE C1265 TYR 0.035 0.002 TYR C1231 ARG 0.010 0.001 ARG C1059 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 624 time to evaluate : 3.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 PHE cc_start: 0.7238 (m-10) cc_final: 0.6914 (m-80) REVERT: A 51 MET cc_start: 0.9058 (mmm) cc_final: 0.8848 (mmm) REVERT: A 188 GLU cc_start: 0.7918 (mp0) cc_final: 0.7710 (mp0) REVERT: B 96 ASP cc_start: 0.7806 (m-30) cc_final: 0.5689 (t0) REVERT: B 226 GLU cc_start: 0.8339 (tp30) cc_final: 0.8112 (tp30) REVERT: C 92 TYR cc_start: 0.7914 (OUTLIER) cc_final: 0.7448 (p90) REVERT: C 213 LEU cc_start: 0.9060 (mt) cc_final: 0.8815 (mt) REVERT: C 224 PHE cc_start: 0.8486 (m-80) cc_final: 0.7928 (m-10) REVERT: C 410 LEU cc_start: 0.8901 (mt) cc_final: 0.8376 (pp) REVERT: C 429 MET cc_start: 0.9396 (mmm) cc_final: 0.9109 (mmm) REVERT: C 504 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7755 (mt-10) REVERT: C 542 ARG cc_start: 0.6639 (mtt-85) cc_final: 0.5631 (tmt-80) REVERT: C 696 ASP cc_start: 0.8767 (t0) cc_final: 0.8257 (t0) REVERT: C 704 MET cc_start: 0.8534 (mtm) cc_final: 0.8267 (mmp) REVERT: C 705 GLU cc_start: 0.9119 (mp0) cc_final: 0.8801 (mp0) REVERT: C 706 ARG cc_start: 0.8799 (mtt-85) cc_final: 0.8537 (mmt90) REVERT: C 738 GLU cc_start: 0.7303 (pm20) cc_final: 0.6740 (pm20) REVERT: C 798 GLN cc_start: 0.8816 (mp10) cc_final: 0.8216 (mp10) REVERT: C 805 MET cc_start: 0.8842 (pmm) cc_final: 0.8416 (pmm) REVERT: C 955 GLN cc_start: 0.8695 (tp40) cc_final: 0.7895 (tm-30) REVERT: C 965 GLN cc_start: 0.7823 (tm-30) cc_final: 0.7414 (tm-30) REVERT: C 976 ARG cc_start: -0.4779 (OUTLIER) cc_final: -0.5631 (ttt-90) REVERT: C 1066 MET cc_start: 0.8439 (mmm) cc_final: 0.8085 (ttm) REVERT: C 1182 ILE cc_start: 0.9295 (mt) cc_final: 0.9090 (mm) REVERT: C 1214 ASP cc_start: 0.8974 (t70) cc_final: 0.8521 (t70) REVERT: C 1272 GLU cc_start: 0.8843 (pm20) cc_final: 0.8569 (pm20) REVERT: C 1273 MET cc_start: 0.9251 (mpp) cc_final: 0.8868 (mtt) REVERT: C 1290 MET cc_start: 0.8867 (mmt) cc_final: 0.8539 (mmp) REVERT: C 1321 GLU cc_start: 0.8880 (mp0) cc_final: 0.8548 (mp0) REVERT: D 76 LYS cc_start: 0.5507 (mmtt) cc_final: 0.4992 (tptp) REVERT: D 128 LEU cc_start: 0.9361 (mt) cc_final: 0.9113 (mm) REVERT: D 130 MET cc_start: 0.8295 (ttm) cc_final: 0.7818 (mtp) REVERT: D 134 ASP cc_start: 0.8984 (m-30) cc_final: 0.8665 (p0) REVERT: D 148 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7776 (tm-30) REVERT: D 180 MET cc_start: 0.7970 (ttp) cc_final: 0.7287 (ttp) REVERT: D 192 MET cc_start: 0.8618 (ptm) cc_final: 0.8220 (ptp) REVERT: D 222 LYS cc_start: 0.8863 (mtmm) cc_final: 0.8607 (tttp) REVERT: D 237 MET cc_start: 0.8926 (mmt) cc_final: 0.8554 (mmt) REVERT: D 264 ASP cc_start: 0.9191 (m-30) cc_final: 0.8915 (m-30) REVERT: D 300 GLN cc_start: 0.8541 (tm-30) cc_final: 0.7880 (tm-30) REVERT: D 360 TYR cc_start: 0.8462 (p90) cc_final: 0.8111 (p90) REVERT: D 435 GLN cc_start: 0.9071 (mt0) cc_final: 0.8695 (mp10) REVERT: D 438 GLU cc_start: 0.8391 (tt0) cc_final: 0.7869 (tt0) REVERT: D 457 TYR cc_start: 0.8915 (m-80) cc_final: 0.8443 (m-10) REVERT: D 487 THR cc_start: 0.9432 (m) cc_final: 0.9176 (t) REVERT: D 587 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8873 (pp) REVERT: D 601 ILE cc_start: 0.9609 (mt) cc_final: 0.9326 (tt) REVERT: D 622 ASP cc_start: 0.8116 (t0) cc_final: 0.7893 (t0) REVERT: D 625 MET cc_start: 0.8871 (mpp) cc_final: 0.8616 (mpp) REVERT: D 743 MET cc_start: 0.5058 (pmm) cc_final: 0.4787 (ppp) REVERT: D 747 MET cc_start: 0.5479 (mpp) cc_final: 0.5078 (mpp) REVERT: D 1040 MET cc_start: 0.1677 (mtm) cc_final: 0.1310 (ptt) REVERT: D 1229 VAL cc_start: 0.8459 (t) cc_final: 0.8143 (t) REVERT: D 1254 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8542 (tt0) REVERT: D 1290 ARG cc_start: 0.7696 (mtt180) cc_final: 0.7471 (mtt-85) REVERT: D 1309 ILE cc_start: 0.9402 (pt) cc_final: 0.8802 (mt) REVERT: D 1352 ILE cc_start: 0.9637 (pt) cc_final: 0.9352 (tp) REVERT: E 10 VAL cc_start: 0.8730 (m) cc_final: 0.8490 (m) REVERT: E 25 ARG cc_start: 0.7692 (mtm-85) cc_final: 0.7477 (ptp-170) REVERT: E 30 MET cc_start: 0.8769 (mtp) cc_final: 0.8500 (ttt) REVERT: E 65 ASP cc_start: 0.8405 (m-30) cc_final: 0.7998 (p0) REVERT: F 104 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8266 (mm-30) REVERT: F 109 GLU cc_start: 0.7025 (pm20) cc_final: 0.6779 (tm-30) REVERT: F 227 GLN cc_start: 0.6854 (mm-40) cc_final: 0.5535 (tm-30) REVERT: F 281 ARG cc_start: 0.9167 (ttt180) cc_final: 0.8961 (ttp80) REVERT: F 338 HIS cc_start: 0.5877 (p90) cc_final: 0.5098 (t70) REVERT: F 365 MET cc_start: 0.8443 (tmm) cc_final: 0.7999 (ptm) REVERT: F 386 LEU cc_start: 0.9128 (tt) cc_final: 0.8818 (mt) REVERT: F 499 LYS cc_start: 0.8476 (pttp) cc_final: 0.8002 (ttmt) REVERT: F 555 GLU cc_start: 0.8701 (mp0) cc_final: 0.8415 (mp0) REVERT: J 42 PHE cc_start: 0.4074 (t80) cc_final: 0.3676 (t80) REVERT: J 50 LEU cc_start: 0.7694 (tp) cc_final: 0.7241 (pt) REVERT: J 78 MET cc_start: 0.5548 (ttp) cc_final: 0.5343 (ttp) outliers start: 30 outliers final: 11 residues processed: 651 average time/residue: 0.5183 time to fit residues: 511.7559 Evaluate side-chains 402 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 388 time to evaluate : 3.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 334 optimal weight: 0.7980 chunk 300 optimal weight: 30.0000 chunk 166 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 202 optimal weight: 8.9990 chunk 160 optimal weight: 1.9990 chunk 310 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 chunk 188 optimal weight: 10.0000 chunk 231 optimal weight: 2.9990 chunk 359 optimal weight: 9.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 75 GLN A 137 ASN B 37 HIS ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS B 117 HIS B 132 HIS C 120 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN C 462 ASN C 613 ASN C 659 GLN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 799 ASN C1157 GLN C1209 GLN ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN D 157 GLN ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 488 ASN D 489 ASN D 606 ASN D 702 GLN D 720 ASN D 951 GLN D1114 GLN D1268 ASN D1326 GLN E 43 ASN F 128 ASN F 210 ASN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 HIS F 464 ASN F 568 ASN ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33809 Z= 0.203 Angle : 0.637 7.639 46192 Z= 0.342 Chirality : 0.043 0.168 5259 Planarity : 0.005 0.061 5591 Dihedral : 16.882 174.680 5643 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.85 % Favored : 94.12 % Rotamer: Outliers : 0.18 % Allowed : 5.57 % Favored : 94.