Starting phenix.real_space_refine on Sun Feb 25 14:13:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nky_12450/02_2024/7nky_12450.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nky_12450/02_2024/7nky_12450.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nky_12450/02_2024/7nky_12450.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nky_12450/02_2024/7nky_12450.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nky_12450/02_2024/7nky_12450.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nky_12450/02_2024/7nky_12450.pdb" } resolution = 3.2 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= 0.001 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 9 6.06 5 P 301 5.49 5 Mg 1 5.21 5 S 223 5.16 5 C 31754 2.51 5 N 9175 2.21 5 O 10379 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 55": "OD1" <-> "OD2" Residue "A GLU 280": "OE1" <-> "OE2" Residue "A GLU 496": "OE1" <-> "OE2" Residue "A GLU 618": "OE1" <-> "OE2" Residue "A PHE 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 905": "OD1" <-> "OD2" Residue "A ASP 909": "OD1" <-> "OD2" Residue "A ASP 1043": "OD1" <-> "OD2" Residue "A GLU 1277": "OE1" <-> "OE2" Residue "A TYR 1453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1181": "OE1" <-> "OE2" Residue "B ASP 1186": "OD1" <-> "OD2" Residue "B GLU 1206": "OE1" <-> "OE2" Residue "C GLU 138": "OE1" <-> "OE2" Residue "E PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 84": "OD1" <-> "OD2" Residue "E TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 116": "OD1" <-> "OD2" Residue "F TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 14": "OE1" <-> "OE2" Residue "H ASP 53": "OD1" <-> "OD2" Residue "H ASP 91": "OD1" <-> "OD2" Residue "H ASP 92": "OD1" <-> "OD2" Residue "H TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 106": "OE1" <-> "OE2" Residue "I ASP 72": "OD1" <-> "OD2" Residue "I GLU 74": "OE1" <-> "OE2" Residue "J ASP 55": "OD1" <-> "OD2" Residue "J GLU 58": "OE1" <-> "OE2" Residue "K GLU 38": "OE1" <-> "OE2" Residue "K GLU 79": "OE1" <-> "OE2" Residue "Z TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 830": "OE1" <-> "OE2" Residue "G ASP 65": "OD1" <-> "OD2" Residue "G TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 684": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 761": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 889": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 94": "OE1" <-> "OE2" Residue "a GLU 97": "OE1" <-> "OE2" Residue "b ASP 24": "OD1" <-> "OD2" Residue "b GLU 52": "OE1" <-> "OE2" Residue "b GLU 63": "OE1" <-> "OE2" Residue "b ASP 68": "OD1" <-> "OD2" Residue "b ARG 78": "NH1" <-> "NH2" Residue "b TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 32": "NH1" <-> "NH2" Residue "c GLU 64": "OE1" <-> "OE2" Residue "c GLU 91": "OE1" <-> "OE2" Residue "d ASP 48": "OD1" <-> "OD2" Residue "d GLU 68": "OE1" <-> "OE2" Residue "e TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 123": "OD1" <-> "OD2" Residue "f GLU 63": "OE1" <-> "OE2" Residue "f TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 92": "OE1" <-> "OE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 51842 Number of models: 1 Model: "" Number of chains: 34 Chain: "P" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 325 Classifications: {'RNA': 16} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 2, 'rna3p_pyr': 12} Link IDs: {'rna2p': 2, 'rna3p': 13} Chain: "N" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 2843 Classifications: {'DNA': 138} Link IDs: {'rna3p': 137} Chain breaks: 1 Chain: "T" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 3022 Classifications: {'DNA': 148} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 147} Chain: "A" Number of atoms: 11092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1410, 11092 Classifications: {'peptide': 1410} Link IDs: {'PTRANS': 65, 'TRANS': 1344} Chain breaks: 5 Chain: "B" Number of atoms: 8865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1116, 8865 Classifications: {'peptide': 1116} Link IDs: {'PTRANS': 50, 'TRANS': 1065} Chain breaks: 6 Chain: "C" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2086 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 11, 'TRANS': 253} Chain: "E" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1752 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "F" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 705 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 80} Chain: "H" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1068 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain breaks: 1 Chain: "I" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 971 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain: "J" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 1 Chain: "L" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 351 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "Y" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 739 Classifications: {'peptide': 98} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 6, 'TRANS': 91} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "Z" Number of atoms: 1252 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1252 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 149} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1444 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 177} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1340 Classifications: {'peptide': 171} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 162} Chain: "O" Number of atoms: 3481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3481 Classifications: {'peptide': 427} Link IDs: {'CIS': 2, 'PCIS': 3, 'PTRANS': 12, 'TRANS': 409} Chain breaks: 3 Chain: "Q" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 404, 3264 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 384} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "a" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 720 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "b" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "c" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 786 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "d" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "e" Number of atoms: 775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 775 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "f" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "g" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 747 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "h" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 7003 SG CYS A 107 81.562 73.910 138.191 1.00 94.55 S ATOM 7027 SG CYS A 110 78.882 72.008 137.277 1.00 93.22 S ATOM 7332 SG CYS A 148 83.230 71.165 136.128 1.00110.66 S ATOM 7470 SG CYS A 167 79.920 74.365 134.989 1.00109.52 S ATOM 6698 SG CYS A 67 52.899 81.490 176.187 1.00 96.18 S ATOM 6720 SG CYS A 70 52.392 78.076 177.565 1.00 86.37 S ATOM 6773 SG CYS A 77 55.486 79.576 177.639 1.00 85.29 S ATOM 25665 SG CYS B1163 57.956 66.442 167.919 1.00 86.50 S ATOM 25683 SG CYS B1166 59.968 68.430 166.101 1.00 86.11 S ATOM 25808 SG CYS B1182 56.321 69.224 166.755 1.00 89.79 S ATOM 25827 SG CYS B1185 57.881 67.678 163.458 1.00 96.76 S ATOM 26794 SG CYS C 86 62.921 87.567 243.830 1.00104.48 S ATOM 26811 SG CYS C 88 61.769 90.233 241.036 1.00133.03 S ATOM 26867 SG CYS C 95 65.637 89.273 242.462 1.00 85.25 S ATOM 31811 SG CYS I 7 137.772 109.539 147.422 1.00154.91 S ATOM 31836 SG CYS I 10 135.318 111.890 146.317 1.00152.97 S ATOM 32002 SG CYS I 29 135.491 107.122 145.587 1.00162.69 S ATOM 32026 SG CYS I 32 136.999 109.925 144.041 1.00158.29 S ATOM 32353 SG CYS I 75 152.844 97.944 188.628 1.00108.56 S ATOM 32375 SG CYS I 78 154.236 101.164 189.867 1.00106.16 S ATOM 32591 SG CYS I 103 150.614 101.536 189.428 1.00103.97 S ATOM 32611 SG CYS I 106 152.481 101.356 186.523 1.00114.87 S ATOM 32783 SG CYS J 7 95.544 91.301 233.968 1.00 61.24 S ATOM 32806 SG CYS J 10 95.382 89.040 237.217 1.00 63.01 S ATOM 33086 SG CYS J 45 98.509 89.437 234.916 1.00 59.59 S ATOM 33092 SG CYS J 46 97.464 92.051 237.233 1.00 58.26 S ATOM 34224 SG CYS L 31 73.513 122.867 214.005 1.00 97.76 S ATOM 34348 SG CYS L 48 70.625 124.899 213.794 1.00 92.96 S ATOM 34371 SG CYS L 51 74.429 126.297 212.872 1.00 97.84 S ATOM 34569 SG CYS Y 7 59.504 126.172 139.405 1.00241.41 S ATOM 34591 SG CYS Y 10 62.580 126.690 137.927 1.00240.25 S ATOM 34698 SG CYS Y 24 61.040 129.657 139.197 1.00244.34 S ATOM 34719 SG CYS Y 27 60.770 127.928 135.290 1.00248.53 S Time building chain proxies: 25.66, per 1000 atoms: 0.49 Number of scatterers: 51842 At special positions: 0 Unit cell: (203.7, 174.3, 274.05, 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 9 29.99 S 223 16.00 P 301 15.00 Mg 1 11.99 O 10379 8.00 N 9175 7.00 C 31754 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: 21.37 Conformation dependent library (CDL) restraints added in 8.