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % 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: -3.60 (0.11), residues: 3845 helix: -2.69 (0.11), residues: 1322 sheet: -1.92 (0.24), residues: 388 loop : -2.29 (0.12), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C1276 HIS 0.010 0.001 HIS C 150 PHE 0.018 0.001 PHE F 266 TYR 0.024 0.002 TYR C1149 ARG 0.009 0.001 ARG C 678 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 553 time to evaluate : 3.772 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 HIS cc_start: 0.8954 (t-90) cc_final: 0.8431 (t-90) REVERT: A 188 GLU cc_start: 0.7931 (mp0) cc_final: 0.7710 (mp0) REVERT: B 96 ASP cc_start: 0.7506 (m-30) cc_final: 0.6132 (t0) REVERT: C 118 LYS cc_start: 0.8372 (pttt) cc_final: 0.7082 (pttt) REVERT: C 130 MET cc_start: 0.8322 (ttm) cc_final: 0.8045 (ttp) REVERT: C 148 GLN cc_start: 0.8758 (tt0) cc_final: 0.8491 (tt0) REVERT: C 213 LEU cc_start: 0.8918 (mt) cc_final: 0.8717 (mt) REVERT: C 224 PHE cc_start: 0.8246 (m-80) cc_final: 0.7762 (m-10) REVERT: C 473 ARG cc_start: 0.7792 (tmm-80) cc_final: 0.7573 (tpt-90) REVERT: C 542 ARG cc_start: 0.6326 (mtt-85) cc_final: 0.5322 (tmt-80) REVERT: C 696 ASP cc_start: 0.8566 (t0) cc_final: 0.8180 (t0) REVERT: C 705 GLU cc_start: 0.9208 (mp0) cc_final: 0.8974 (mp0) REVERT: C 732 ILE cc_start: 0.8683 (pt) cc_final: 0.8429 (mm) REVERT: C 768 MET cc_start: 0.8085 (ttp) cc_final: 0.7703 (mtm) REVERT: C 794 LEU cc_start: 0.9341 (tp) cc_final: 0.8916 (tp) REVERT: C 798 GLN cc_start: 0.8839 (mp10) cc_final: 0.8204 (mp10) REVERT: C 816 ILE cc_start: 0.9224 (pt) cc_final: 0.8950 (pt) REVERT: C 850 ILE cc_start: 0.9026 (mm) cc_final: 0.8783 (mm) REVERT: C 903 ARG cc_start: 0.8615 (ttt180) cc_final: 0.8353 (ttp80) REVERT: C 955 GLN cc_start: 0.8741 (tp40) cc_final: 0.8230 (tm-30) REVERT: C 965 GLN cc_start: 0.6693 (tm-30) cc_final: 0.6484 (tm-30) REVERT: C 1023 HIS cc_start: 0.6887 (m170) cc_final: 0.6567 (m170) REVERT: C 1214 ASP cc_start: 0.9009 (t70) cc_final: 0.8355 (t70) REVERT: C 1240 ASP cc_start: 0.8777 (m-30) cc_final: 0.8409 (t0) REVERT: C 1243 MET cc_start: 0.8996 (tmm) cc_final: 0.7796 (ttm) REVERT: C 1253 LEU cc_start: 0.9445 (tp) cc_final: 0.9072 (tp) REVERT: C 1276 TRP cc_start: 0.8461 (m-10) cc_final: 0.8068 (m-90) REVERT: C 1290 MET cc_start: 0.8975 (mmt) cc_final: 0.8109 (mmp) REVERT: C 1304 MET cc_start: 0.8316 (tpp) cc_final: 0.7825 (mmt) REVERT: D 29 MET cc_start: 0.7996 (ttp) cc_final: 0.7100 (tmm) REVERT: D 76 LYS cc_start: 0.5292 (mmtt) cc_final: 0.4824 (tptp) REVERT: D 113 HIS cc_start: 0.9094 (t-90) cc_final: 0.8693 (t-170) REVERT: D 130 MET cc_start: 0.8159 (ttm) cc_final: 0.7671 (mtp) REVERT: D 134 ASP cc_start: 0.8798 (m-30) cc_final: 0.8434 (m-30) REVERT: D 192 MET cc_start: 0.8385 (ptt) cc_final: 0.8125 (ptp) REVERT: D 235 GLU cc_start: 0.8869 (pm20) cc_final: 0.8619 (pm20) REVERT: D 237 MET cc_start: 0.9002 (mmt) cc_final: 0.8685 (mmt) REVERT: D 264 ASP cc_start: 0.9184 (m-30) cc_final: 0.8962 (m-30) REVERT: D 269 TYR cc_start: 0.8916 (m-80) cc_final: 0.8623 (m-80) REVERT: D 360 TYR cc_start: 0.8506 (p90) cc_final: 0.8105 (p90) REVERT: D 370 LYS cc_start: 0.9467 (tppt) cc_final: 0.9175 (tppt) REVERT: D 372 MET cc_start: 0.9375 (ttm) cc_final: 0.9139 (ttm) REVERT: D 435 GLN cc_start: 0.9121 (mt0) cc_final: 0.8486 (mp10) REVERT: D 438 GLU cc_start: 0.8346 (tt0) cc_final: 0.7499 (tt0) REVERT: D 445 LYS cc_start: 0.9084 (mttt) cc_final: 0.7987 (mmtt) REVERT: D 457 TYR cc_start: 0.8556 (m-80) cc_final: 0.7882 (m-10) REVERT: D 487 THR cc_start: 0.9442 (m) cc_final: 0.9201 (t) REVERT: D 525 MET cc_start: 0.8602 (mtp) cc_final: 0.8331 (mtt) REVERT: D 625 MET cc_start: 0.8687 (mpp) cc_final: 0.8329 (mpp) REVERT: D 790 THR cc_start: 0.8340 (p) cc_final: 0.8138 (p) REVERT: D 869 CYS cc_start: 0.8449 (m) cc_final: 0.8248 (m) REVERT: D 995 TYR cc_start: 0.7769 (m-80) cc_final: 0.7524 (m-80) REVERT: D 1286 LYS cc_start: 0.8976 (pttt) cc_final: 0.8734 (mmmt) REVERT: D 1290 ARG cc_start: 0.7826 (mtt180) cc_final: 0.7471 (mtt-85) REVERT: D 1309 ILE cc_start: 0.9260 (pt) cc_final: 0.8767 (mt) REVERT: E 25 ARG cc_start: 0.7767 (mtm-85) cc_final: 0.6948 (ptp-170) REVERT: E 31 GLN cc_start: 0.8496 (tp40) cc_final: 0.8178 (tp40) REVERT: E 71 GLU cc_start: 0.7912 (tp30) cc_final: 0.7629 (mm-30) REVERT: F 104 GLU cc_start: 0.8376 (mm-30) cc_final: 0.8081 (mm-30) REVERT: F 109 GLU cc_start: 0.7167 (pm20) cc_final: 0.6779 (tm-30) REVERT: F 227 GLN cc_start: 0.6666 (mm-40) cc_final: 0.5233 (tm-30) REVERT: F 445 ASP cc_start: 0.9194 (p0) cc_final: 0.8858 (p0) REVERT: F 470 MET cc_start: 0.8672 (mmt) cc_final: 0.8100 (mmt) REVERT: F 499 LYS cc_start: 0.8391 (pttp) cc_final: 0.7965 (ttmt) REVERT: J 17 HIS cc_start: 0.6361 (m170) cc_final: 0.5840 (m170) REVERT: J 50 LEU cc_start: 0.7761 (tp) cc_final: 0.7415 (pt) outliers start: 6 outliers final: 0 residues processed: 558 average time/residue: 0.4882 time to fit residues: 436.6050 Evaluate side-chains 385 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 4.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 199 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 chunk 299 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 99 optimal weight: 2.9990 chunk 360 optimal weight: 0.8980 chunk 389 optimal weight: 7.9990 chunk 320 optimal weight: 2.9990 chunk 357 optimal weight: 0.7980 chunk 122 optimal weight: 5.9990 chunk 289 optimal weight: 8.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 387 ASN ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1244 HIS ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D 716 GLN D1010 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33809 Z= 0.205 Angle : 0.599 8.576 46192 Z= 0.321 Chirality : 0.042 0.216 5259 Planarity : 0.004 0.074 5591 Dihedral : 16.633 179.300 5643 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.50 % Favored : 93.47 % Rotamer: Outliers : 0.12 % Allowed : 5.66 % Favored : 94.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % 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: -2.92 (0.12), residues: 3845 helix: -1.87 (0.13), residues: 1334 sheet: -1.52 (0.25), residues: 376 loop : -2.07 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 115 HIS 0.008 0.001 HIS C 150 PHE 0.017 0.001 PHE F 259 TYR 0.018 0.001 TYR C1149 ARG 0.011 0.000 ARG C 678 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 495 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 491 time to evaluate : 3.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 HIS cc_start: 0.8917 (t-90) cc_final: 0.8426 (t-90) REVERT: A 58 GLU cc_start: 0.8494 (tt0) cc_final: 0.7950 (tp30) REVERT: A 183 ILE cc_start: 0.9304 (tt) cc_final: 0.8967 (mm) REVERT: A 186 ASN cc_start: 0.8850 (m110) cc_final: 0.7936 (p0) REVERT: A 188 GLU cc_start: 0.7951 (mp0) cc_final: 0.7404 (mp0) REVERT: B 96 ASP cc_start: 0.7455 (m-30) cc_final: 0.6056 (t0) REVERT: C 130 MET cc_start: 0.8382 (ttm) cc_final: 0.7721 (ttm) REVERT: C 213 LEU cc_start: 0.8889 (mt) cc_final: 0.8689 (mt) REVERT: C 224 PHE cc_start: 0.8300 (m-80) cc_final: 0.7822 (m-10) REVERT: C 386 GLU cc_start: 0.7710 (mm-30) cc_final: 0.6084 (pt0) REVERT: C 410 LEU cc_start: 0.8568 (mp) cc_final: 0.8217 (pp) REVERT: C 616 ILE cc_start: 0.9298 (mt) cc_final: 0.9068 (mt) REVERT: C 667 LEU cc_start: 0.8833 (mt) cc_final: 0.8380 (tt) REVERT: C 741 MET cc_start: 0.7506 (ptt) cc_final: 0.7006 (ptp) REVERT: C 850 ILE cc_start: 0.9113 (mm) cc_final: 0.8848 (mm) REVERT: C 903 ARG cc_start: 0.8601 (ttt180) cc_final: 0.8244 (ttp80) REVERT: C 1021 LEU cc_start: 0.5216 (mt) cc_final: 0.4956 (pp) REVERT: C 1023 HIS cc_start: 0.7001 (m170) cc_final: 0.6661 (m170) REVERT: C 1119 MET cc_start: 0.8419 (mmp) cc_final: 0.8129 (tpp) REVERT: C 1170 MET cc_start: 0.9409 (mmm) cc_final: 0.9203 (mmm) REVERT: C 1214 ASP cc_start: 0.8942 (t70) cc_final: 0.8447 (t70) REVERT: C 1240 ASP cc_start: 0.8730 (m-30) cc_final: 0.8355 (t0) REVERT: C 1272 GLU cc_start: 0.8910 (pm20) cc_final: 0.8525 (pm20) REVERT: C 1276 TRP cc_start: 0.8551 (m-10) cc_final: 0.8243 (m-90) REVERT: D 76 LYS cc_start: 0.5258 (mmtt) cc_final: 0.4785 (tptp) REVERT: D 130 MET cc_start: 0.8053 (ttm) cc_final: 0.7594 (ttm) REVERT: D 180 MET cc_start: 0.7603 (ttm) cc_final: 0.7260 (ttp) REVERT: D 192 MET cc_start: 0.8389 (ptt) cc_final: 0.8095 (ptp) REVERT: D 330 MET cc_start: 0.8224 (mmm) cc_final: 0.7935 (mmm) REVERT: D 360 TYR cc_start: 0.8464 (p90) cc_final: 0.8087 (p90) REVERT: D 435 GLN cc_start: 0.9039 (mt0) cc_final: 0.8415 (mp10) REVERT: D 445 LYS cc_start: 0.9078 (mttt) cc_final: 0.8436 (mttt) REVERT: D 457 TYR cc_start: 0.8604 (m-80) cc_final: 0.8094 (m-10) REVERT: D 487 THR cc_start: 0.9462 (m) cc_final: 0.9221 (t) REVERT: D 605 LEU cc_start: 0.9461 (mp) cc_final: 0.9229 (mp) REVERT: D 747 MET cc_start: 0.5159 (mpp) cc_final: 0.4787 (mpp) REVERT: D 869 CYS cc_start: 0.8475 (m) cc_final: 0.8180 (m) REVERT: D 1040 MET cc_start: 0.1077 (ptt) cc_final: 0.0751 (ptp) REVERT: D 1101 LEU cc_start: 0.7197 (mp) cc_final: 0.6700 (pt) REVERT: D 1290 ARG cc_start: 0.7868 (mtt180) cc_final: 0.7479 (mtt-85) REVERT: D 1309 ILE cc_start: 0.9234 (pt) cc_final: 0.8935 (mt) REVERT: D 1325 PHE cc_start: 0.8797 (p90) cc_final: 0.8593 (p90) REVERT: D 1326 GLN cc_start: 0.8680 (mt0) cc_final: 0.7937 (mt0) REVERT: E 71 GLU cc_start: 0.8002 (tp30) cc_final: 0.7602 (mm-30) REVERT: F 102 MET cc_start: 0.8452 (ttp) cc_final: 0.7611 (tmm) REVERT: F 104 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8172 (mm-30) REVERT: F 227 GLN cc_start: 0.6666 (mm-40) cc_final: 0.5208 (tm-30) REVERT: F 276 MET cc_start: 0.8935 (tpp) cc_final: 0.8692 (tmm) REVERT: F 499 LYS cc_start: 0.8496 (pttp) cc_final: 0.8016 (ttmt) REVERT: J 50 LEU cc_start: 0.7683 (tp) cc_final: 0.7327 (pt) outliers start: 4 outliers final: 1 residues processed: 494 average time/residue: 0.4357 time to fit residues: 351.3243 Evaluate side-chains 361 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 360 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 355 optimal weight: 9.9990 chunk 270 optimal weight: 0.4980 chunk 186 optimal weight: 10.0000 chunk 39 optimal weight: 30.0000 chunk 171 optimal weight: 10.0000 chunk 241 optimal weight: 10.0000 chunk 361 optimal weight: 9.9990 chunk 382 optimal weight: 10.0000 chunk 188 optimal weight: 9.9990 chunk 342 optimal weight: 20.0000 chunk 103 optimal weight: 9.9990 overall best weight: 8.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 HIS ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 GLN ** C 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 767 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 798 GLN C 952 GLN ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 ASN ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 HIS D 489 ASN ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1227 HIS F 242 HIS ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 ASN F 472 GLN ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 33809 Z= 0.451 Angle : 0.818 12.709 46192 Z= 0.431 Chirality : 0.048 0.246 5259 Planarity : 0.006 0.053 5591 Dihedral : 16.767 177.908 5643 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.75 % Favored : 90.22 % Rotamer: Outliers : 0.15 % Allowed : 6.15 % Favored : 93.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.12), residues: 3845 helix: -1.78 (0.13), residues: 1327 sheet: -1.72 (0.24), residues: 366 loop : -2.25 (0.13), residues: 2152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 33 HIS 0.008 0.002 HIS D 419 PHE 0.033 0.003 PHE C 972 TYR 0.026 0.003 TYR C1231 ARG 0.010 0.001 ARG C 678 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 415 time to evaluate : 3.