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1801 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 110 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 107 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 148 " pdb="ZN ZN A1801 " - pdb=" SG CYS A 167 " pdb=" ZN A1802 " pdb="ZN ZN A1802 " - pdb=" NE2 HIS A 80 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 70 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 77 " pdb="ZN ZN A1802 " - pdb=" SG CYS A 67 " pdb=" ZN B1301 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1185 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1163 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1182 " pdb="ZN ZN B1301 " - pdb=" SG CYS B1166 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 95 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 88 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 86 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 29 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 10 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 7 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 32 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 103 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 75 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 106 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 78 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 10 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 46 " pdb=" ZN L 101 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 51 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 31 " pdb="ZN ZN L 101 " - pdb=" SG CYS L 48 " pdb=" ZN Y 300 " pdb="ZN ZN Y 300 " - pdb=" SG CYS Y 10 " pdb="ZN ZN Y 300 " - pdb=" SG CYS Y 24 " pdb="ZN ZN Y 300 " - pdb=" SG CYS Y 7 " pdb="ZN ZN Y 300 " - pdb=" SG CYS Y 27 " Number of angles added : 39 11296 Ramachandran restraints generated. 5648 Oldfield, 0 Emsley, 5648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10764 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 70 sheets defined 40.2% alpha, 17.0% beta 127 base pairs and 254 stacking pairs defined. Time for finding SS restraints: 21.49 Creating SS restraints... Processing helix chain 'A' and resid 23 through 31 Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 55 through 59 Processing helix chain 'A' and resid 95 through 106 Processing helix chain 'A' and resid 119 through 128 removed outlier: 3.718A pdb=" N ILE A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 145 removed outlier: 4.152A pdb=" N THR A 144 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS A 145 " --> pdb=" O LEU A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 214 Processing helix chain 'A' and resid 215 through 222 removed outlier: 3.632A pdb=" N LEU A 222 " --> pdb=" O ASP A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 235 Processing helix chain 'A' and resid 243 through 247 Processing helix chain 'A' and resid 260 through 282 Processing helix chain 'A' and resid 287 through 305 Processing helix chain 'A' and resid 324 through 331 removed outlier: 4.505A pdb=" N GLY A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 374 Processing helix chain 'A' and resid 384 through 395 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 471 through 473 No H-bonds generated for 'chain 'A' and resid 471 through 473' Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.636A pdb=" N TYR A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 524 through 536 Processing helix chain 'A' and resid 542 through 553 Processing helix chain 'A' and resid 574 through 580 removed outlier: 3.664A pdb=" N VAL A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 623 Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 661 Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.787A pdb=" N THR A 669 " --> pdb=" O GLY A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 699 Processing helix chain 'A' and resid 709 through 737 Processing helix chain 'A' and resid 741 through 750 Processing helix chain 'A' and resid 754 through 763 Processing helix chain 'A' and resid 809 through 845 removed outlier: 3.871A pdb=" N ALA A 832 " --> pdb=" O ALA A 828 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 871 Processing helix chain 'A' and resid 874 through 878 Processing helix chain 'A' and resid 889 through 898 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 915 through 920 Processing helix chain 'A' and resid 922 through 947 Processing helix chain 'A' and resid 959 through 972 Processing helix chain 'A' and resid 982 through 997 Processing helix chain 'A' and resid 1004 through 1015 Processing helix chain 'A' and resid 1015 through 1026 Processing helix chain 'A' and resid 1027 through 1033 Processing helix chain 'A' and resid 1038 through 1057 Processing helix chain 'A' and resid 1063 through 1079 Proline residue: A1075 - end of helix removed outlier: 3.772A pdb=" N GLN A1078 " --> pdb=" O GLU A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1106 Processing helix chain 'A' and resid 1127 through 1139 Processing helix chain 'A' and resid 1143 through 1146 No H-bonds generated for 'chain 'A' and resid 1143 through 1146' Processing helix chain 'A' and resid 1163 through 1165 No H-bonds generated for 'chain 'A' and resid 1163 through 1165' Processing helix chain 'A' and resid 1166 through 1175 removed outlier: 4.095A pdb=" N ILE A1170 " --> pdb=" O ASP A1166 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1206 Processing helix chain 'A' and resid 1208 through 1220 Processing helix chain 'A' and resid 1255 through 1271 removed outlier: 3.899A pdb=" N MET A1259 " --> pdb=" O GLU A1255 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS A1261 " --> pdb=" O ASP A1257 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LYS A1262 " --> pdb=" O HIS A1258 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE A1271 " --> pdb=" O MET A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1312 through 1317 removed outlier: 3.871A pdb=" N VAL A1316 " --> pdb=" O ASN A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1340 Processing helix chain 'A' and resid 1340 through 1359 removed outlier: 4.416A pdb=" N ASP A1359 " --> pdb=" O VAL A1355 " (cutoff:3.500A) Processing helix chain 'A' and resid 1364 through 1377 removed outlier: 3.863A pdb=" N MET A1368 " --> pdb=" O ASN A1364 " (cutoff:3.500A) Processing helix chain 'A' and resid 1388 through 1392 Processing helix chain 'A' and resid 1395 through 1402 removed outlier: 3.638A pdb=" N PHE A1402 " --> pdb=" O MET A1398 " (cutoff:3.500A) Processing helix chain 'A' and resid 1404 through 1416 removed outlier: 3.736A pdb=" N ILE A1408 " --> pdb=" O GLU A1404 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1431 Processing helix chain 'A' and resid 1446 through 1454 Processing helix chain 'B' and resid 26 through 41 removed outlier: 3.716A pdb=" N TRP B 31 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 66 removed outlier: 4.675A pdb=" N LEU B 59 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLN B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ASP B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 121 Processing helix chain 'B' and resid 185 through 192 Processing helix chain 'B' and resid 282 through 290 Processing helix chain 'B' and resid 293 through 302 Processing helix chain 'B' and resid 308 through 321 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 326 through 339 Processing helix chain 'B' and resid 348 through 359 Processing helix chain 'B' and resid 371 through 390 Processing helix chain 'B' and resid 400 through 402 No H-bonds generated for 'chain 'B' and resid 400 through 402' Processing helix chain 'B' and resid 408 through 435 Processing helix chain 'B' and resid 450 through 464 Processing helix chain 'B' and resid 487 through 496 Processing helix chain 'B' and resid 509 through 513 Processing helix chain 'B' and resid 515 through 519 Processing helix chain 'B' and resid 551 through 562 Processing helix chain 'B' and resid 592 through 607 Processing helix chain 'B' and resid 654 through 668 removed outlier: 3.713A pdb=" N ASP B 668 " --> pdb=" O THR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 687 Processing helix chain 'B' and resid 696 through 701 removed outlier: 3.673A pdb=" N ILE B 701 " --> pdb=" O GLU B 698 " (cutoff:3.500A) Processing helix chain 'B' and resid 744 through 749 removed outlier: 3.531A pdb=" N LEU B 749 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 755 removed outlier: 3.558A pdb=" N ILE B 755 " --> pdb=" O ALA B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 762 Processing helix chain 'B' and resid 763 through 777 removed outlier: 4.412A pdb=" N LYS B 775 " --> pdb=" O SER B 771 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLN B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 813 Processing helix chain 'B' and resid 843 through 849 Processing helix chain 'B' and resid 1015 through 1021 removed outlier: 4.231A pdb=" N SER B1019 " --> pdb=" O HIS B1015 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1039 removed outlier: 4.193A pdb=" N LEU B1026 " --> pdb=" O THR B1022 " (cutoff:3.500A) Processing helix chain 'B' and resid 1051 through 1063 Processing helix chain 'B' and resid 1098 through 1103 Processing helix chain 'B' and resid 1131 through 1142 Processing helix chain 'B' and resid 1143 through 1152 Processing helix chain 'B' and resid 1197 through 1210 Processing helix chain 'C' and resid 26 through 40 Processing helix chain 'C' and resid 59 through 70 