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.7932 (mp0) cc_final: 0.7729 (mp0) REVERT: B 96 ASP cc_start: 0.7347 (m-30) cc_final: 0.5843 (t0) REVERT: C 85 CYS cc_start: 0.8546 (m) cc_final: 0.8212 (m) REVERT: C 130 MET cc_start: 0.8355 (ttm) cc_final: 0.7852 (ttm) REVERT: C 213 LEU cc_start: 0.8939 (mt) cc_final: 0.8727 (mt) REVERT: C 245 ARG cc_start: 0.7081 (mtt180) cc_final: 0.6492 (mmp80) REVERT: C 410 LEU cc_start: 0.8640 (mp) cc_final: 0.8137 (pp) REVERT: C 659 GLN cc_start: 0.8694 (pt0) cc_final: 0.8312 (tt0) REVERT: C 685 MET cc_start: 0.8994 (mmt) cc_final: 0.8616 (tpp) REVERT: C 696 ASP cc_start: 0.8612 (t0) cc_final: 0.8342 (t0) REVERT: C 768 MET cc_start: 0.8959 (mtp) cc_final: 0.8733 (mtm) REVERT: C 781 ASP cc_start: 0.8076 (m-30) cc_final: 0.7697 (m-30) REVERT: C 1214 ASP cc_start: 0.8960 (t70) cc_final: 0.8533 (t70) REVERT: C 1240 ASP cc_start: 0.8910 (m-30) cc_final: 0.8466 (t0) REVERT: C 1256 GLN cc_start: 0.9210 (mm110) cc_final: 0.8261 (mp10) REVERT: C 1272 GLU cc_start: 0.9100 (pm20) cc_final: 0.8401 (pm20) REVERT: C 1276 TRP cc_start: 0.8774 (m-10) cc_final: 0.8241 (m-90) REVERT: C 1321 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8190 (tp30) REVERT: D 76 LYS cc_start: 0.5314 (mmtt) cc_final: 0.4932 (tptp) REVERT: D 130 MET cc_start: 0.8206 (ttm) cc_final: 0.7601 (ttm) REVERT: D 180 MET cc_start: 0.7856 (ttm) cc_final: 0.7097 (ttp) REVERT: D 192 MET cc_start: 0.8782 (ptt) cc_final: 0.8573 (ptp) REVERT: D 237 MET cc_start: 0.9129 (tpp) cc_final: 0.8921 (tpp) REVERT: D 298 MET cc_start: 0.8794 (ptp) cc_final: 0.8374 (ptp) REVERT: D 360 TYR cc_start: 0.8378 (p90) cc_final: 0.8063 (p90) REVERT: D 429 LEU cc_start: 0.8802 (mm) cc_final: 0.8463 (mt) REVERT: D 435 GLN cc_start: 0.9113 (mt0) cc_final: 0.8581 (mp10) REVERT: D 457 TYR cc_start: 0.8969 (m-80) cc_final: 0.7630 (m-10) REVERT: D 525 MET cc_start: 0.8684 (mtt) cc_final: 0.8483 (mtt) REVERT: D 747 MET cc_start: 0.5018 (mpp) cc_final: 0.4806 (mpp) REVERT: D 1040 MET cc_start: 0.1359 (ptt) cc_final: 0.0967 (ptp) REVERT: D 1075 ARG cc_start: 0.4659 (mmt90) cc_final: 0.2867 (mmp-170) REVERT: D 1189 MET cc_start: 0.5076 (ttm) cc_final: 0.4841 (ttt) REVERT: D 1254 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8662 (mt-10) REVERT: D 1290 ARG cc_start: 0.7730 (mmt180) cc_final: 0.7260 (mtt-85) REVERT: F 102 MET cc_start: 0.8167 (ttp) cc_final: 0.7627 (tmm) REVERT: F 104 GLU cc_start: 0.8408 (mm-30) cc_final: 0.8150 (mm-30) REVERT: F 276 MET cc_start: 0.8870 (tpp) cc_final: 0.8665 (tmm) REVERT: F 277 MET cc_start: 0.7988 (mtm) cc_final: 0.7508 (mtp) REVERT: F 297 MET cc_start: 0.5871 (mtm) cc_final: 0.5619 (ptt) REVERT: F 473 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: F 499 LYS cc_start: 0.8487 (pttp) cc_final: 0.8037 (ttmm) REVERT: F 571 TYR cc_start: 0.6516 (m-80) cc_final: 0.6197 (m-80) REVERT: J 50 LEU cc_start: 0.7443 (tp) cc_final: 0.7026 (pt) REVERT: J 58 ARG cc_start: 0.7372 (mtt90) cc_final: 0.7156 (mtt90) REVERT: J 78 MET cc_start: 0.6072 (ttp) cc_final: 0.4949 (tpp) outliers start: 5 outliers final: 0 residues processed: 420 average time/residue: 0.4101 time to fit residues: 286.2132 Evaluate side-chains 315 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 314 time to evaluate : 3.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 318 optimal weight: 2.9990 chunk 217 optimal weight: 7.9990 chunk 5 optimal weight: 0.5980 chunk 285 optimal weight: 40.0000 chunk 157 optimal weight: 5.9990 chunk 326 optimal weight: 8.9990 chunk 264 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 195 optimal weight: 2.9990 chunk 343 optimal weight: 30.0000 chunk 96 optimal weight: 8.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 GLN ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN D1326 GLN E 43 ASN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 362 ASN ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 105 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33809 Z= 0.202 Angle : 0.607 8.382 46192 Z= 0.321 Chirality : 0.043 0.188 5259 Planarity : 0.004 0.057 5591 Dihedral : 16.416 177.557 5643 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.22 % Favored : 93.76 % Rotamer: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % 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: -2.56 (0.13), residues: 3845 helix: -1.34 (0.14), residues: 1335 sheet: -1.45 (0.25), residues: 366 loop : -2.00 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 580 HIS 0.007 0.001 HIS J 17 PHE 0.024 0.001 PHE C 972 TYR 0.033 0.002 TYR J 37 ARG 0.008 0.000 ARG C1246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 476 time to evaluate : 4.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 HIS cc_start: 0.8727 (t-90) cc_final: 0.8454 (t-90) REVERT: A 79 LEU cc_start: 0.8867 (pt) cc_final: 0.8649 (tp) REVERT: A 183 ILE cc_start: 0.9187 (tt) cc_final: 0.8839 (mm) REVERT: A 186 ASN cc_start: 0.8864 (m110) cc_final: 0.8079 (p0) REVERT: A 188 GLU cc_start: 0.7846 (mp0) cc_final: 0.7377 (mp0) REVERT: B 96 ASP cc_start: 0.7288 (m-30) cc_final: 0.5823 (t0) REVERT: B 198 LEU cc_start: 0.8877 (mt) cc_final: 0.8607 (pp) REVERT: C 85 CYS cc_start: 0.8308 (m) cc_final: 0.7978 (m) REVERT: C 410 LEU cc_start: 0.8600 (mp) cc_final: 0.8168 (pp) REVERT: C 667 LEU cc_start: 0.9067 (mp) cc_final: 0.8588 (tt) REVERT: C 696 ASP cc_start: 0.8533 (t0) cc_final: 0.8282 (t0) REVERT: C 781 ASP cc_start: 0.8139 (m-30) cc_final: 0.7803 (m-30) REVERT: C 850 ILE cc_start: 0.9230 (mm) cc_final: 0.8938 (mm) REVERT: C 1021 LEU cc_start: 0.4962 (mt) cc_final: 0.4446 (pp) REVERT: C 1073 LYS cc_start: 0.9194 (mmmt) cc_final: 0.8598 (mttt) REVERT: C 1107 MET cc_start: 0.4463 (mmt) cc_final: 0.3364 (mtm) REVERT: C 1164 PHE cc_start: 0.8525 (m-10) cc_final: 0.8319 (m-80) REVERT: C 1214 ASP cc_start: 0.8896 (t70) cc_final: 0.8271 (t70) REVERT: C 1240 ASP cc_start: 0.8660 (m-30) cc_final: 0.8404 (t0) REVERT: C 1253 LEU cc_start: 0.9481 (tp) cc_final: 0.9199 (tp) REVERT: C 1272 GLU cc_start: 0.8940 (pm20) cc_final: 0.8350 (pm20) REVERT: C 1276 TRP cc_start: 0.8496 (m-10) cc_final: 0.8080 (m-90) REVERT: C 1321 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8138 (tp30) REVERT: D 29 MET cc_start: 0.8218 (ptp) cc_final: 0.7973 (ptp) REVERT: D 76 LYS cc_start: 0.5336 (mmtt) cc_final: 0.4773 (tptp) REVERT: D 130 MET cc_start: 0.8115 (ttm) cc_final: 0.7434 (ttm) REVERT: D 180 MET cc_start: 0.7700 (ttm) cc_final: 0.7107 (ttp) REVERT: D 192 MET cc_start: 0.8502 (ptt) cc_final: 0.8079 (ptp) REVERT: D 298 MET cc_start: 0.8802 (ptp) cc_final: 0.8091 (ptp) REVERT: D 299 LEU cc_start: 0.9325 (tp) cc_final: 0.9034 (tp) REVERT: D 360 TYR cc_start: 0.8422 (p90) cc_final: 0.7989 (p90) REVERT: D 429 LEU cc_start: 0.8843 (mm) cc_final: 0.8581 (mt) REVERT: D 435 GLN cc_start: 0.9018 (mt0) cc_final: 0.8493 (mp10) REVERT: D 525 MET cc_start: 0.8817 (mtt) cc_final: 0.8591 (mtt) REVERT: D 719 PHE cc_start: 0.3832 (m-10) cc_final: 0.3481 (m-10) REVERT: D 1040 MET cc_start: 0.1712 (ptt) cc_final: 0.1323 (ptp) REVERT: D 1075 ARG cc_start: 0.4553 (mmt90) cc_final: 0.2834 (mmp-170) REVERT: D 1210 ILE cc_start: 0.8329 (mm) cc_final: 0.8101 (mt) REVERT: D 1254 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8603 (mt-10) REVERT: D 1286 LYS cc_start: 0.9036 (pttt) cc_final: 0.8800 (mmmt) REVERT: D 1290 ARG cc_start: 0.7864 (mmt180) cc_final: 0.7506 (mtt-85) REVERT: D 1330 ARG cc_start: 0.6868 (mmt180) cc_final: 0.6535 (mmt180) REVERT: F 102 MET cc_start: 0.8212 (ttp) cc_final: 0.7638 (tmm) REVERT: F 104 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8055 (mm-30) REVERT: F 227 GLN cc_start: 0.6710 (mm-40) cc_final: 0.5238 (tm-30) REVERT: F 277 MET cc_start: 0.7952 (mtm) cc_final: 0.7299 (mtp) REVERT: F 416 VAL cc_start: 0.9037 (t) cc_final: 0.8832 (t) REVERT: F 499 LYS cc_start: 0.8312 (pttp) cc_final: 0.7882 (ttmt) REVERT: F 571 TYR cc_start: 0.6430 (m-80) cc_final: 0.6084 (m-80) REVERT: J 18 ILE cc_start: 0.7335 (pt) cc_final: 0.7010 (pt) REVERT: J 50 LEU cc_start: 0.7460 (tp) cc_final: 0.7041 (pt) REVERT: J 58 ARG cc_start: 0.7227 (mtt90) cc_final: 0.6599 (tpp80) REVERT: J 78 MET cc_start: 0.6262 (ttp) cc_final: 0.5253 (tpt) outliers start: 1 outliers final: 0 residues processed: 477 average time/residue: 0.4316 time to fit residues: 338.7080 Evaluate side-chains 351 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 351 time to evaluate : 3.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 128 optimal weight: 6.9990 chunk 344 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 224 optimal weight: 4.9990 chunk 94 optimal weight: 20.0000 chunk 383 optimal weight: 10.0000 chunk 318 optimal weight: 8.9990 chunk 177 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 126 optimal weight: 8.9990 chunk 201 optimal weight: 0.4980 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN D1326 GLN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 33809 Z= 0.309 Angle : 0.685 9.906 46192 Z= 0.359 Chirality : 0.044 0.233 5259 Planarity : 0.005 0.072 5591 Dihedral : 16.376 179.686 5643 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.18 % Favored : 90.77 % Rotamer: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % 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: -2.57 (0.13), residues: 3845 helix: -1.31 (0.14), residues: 1339 sheet: -1.39 (0.26), residues: 336 loop : -2.05 (0.13), residues: 2170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 33 HIS 0.013 0.001 HIS J 17 PHE 0.028 0.002 PHE A 8 TYR 0.032 0.002 TYR J 37 ARG 0.008 0.001 ARG C1246 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 425 time to evaluate : 3.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 HIS cc_start: 0.8752 (t-90) cc_final: 0.8531 (t-90) REVERT: A 131 CYS cc_start: 0.9012 (m) cc_final: 0.8802 (m) REVERT: A 188 GLU cc_start: 0.7881 (mp0) cc_final: 0.7663 (mp0) REVERT: C 85 CYS cc_start: 0.8403 (m) cc_final: 0.8028 (m) REVERT: C 245 ARG cc_start: 0.7097 (mtt180) cc_final: 0.6374 (mmp80) REVERT: C 410 LEU cc_start: 0.8595 (mp) cc_final: 0.8076 (pp) REVERT: C 696 ASP cc_start: 0.8527 (t0) cc_final: 0.8303 (t0) REVERT: C 781 ASP cc_start: 0.8059 (m-30) cc_final: 0.7839 (m-30) REVERT: C 1107 MET cc_start: 0.4454 (mmt) cc_final: 0.3487 (mtm) REVERT: C 1164 PHE cc_start: 0.8630 (m-10) cc_final: 0.8421 (m-80) REVERT: C 1214 ASP cc_start: 0.8900 (t70) cc_final: 0.8385 (t70) REVERT: C 1240 ASP cc_start: 0.8829 (m-30) cc_final: 0.8389 (t0) REVERT: C 1272 GLU cc_start: 0.8985 (pm20) cc_final: 0.8502 (pm20) REVERT: C 1273 MET cc_start: 0.8792 (mmm) cc_final: 0.8365 (mmm) REVERT: C 1321 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8484 (tp30) REVERT: D 76 LYS cc_start: 0.5266 (mmtt) cc_final: 0.4719 (tptp) REVERT: D 130 MET cc_start: 0.8092 (ttm) cc_final: 0.7452 (ttm) REVERT: D 180 MET cc_start: 0.7727 (ttm) cc_final: 0.7161 (ttp) REVERT: D 192 MET cc_start: 0.8922 (ptt) cc_final: 0.8561 (ptp) REVERT: D 298 MET cc_start: 0.8755 (ptp) cc_final: 0.8035 (ptp) REVERT: D 400 MET cc_start: 0.8444 (ttm) cc_final: 0.7354 (tpp) REVERT: D 435 GLN cc_start: 0.9024 (mt0) cc_final: 0.8537 (mp10) REVERT: D 475 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8420 (mm-30) REVERT: D 525 MET cc_start: 0.8905 (mtt) cc_final: 0.8623 (mtt) REVERT: D 604 MET cc_start: 0.9252 (tpp) cc_final: 0.8986 (ttm) REVERT: D 719 PHE cc_start: 0.3915 (m-10) cc_final: 0.3574 (m-10) REVERT: D 1075 ARG cc_start: 0.4691 (mmt90) cc_final: 0.2996 (mmp-170) REVERT: D 1254 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8573 (mt-10) REVERT: D 1290 ARG cc_start: 0.7797 (mmt180) cc_final: 0.7353 (mtt-85) REVERT: D 1309 ILE cc_start: 0.9326 (pt) cc_final: 0.8927 (mt) REVERT: F 102 MET cc_start: 0.8165 (ttp) cc_final: 0.7579 (tmm) REVERT: F 104 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8084 (mm-30) REVERT: F 489 MET cc_start: 0.8216 (mpp) cc_final: 0.7916 (mmt) REVERT: F 499 LYS cc_start: 0.8413 (pttp) cc_final: 0.8035 (ttmt) REVERT: F 571 TYR cc_start: 0.6432 (m-80) cc_final: 0.5911 (m-80) REVERT: J 18 ILE cc_start: 0.7411 (pt) cc_final: 0.7103 (pt) REVERT: J 50 LEU cc_start: 0.7567 (tp) cc_final: 0.7213 (pt) REVERT: J 58 ARG cc_start: 0.7119 (mtt90) cc_final: 0.6873 (tpp80) REVERT: J 78 MET cc_start: 0.6141 (ttp) cc_final: 0.5182 (tpt) outliers start: 0 outliers final: 0 residues processed: 425 average time/residue: 0.4250 time to fit residues: 298.9125 Evaluate side-chains 321 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 321 time to evaluate : 3.