Processing helix chain 'C' and resid 167 through 171 Processing helix chain 'C' and resid 196 through 201 Processing helix chain 'C' and resid 206 through 210 Processing helix chain 'C' and resid 239 through 267 removed outlier: 3.544A pdb=" N VAL C 244 " --> pdb=" O VAL C 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 27 Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 46 Processing helix chain 'E' and resid 65 through 72 Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 117 through 123 removed outlier: 3.592A pdb=" N LEU E 123 " --> pdb=" O SER E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 141 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 182 through 189 Processing helix chain 'F' and resid 69 through 71 No H-bonds generated for 'chain 'F' and resid 69 through 71' Processing helix chain 'F' and resid 86 through 103 Processing helix chain 'F' and resid 116 through 128 Processing helix chain 'H' and resid 128 through 134 removed outlier: 4.442A pdb=" N ASN H 133 " --> pdb=" O ARG H 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'J' and resid 14 through 16 No H-bonds generated for 'chain 'J' and resid 14 through 16' Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 40 Processing helix chain 'J' and resid 43 through 52 Processing helix chain 'J' and resid 56 through 62 removed outlier: 4.012A pdb=" N ARG J 62 " --> pdb=" O GLU J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 10 Processing helix chain 'K' and resid 39 through 53 removed outlier: 3.610A pdb=" N GLY K 43 " --> pdb=" O ASP K 39 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 110 removed outlier: 3.705A pdb=" N ASN K 110 " --> pdb=" O GLU K 106 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 23 Processing helix chain 'Y' and resid 27 through 35 Processing helix chain 'Y' and resid 37 through 41 removed outlier: 3.643A pdb=" N CYS Y 41 " --> pdb=" O SER Y 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 37 through 41' Processing helix chain 'Y' and resid 58 through 65 Processing helix chain 'Y' and resid 83 through 88 Processing helix chain 'Z' and resid 296 through 315 Processing helix chain 'Z' and resid 341 through 350 Processing helix chain 'Z' and resid 364 through 366 No H-bonds generated for 'chain 'Z' and resid 364 through 366' Processing helix chain 'Z' and resid 367 through 372 Processing helix chain 'D' and resid 51 through 76 removed outlier: 3.720A pdb=" N LYS D 76 " --> pdb=" O ARG D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 134 Processing helix chain 'D' and resid 138 through 151 removed outlier: 4.298A pdb=" N LYS D 142 " --> pdb=" O ASN D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 171 Processing helix chain 'D' and resid 173 through 183 Processing helix chain 'D' and resid 187 through 195 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 19 through 20 No H-bonds generated for 'chain 'G' and resid 19 through 20' Processing helix chain 'G' and resid 21 through 35 Processing helix chain 'G' and resid 50 through 54 Processing helix chain 'G' and resid 112 through 115 Processing helix chain 'O' and resid 84 through 94 removed outlier: 4.373A pdb=" N LEU O 88 " --> pdb=" O ASP O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 335 through 342 removed outlier: 4.398A pdb=" N GLU O 339 " --> pdb=" O GLU O 335 " (cutoff:3.500A) Processing helix chain 'O' and resid 353 through 366 Processing helix chain 'O' and resid 377 through 381 Processing helix chain 'O' and resid 427 through 432 removed outlier: 4.004A pdb=" N SER O 431 " --> pdb=" O THR O 428 " (cutoff:3.500A) Processing helix chain 'O' and resid 454 through 469 Processing helix chain 'Q' and resid 612 through 617 removed outlier: 4.219A pdb=" N GLU Q 616 " --> pdb=" O LEU Q 612 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N SER Q 617 " --> pdb=" O PRO Q 613 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 612 through 617' Processing helix chain 'Q' and resid 635 through 647 removed outlier: 3.685A pdb=" N THR Q 639 " --> pdb=" O ARG Q 635 " (cutoff:3.500A) Processing helix chain 'Q' and resid 790 through 820 removed outlier: 4.250A pdb=" N GLU Q 794 " --> pdb=" O GLU Q 790 " (cutoff:3.500A) Processing helix chain 'Q' and resid 864 through 866 No H-bonds generated for 'chain 'Q' and resid 864 through 866' Processing helix chain 'Q' and resid 906 through 918 Processing helix chain 'Q' and resid 930 through 940 Processing helix chain 'Q' and resid 942 through 947 Processing helix chain 'Q' and resid 948 through 954 removed outlier: 3.680A pdb=" N ASN Q 951 " --> pdb=" O GLY Q 948 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU Q 953 " --> pdb=" O TRP Q 950 " (cutoff:3.500A) Processing helix chain 'a' and resid 46 through 57 removed outlier: 3.851A pdb=" N ARG a 52 " --> pdb=" O LEU a 48 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR a 54 " --> pdb=" O GLU a 50 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN a 55 " --> pdb=" O ILE a 51 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LYS a 56 " --> pdb=" O ARG a 52 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N SER a 57 " --> pdb=" O ARG a 53 " (cutoff:3.500A) Processing helix chain 'a' and resid 63 through 79 removed outlier: 3.871A pdb=" N ASP a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE a 78 " --> pdb=" O ILE a 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 115 Processing helix chain 'a' and resid 120 through 132 removed outlier: 3.646A pdb=" N ILE a 124 " --> pdb=" O MET a 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 77 removed outlier: 3.966A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 94 Processing helix chain 'c' and resid 17 through 21 Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.296A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 90 Processing helix chain 'c' and resid 90 through 97 Processing helix chain 'c' and resid 112 through 116 Processing helix chain 'd' and resid 34 through 46 Processing helix chain 'd' and resid 52 through 81 Processing helix chain 'd' and resid 87 through 99 removed outlier: 3.627A pdb=" N ILE d 91 " --> pdb=" O THR d 87 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU d 99 " --> pdb=" O VAL d 95 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 121 removed outlier: 4.597A pdb=" N HIS d 106 " --> pdb=" O GLU d 102 " (cutoff:3.500A) Processing helix chain 'e' and resid 44 through 57 Processing helix chain 'e' and resid 63 through 79 removed outlier: 4.389A pdb=" N ASP e 77 " --> pdb=" O GLU e 73 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE e 78 " --> pdb=" O ILE e 74 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 132 removed outlier: 3.640A pdb=" N ILE e 124 " --> pdb=" O MET e 120 " (cutoff:3.500A) Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 30 through 42 Processing helix chain 'f' and resid 48 through 77 removed outlier: 4.357A pdb=" N GLU f 52 " --> pdb=" O GLY f 48 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP f 68 " --> pdb=" O ASN f 64 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 94 Processing helix chain 'g' and resid 16 through 22 Processing helix chain 'g' and resid 26 through 37 Processing helix chain 'g' and resid 45 through 74 removed outlier: 4.630A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR g 50 " --> pdb=" O GLY g 46 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 90 Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'h' and resid 34 through 46 removed outlier: 3.817A pdb=" N LYS h 40 " --> pdb=" O ILE h 36 " (cutoff:3.500A) Processing helix chain 'h' and resid 52 through 81 Processing helix chain 'h' and resid 87 through 99 Processing helix chain 'h' and resid 100 through 121 Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 12 removed outlier: 4.427A pdb=" N HIS B1195 " --> pdb=" O ARG A 12 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1418 through 1419 removed outlier: 3.906A pdb=" N GLU A 16 " --> pdb=" O TYR B1217 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR B1217 " --> pdb=" O GLU A 16 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 33 through 34 removed outlier: 6.768A pdb=" N ALA A 33 " --> pdb=" O HIS A 83 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ASP A 85 " --> pdb=" O ALA A 33 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N THR A 237 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 151 through 153 Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 250 through 251 Processing sheet with id=AA7, first strand: chain 'A' and resid 343 through 345 removed outlier: 3.690A pdb=" N LEU B1128 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1104 through 1105 removed outlier: 7.782A pdb=" N PHE A 468 " --> pdb=" O ARG A 350 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL A 352 " --> pdb=" O PHE A 468 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU A 470 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N SER A 354 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 375 through 379 removed outlier: 4.339A pdb=" N TYR A 404 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N HIS A 435 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ALA A 402 " --> pdb=" O HIS A 435 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 