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 369 optimal weight: 10.0000 chunk 43 optimal weight: 30.0000 chunk 218 optimal weight: 10.0000 chunk 279 optimal weight: 1.9990 chunk 216 optimal weight: 5.9990 chunk 322 optimal weight: 7.9990 chunk 213 optimal weight: 10.0000 chunk 381 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 232 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 HIS ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 GLN ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 673 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C1023 HIS ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 477 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 716 GLN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 33809 Z= 0.328 Angle : 0.694 9.920 46192 Z= 0.364 Chirality : 0.045 0.195 5259 Planarity : 0.005 0.071 5591 Dihedral : 16.435 178.497 5643 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.87 % Favored : 91.11 % Rotamer: Outliers : 0.03 % Allowed : 2.42 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % 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: -2.52 (0.13), residues: 3845 helix: -1.25 (0.14), residues: 1327 sheet: -1.31 (0.26), residues: 345 loop : -2.05 (0.13), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP C1276 HIS 0.009 0.001 HIS J 17 PHE 0.026 0.002 PHE C 53 TYR 0.032 0.002 TYR J 37 ARG 0.007 0.001 ARG C1246 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 405 time to evaluate : 3.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 HIS cc_start: 0.8777 (t-90) cc_final: 0.8528 (t-90) REVERT: A 131 CYS cc_start: 0.8969 (m) cc_final: 0.8705 (m) REVERT: A 188 GLU cc_start: 0.7891 (mp0) cc_final: 0.7677 (mp0) REVERT: B 198 LEU cc_start: 0.8986 (mt) cc_final: 0.8669 (pp) REVERT: C 85 CYS cc_start: 0.8448 (m) cc_final: 0.8216 (m) REVERT: C 245 ARG cc_start: 0.7134 (mtt180) cc_final: 0.6443 (mmp80) REVERT: C 410 LEU cc_start: 0.8602 (mp) cc_final: 0.8045 (pp) REVERT: C 659 GLN cc_start: 0.8700 (tt0) cc_final: 0.8388 (tm-30) REVERT: C 696 ASP cc_start: 0.8589 (t0) cc_final: 0.8317 (t0) REVERT: C 781 ASP cc_start: 0.7966 (m-30) cc_final: 0.7760 (m-30) REVERT: C 1164 PHE cc_start: 0.8691 (m-10) cc_final: 0.8464 (m-80) REVERT: C 1214 ASP cc_start: 0.8854 (t70) cc_final: 0.8344 (t70) REVERT: C 1240 ASP cc_start: 0.8825 (m-30) cc_final: 0.8397 (t0) REVERT: C 1253 LEU cc_start: 0.9580 (tp) cc_final: 0.9378 (tp) REVERT: C 1272 GLU cc_start: 0.9100 (pm20) cc_final: 0.8632 (pm20) REVERT: C 1273 MET cc_start: 0.8748 (mmm) cc_final: 0.7922 (mmm) REVERT: C 1321 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8055 (tp30) REVERT: D 130 MET cc_start: 0.8161 (ttm) cc_final: 0.7562 (ttm) REVERT: D 180 MET cc_start: 0.7809 (ttm) cc_final: 0.7083 (ttp) REVERT: D 192 MET cc_start: 0.8923 (ptt) cc_final: 0.8639 (ptp) REVERT: D 298 MET cc_start: 0.8737 (ptp) cc_final: 0.7977 (ptp) REVERT: D 400 MET cc_start: 0.8561 (ttm) cc_final: 0.7483 (tpp) REVERT: D 435 GLN cc_start: 0.8999 (mt0) cc_final: 0.8551 (mp10) REVERT: D 457 TYR cc_start: 0.9097 (m-10) cc_final: 0.8789 (m-10) REVERT: D 475 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8733 (mm-30) REVERT: D 719 PHE cc_start: 0.3676 (m-10) cc_final: 0.3289 (m-10) REVERT: D 1040 MET cc_start: 0.2007 (ptt) cc_final: 0.1629 (ptp) REVERT: D 1075 ARG cc_start: 0.5262 (mtt-85) cc_final: 0.3933 (mmp-170) REVERT: D 1254 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8638 (mt-10) REVERT: D 1290 ARG cc_start: 0.7694 (mmt180) cc_final: 0.7241 (mtt-85) REVERT: D 1309 ILE cc_start: 0.9359 (pt) cc_final: 0.8841 (mt) REVERT: F 102 MET cc_start: 0.8074 (ttp) cc_final: 0.7471 (tmm) REVERT: F 104 GLU cc_start: 0.8314 (mm-30) cc_final: 0.8058 (mm-30) REVERT: F 499 LYS cc_start: 0.8415 (pttp) cc_final: 0.8029 (ttmt) REVERT: J 18 ILE cc_start: 0.7578 (pt) cc_final: 0.7246 (pt) REVERT: J 58 ARG cc_start: 0.7083 (mtt90) cc_final: 0.6822 (tpp80) outliers start: 1 outliers final: 0 residues processed: 406 average time/residue: 0.4175 time to fit residues: 282.1458 Evaluate side-chains 311 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 3.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 236 optimal weight: 10.0000 chunk 152 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 chunk 114 optimal weight: 0.5980 chunk 74 optimal weight: 7.9990 chunk 73 optimal weight: 0.8980 chunk 242 optimal weight: 3.9990 chunk 260 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 300 optimal weight: 20.0000 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN C1023 HIS ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 364 HIS D 489 ASN ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1326 GLN E 75 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 383 ASN ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33809 Z= 0.221 Angle : 0.619 11.672 46192 Z= 0.325 Chirality : 0.043 0.209 5259 Planarity : 0.004 0.066 5591 Dihedral : 16.391 176.859 5643 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.33 % Favored : 92.64 % Rotamer: Outliers : 0.03 % Allowed : 1.30 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % 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: -2.23 (0.13), residues: 3845 helix: -0.99 (0.14), residues: 1329 sheet: -1.13 (0.27), residues: 351 loop : -1.89 (0.13), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP C1276 HIS 0.006 0.001 HIS J 17 PHE 0.020 0.001 PHE C 972 TYR 0.032 0.002 TYR J 37 ARG 0.006 0.000 ARG C1246 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 433 time to evaluate : 3.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 HIS cc_start: 0.8719 (t-90) cc_final: 0.8485 (t-90) REVERT: A 131 CYS cc_start: 0.8845 (m) cc_final: 0.8526 (m) REVERT: A 188 GLU cc_start: 0.7893 (mp0) cc_final: 0.7653 (mp0) REVERT: B 185 TYR cc_start: 0.9096 (p90) cc_final: 0.8783 (p90) REVERT: B 198 LEU cc_start: 0.8926 (mt) cc_final: 0.8708 (pp) REVERT: C 85 CYS cc_start: 0.8370 (m) cc_final: 0.8167 (m) REVERT: C 118 LYS cc_start: 0.8335 (pttt) cc_final: 0.8026 (pttp) REVERT: C 245 ARG cc_start: 0.7096 (mtt180) cc_final: 0.6288 (mmp80) REVERT: C 410 LEU cc_start: 0.8591 (mp) cc_final: 0.8063 (pp) REVERT: C 429 MET cc_start: 0.9448 (mmm) cc_final: 0.9228 (mmm) REVERT: C 680 LEU cc_start: 0.9512 (mt) cc_final: 0.9307 (mm) REVERT: C 696 ASP cc_start: 0.8550 (t0) cc_final: 0.8306 (t0) REVERT: C 741 MET cc_start: 0.7272 (ptt) cc_final: 0.7032 (ptt) REVERT: C 781 ASP cc_start: 0.7997 (m-30) cc_final: 0.7762 (m-30) REVERT: C 850 ILE cc_start: 0.9136 (mm) cc_final: 0.8900 (mm) REVERT: C 952 GLN cc_start: 0.9289 (mt0) cc_final: 0.9063 (mt0) REVERT: C 1214 ASP cc_start: 0.8837 (t70) cc_final: 0.8288 (t70) REVERT: C 1238 LEU cc_start: 0.9263 (mp) cc_final: 0.8831 (mp) REVERT: C 1240 ASP cc_start: 0.8799 (m-30) cc_final: 0.8385 (t0) REVERT: C 1253 LEU cc_start: 0.9536 (tp) cc_final: 0.9249 (tp) REVERT: C 1273 MET cc_start: 0.8696 (mmm) cc_final: 0.8412 (mmm) REVERT: C 1321 GLU cc_start: 0.8849 (mm-30) cc_final: 0.7872 (tp30) REVERT: D 130 MET cc_start: 0.8118 (ttm) cc_final: 0.7532 (ttm) REVERT: D 180 MET cc_start: 0.7718 (ttm) cc_final: 0.7065 (ttp) REVERT: D 370 LYS cc_start: 0.9284 (mmtm) cc_final: 0.9052 (mmtm) REVERT: D 407 VAL cc_start: 0.9153 (m) cc_final: 0.8754 (p) REVERT: D 435 GLN cc_start: 0.8980 (mt0) cc_final: 0.8469 (mp10) REVERT: D 457 TYR cc_start: 0.8966 (m-10) cc_final: 0.8588 (m-10) REVERT: D 465 GLN cc_start: 0.8856 (mp10) cc_final: 0.8347 (mp10) REVERT: D 475 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8520 (mm-30) REVERT: D 605 LEU cc_start: 0.9519 (mp) cc_final: 0.9314 (mp) REVERT: D 719 PHE cc_start: 0.3612 (m-10) cc_final: 0.3254 (m-10) REVERT: D 725 MET cc_start: 0.9059 (tmm) cc_final: 0.8805 (tmm) REVERT: D 1075 ARG cc_start: 0.5529 (mtt-85) cc_final: 0.4071 (mmp-170) REVERT: D 1254 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8472 (mt-10) REVERT: D 1286 LYS cc_start: 0.9035 (pttt) cc_final: 0.8827 (mmmt) REVERT: D 1290 ARG cc_start: 0.7780 (mmt180) cc_final: 0.7378 (mtt-85) REVERT: D 1309 ILE cc_start: 0.9308 (pt) cc_final: 0.8888 (mt) REVERT: F 277 MET cc_start: 0.9414 (tmm) cc_final: 0.9206 (tmm) REVERT: F 489 MET cc_start: 0.8455 (mpp) cc_final: 0.8005 (mpp) REVERT: J 17 HIS cc_start: 0.6459 (m170) cc_final: 0.6154 (m170) REVERT: J 18 ILE cc_start: 0.7441 (pt) cc_final: 0.6590 (mt) outliers start: 1 outliers final: 0 residues processed: 434 average time/residue: 0.4300 time to fit residues: 308.5141 Evaluate side-chains 326 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 3.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 347 optimal weight: 7.9990 chunk 365 optimal weight: 4.9990 chunk 333 optimal weight: 0.7980 chunk 355 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 chunk 154 optimal weight: 0.0470 chunk 279 optimal weight: 10.0000 chunk 109 optimal weight: 10.0000 chunk 321 optimal weight: 7.9990 chunk 336 optimal weight: 6.9990 chunk 354 optimal weight: 0.9980 overall best weight: 2.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN D 606 ASN ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 921 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1326 GLN ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.4863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33809 Z= 0.205 Angle : 0.612 9.673 46192 Z= 0.319 Chirality : 0.042 0.191 5259 Planarity : 0.004 0.064 5591 Dihedral : 16.379 177.602 5643 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.18 % Favored : 92.77 % Rotamer: Outliers : 0.03 % Allowed : 0.79 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % 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: -2.09 (0.13), residues: 3845 helix: -0.88 (0.14), residues: 1337 sheet: -0.97 (0.28), residues: 343 loop : -1.82 (0.13), residues: 2165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP C1276 HIS 0.005 0.001 HIS J 17 PHE 0.017 0.001 PHE C 972 TYR 0.032 0.002 TYR J 37 ARG 0.006 0.000 ARG C 540 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 427 time to evaluate : 3.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 HIS cc_start: 0.8742 (t-90) cc_final: 0.8477 (t-90) REVERT: A 131 CYS cc_start: 0.8916 (m) cc_final: 0.8610 (m) REVERT: A 188 GLU cc_start: 0.7878 (mp0) cc_final: 0.7631 (mp0) REVERT: B 185 TYR cc_start: 0.9045 (p90) cc_final: 0.8721 (p90) REVERT: C 386 GLU cc_start: 0.7450 (mm-30) cc_final: 0.7019 (tp30) REVERT: C 410 LEU cc_start: 0.8599 (mp) cc_final: 0.8108 (pp) REVERT: C 429 MET cc_start: 0.9435 (mmm) cc_final: 0.9193 (mmm) REVERT: C 696 ASP cc_start: 0.8474 (t0) cc_final: 0.8250 (t0) REVERT: C 781 ASP cc_start: 0.7897 (m-30) cc_final: 0.7656 (m-30) REVERT: C 850 ILE cc_start: 0.9125 (mm) cc_final: 0.8900 (mm) REVERT: C 952 GLN cc_start: 0.9292 (mt0) cc_final: 0.9060 (mt0) REVERT: C 1164 PHE cc_start: 0.8470 (m-10) cc_final: 0.8197 (m-10) REVERT: C 1214 ASP cc_start: 0.8911 (t70) cc_final: 0.8320 (t70) REVERT: C 1238 LEU cc_start: 0.9254 (mp) cc_final: 0.8853 (mp) REVERT: C 1240 ASP cc_start: 0.8777 (m-30) cc_final: 0.8406 (t0) REVERT: C 1272 GLU cc_start: 0.8944 (pm20) cc_final: 0.8364 (pm20) REVERT: C 1321 GLU cc_start: 0.8870 (mm-30) cc_final: 0.7931 (tp30) REVERT: D 130 MET cc_start: 0.8099 (ttm) cc_final: 0.7534 (ttm) REVERT: D 180 MET cc_start: 0.7674 (ttm) cc_final: 0.6999 (ttp) REVERT: D 289 ASP cc_start: 0.8489 (m-30) cc_final: 0.7995 (t0) REVERT: D 370 LYS cc_start: 0.9295 (mmtm) cc_final: 0.9082 (mmtm) REVERT: D 407 VAL cc_start: 0.9157 (m) cc_final: 0.8779 (p) REVERT: D 435 GLN cc_start: 0.8960 (mt0) cc_final: 0.8455 (mp10) REVERT: D 457 TYR cc_start: 0.8903 (m-10) cc_final: 0.8457 (m-10) REVERT: D 475 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8553 (mm-30) REVERT: D 604 MET cc_start: 0.9230 (tpp) cc_final: 0.9018 (tpp) REVERT: D 719 PHE cc_start: 0.3638 (m-10) cc_final: 0.3293 (m-10) REVERT: D 725 MET cc_start: 0.9059 (tmm) cc_final: 0.8806 (tmm) REVERT: D 1075 ARG cc_start: 0.5605 (mtt-85) cc_final: 0.4130 (mmp-170) REVERT: D 1143 ASP cc_start: 0.8421 (m-30) cc_final: 0.8170 (t0) REVERT: D 1254 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8495 (mt-10) REVERT: D 1256 ILE cc_start: 0.9429 (pt) cc_final: 0.9065 (tt) REVERT: D 1286 LYS cc_start: 0.9073 (pttt) cc_final: 0.8805 (mmmt) REVERT: D 1290 ARG cc_start: 0.7725 (mmt180) cc_final: 0.7336 (mtt-85) REVERT: D 1309 ILE cc_start: 0.9321 (pt) cc_final: 0.8853 (mt) REVERT: F 227 GLN cc_start: 0.6790 (mm-40) cc_final: 0.5253 (tm-30) REVERT: F 277 MET cc_start: 0.9423 (tmm) cc_final: 0.9216 (tmm) REVERT: F 489 MET cc_start: 0.8479 (mpp) cc_final: 0.7950 (mpp) REVERT: J 17 HIS cc_start: 0.6292 (m170) cc_final: 0.6024 (m170) outliers start: 1 outliers final: 0 residues processed: 428 average time/residue: 0.4156 time to fit residues: 295.2960 Evaluate side-chains 335 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 335 time to evaluate : 3.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 233 optimal weight: 10.0000 chunk 376 optimal weight: 10.0000 chunk 229 optimal weight: 6.9990 chunk 178 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 394 optimal weight: 20.0000 chunk 363 optimal weight: 8.9990 chunk 314 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 242 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 357 GLN ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 33809 Z= 0.192 Angle : 0.604 9.650 46192 Z= 0.314 Chirality : 0.042 0.201 5259 Planarity : 0.004 0.062 5591 Dihedral : 16.372 177.707 5643 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.92 % Favored : 93.06 % Rotamer: Outliers : 0.03 % Allowed : 0.24 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.13), residues: 3845 helix: -0.78 (0.14), residues: 1343 sheet: -0.89 (0.27), residues: 355 loop : -1.74 (0.13), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP C1276 HIS 0.005 0.001 HIS J 17 PHE 0.019 0.001 PHE D1325 TYR 0.040 0.001 TYR C1229 ARG 0.010 0.000 ARG C1246 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7690 Ramachandran restraints generated. 3845 Oldfield, 0 Emsley, 3845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 429 time to evaluate : 3.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 HIS cc_start: 0.8752 (t-90) cc_final: 0.8495 (t-90) REVERT: A 131 CYS cc_start: 0.8874 (m) cc_final: 0.8600 (m) REVERT: A 186 ASN cc_start: 0.8934 (m110) cc_final: 0.8659 (m110) REVERT: A 188 GLU cc_start: 0.7892 (mp0) cc_final: 0.7608 (mp0) REVERT: A 201 LEU cc_start: 0.9160 (tp) cc_final: 0.8919 (tt) REVERT: A 226 GLU cc_start: 0.8223 (tt0) cc_final: 0.7888 (tm-30) REVERT: B 185 TYR cc_start: 0.9081 (p90) cc_final: 0.8679 (p90) REVERT: C 85 CYS cc_start: 0.8167 (m) cc_final: 0.7931 (m) REVERT: C 245 ARG cc_start: 0.7036 (mtt180) cc_final: 0.6257 (mmp80) REVERT: C 386 GLU cc_start: 0.7345 (mm-30) cc_final: 0.6924 (tp30) REVERT: C 410 LEU cc_start: 0.8582 (mp) cc_final: 0.8098 (pp) REVERT: C 429 MET cc_start: 0.9417 (mmm) cc_final: 0.9167 (mmm) REVERT: C 533 LEU cc_start: 0.9151 (mp) cc_final: 0.8882 (mp) REVERT: C 696 ASP cc_start: 0.8463 (t0) cc_final: 0.8249 (t0) REVERT: C 952 GLN cc_start: 0.9285 (mt0) cc_final: 0.9030 (mt0) REVERT: C 1164 PHE cc_start: 0.8442 (m-10) cc_final: 0.8142 (m-10) REVERT: C 1214 ASP cc_start: 0.8847 (t70) cc_final: 0.8357 (t70) REVERT: C 1238 LEU cc_start: 0.9260 (mp) cc_final: 0.8835 (mp) REVERT: C 1240 ASP cc_start: 0.8793 (m-30) cc_final: 0.8389 (t0) REVERT: C 1253 LEU cc_start: 0.9557 (tp) cc_final: 0.9269 (tp) REVERT: C 1321 GLU cc_start: 0.8841 (mm-30) cc_final: 0.7811 (tp30) REVERT: D 134 ASP cc_start: 0.8644 (m-30) cc_final: 0.8198 (m-30) REVERT: D 180 MET cc_start: 0.7605 (ttm) cc_final: 0.6933 (ttp) REVERT: D 299 LEU cc_start: 0.9207 (tp) cc_final: 0.8995 (tp) REVERT: D 370 LYS cc_start: 0.9299 (mmtm) cc_final: 0.9056 (mmtm) REVERT: D 400 MET cc_start: 0.8404 (tpp) cc_final: 0.8157 (tpp) REVERT: D 407 VAL cc_start: 0.9147 (m) cc_final: 0.8789 (p) REVERT: D 435 GLN cc_start: 0.8965 (mt0) cc_final: 0.8351 (mp10) REVERT: D 457 TYR cc_start: 0.8755 (m-10) cc_final: 0.8214 (m-10) REVERT: D 475 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8513 (mm-30) REVERT: D 719 PHE cc_start: 0.3521 (m-10) cc_final: 0.3170 (m-10) REVERT: D 725 MET cc_start: 0.9071 (tmm) cc_final: 0.8837 (tmm) REVERT: D 921 GLN cc_start: 0.8805 (mt0) cc_final: 0.8533 (mt0) REVERT: D 1075 ARG cc_start: 0.5598 (mtt-85) cc_final: 0.4090 (mmp-170) REVERT: D 1143 ASP cc_start: 0.8537 (m-30) cc_final: 0.8176 (t0) REVERT: D 1254 GLU cc_start: 0.8800 (mt-10) cc_final: 0.8450 (mt-10) REVERT: D 1256 ILE cc_start: 0.9444 (pt) cc_final: 0.9088 (tt) REVERT: D 1286 LYS cc_start: 0.9093 (pttt) cc_final: 0.8805 (mttt) REVERT: D 1290 ARG cc_start: 0.7724 (mmt180) cc_final: 0.7371 (mtt-85) REVERT: D 1309 ILE cc_start: 0.9324 (pt) cc_final: 0.8850 (mt) REVERT: E 73 GLN cc_start: 0.8971 (mt0) cc_final: 0.8618 (mp10) REVERT: F 227 GLN cc_start: 0.6799 (mm-40) cc_final: 0.5339 (tm-30) REVERT: F 277 MET cc_start: 0.9417 (tmm) cc_final: 0.9212 (tmm) REVERT: F 378 GLU cc_start: 0.9082 (tt0) cc_final: 0.8793 (pp20) REVERT: F 489 MET cc_start: 0.8535 (mpp) cc_final: 0.7972 (mpp) REVERT: J 17 HIS cc_start: 0.6398 (m170) cc_final: 0.6149 (m170) REVERT: J 18 ILE cc_start: 0.7410 (pt) cc_final: 0.6861 (mt) REVERT: J 58 ARG cc_start: 0.6826 (mtt-85) cc_final: 0.6229 (ttm170) outliers start: 1 outliers final: 1 residues processed: 430 average time/residue: 0.4179 time to fit residues: 299.5787 Evaluate side-chains 346 residues out of total 3327 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 345 time to evaluate : 3.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 396 random chunks: chunk 249 optimal weight: 10.0000 chunk 334 optimal weight: 0.0570 chunk 96 optimal weight: 20.0000 chunk 289 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 314 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 323 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 overall best weight: 4.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 760 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 856 ASN ** C1072 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 489 ASN ** D 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.120292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.093461 restraints weight = 101370.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.092523 restraints weight = 90968.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.093220 restraints weight = 76141.601| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 33809 Z= 0.252 Angle : 0.642 10.206 46192 Z= 0.334 Chirality : 0.043 0.200 5259 Planarity : 0.004 0.060 5591 Dihedral : 16.442 179.507 5643 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.27 % Favored : 91.70 % Rotamer: Outliers : 0.03 % Allowed : 0.33 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.68 % 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: -2.07 (0.13), residues: 3845 helix: -0.88 (0.14), residues: 1361 sheet: -0.92 (0.27), residues: 357 loop : -1.80 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP C1276 HIS 0.005 0.001 HIS J 17 PHE 0.028 0.002 PHE B 35 TYR 0.032 0.002 TYR C1229 ARG 0.011 0.000 ARG C1246 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6988.12 seconds wall clock time: 126 minutes 44.39 seconds (7604.39 seconds total)