540 through 541 Processing sheet with id=AB2, first strand: chain 'A' and resid 588 through 590 removed outlier: 6.759A pdb=" N LEU A 606 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 849 through 851 removed outlier: 3.968A pdb=" N THR A 855 " --> pdb=" O HIS A 851 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 879 through 882 Processing sheet with id=AB5, first strand: chain 'A' and resid 1116 through 1117 Processing sheet with id=AB6, first strand: chain 'A' and resid 1141 through 1142 removed outlier: 6.542A pdb=" N THR A1141 " --> pdb=" O LEU A1273 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1147 through 1151 removed outlier: 4.358A pdb=" N LEU A1236 " --> pdb=" O LEU A1197 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1282 through 1292 Processing sheet with id=AB9, first strand: chain 'A' and resid 1442 through 1445 removed outlier: 4.900A pdb=" N ASP F 145 " --> pdb=" O ILE F 74 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 109 through 111 removed outlier: 5.572A pdb=" N PHE B 92 " --> pdb=" O LYS B 133 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N LYS B 133 " --> pdb=" O PHE B 92 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LYS B 94 " --> pdb=" O ASP B 131 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLY B 127 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N SER B 125 " --> pdb=" O PRO B 100 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N SER B 126 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG B 169 " --> pdb=" O SER B 126 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU B 128 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AC3, first strand: chain 'B' and resid 404 through 407 removed outlier: 5.849A pdb=" N ALA B 214 " --> pdb=" O ASN B 499 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 223 through 226 removed outlier: 5.273A pdb=" N HIS B 236 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU B 258 " --> pdb=" O HIS B 236 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN B 255 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 544 through 545 Processing sheet with id=AC6, first strand: chain 'B' and resid 650 through 651 removed outlier: 3.830A pdb=" N GLU B 641 " --> pdb=" O GLU B 650 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 564 through 565 removed outlier: 3.648A pdb=" N VAL B 589 " --> pdb=" O GLU B 564 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N TRP B 586 " --> pdb=" O VAL B 582 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VAL B 582 " --> pdb=" O TRP B 586 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY B 588 " --> pdb=" O VAL B 580 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 793 through 796 removed outlier: 6.682A pdb=" N PHE B 963 " --> pdb=" O VAL B 954 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL B 954 " --> pdb=" O PHE B 963 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LYS B 965 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N VAL B 952 " --> pdb=" O LYS B 965 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG B 967 " --> pdb=" O ASP B 950 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N THR B 971 " --> pdb=" O ASN B 946 " (cutoff:3.500A) removed outlier: 8.510A pdb=" N ASN B 946 " --> pdb=" O THR B 971 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1069 through 1070 removed outlier: 6.873A pdb=" N MET B 839 " --> pdb=" O GLY B 991 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N THR B 993 " --> pdb=" O MET B 839 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N MET B 841 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N LEU B1010 " --> pdb=" O ASN B 822 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N ILE B 824 " --> pdb=" O LEU B1010 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ILE B1012 " --> pdb=" O ILE B 824 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA B 826 " --> pdb=" O ILE B1012 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE B1086 " --> pdb=" O ILE B 827 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 873 through 874 Processing sheet with id=AD2, first strand: chain 'B' and resid 910 through 912 removed outlier: 4.384A pdb=" N ILE B 912 " --> pdb=" O THR B 939 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR B 939 " --> pdb=" O ILE B 912 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 1001 through 1002 Processing sheet with id=AD4, first strand: chain 'B' and resid 1172 through 1174 Processing sheet with id=AD5, first strand: chain 'C' and resid 7 through 13 removed outlier: 7.135A pdb=" N ASP C 19 " --> pdb=" O ARG C 11 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ALA C 13 " --> pdb=" O ASN C 17 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ASN C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 118 through 120 removed outlier: 7.021A pdb=" N GLU C 152 " --> pdb=" O ASN C 54 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ASN C 54 " --> pdb=" O GLU C 152 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LYS C 154 " --> pdb=" O GLU C 52 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LYS C 160 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ILE C 46 " --> pdb=" O LYS C 160 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY C 162 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N LEU C 44 " --> pdb=" O GLY C 162 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N VAL L 65 " --> pdb=" O VAL C 51 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 72 through 74 removed outlier: 4.877A pdb=" N GLN C 73 " --> pdb=" O GLY C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 111 through 114 removed outlier: 6.227A pdb=" N THR C 111 " --> pdb=" O LYS C 146 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N LYS C 146 " --> pdb=" O THR C 111 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL C 113 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 60 through 62 removed outlier: 6.704A pdb=" N TRP E 79 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N VAL E 111 " --> pdb=" O TRP E 79 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N GLU E 81 " --> pdb=" O VAL E 111 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 152 through 155 Processing sheet with id=AE2, first strand: chain 'H' and resid 4 through 16 removed outlier: 3.541A pdb=" N ALA H 29 " --> pdb=" O GLN H 11 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA H 140 " --> pdb=" O GLY H 99 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'I' and resid 15 through 19 removed outlier: 3.945A pdb=" N TYR I 34 " --> pdb=" O CYS I 29 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'I' and resid 70 through 71 Processing sheet with id=AE5, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AE6, first strand: chain 'Y' and resid 13 through 15 Processing sheet with id=AE7, first strand: chain 'Y' and resid 72 through 78 removed outlier: 7.089A pdb=" N GLY Y 48 " --> pdb=" O ILE Y 76 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL Y 78 " --> pdb=" O PHE Y 46 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N PHE Y 46 " --> pdb=" O VAL Y 78 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER Z 324 " --> pdb=" O GLU Z 338 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N GLN Z 359 " --> pdb=" O ARG Z 291 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Z' and resid 837 through 840 removed outlier: 4.061A pdb=" N ASP Z 821 " --> pdb=" O THR Z 828 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N GLU Z 830 " --> pdb=" O VAL Z 819 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL Z 819 " --> pdb=" O GLU Z 830 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N THR Z 804 " --> pdb=" O TYR Z 848 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR Z 846 " --> pdb=" O ARG Z 806 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 5 through 6 removed outlier: 4.056A pdb=" N SER G 8 " --> pdb=" O SER D 6 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS G 73 " --> pdb=" O ASP G 55 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ASP G 55 " --> pdb=" O LYS G 73 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'G' and resid 38 through 39 removed outlier: 7.153A pdb=" N VAL G 77 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N VAL G 48 " --> pdb=" O ARG G 75 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ARG G 75 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 36 through 38 Processing sheet with id=AF3, first strand: chain 'G' and resid 85 through 94 removed outlier: 6.724A pdb=" N GLU G 100 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N PHE G 99 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL G 110 " --> pdb=" O PHE G 99 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LYS G 107 " --> pdb=" O ILE G 157 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA G 159 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N SER G 156 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N SER G 152 " --> pdb=" O SER G 156 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N HIS G 158 " --> pdb=" O CYS G 150 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N CYS G 150 " --> pdb=" O HIS G 158 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE G 160 " --> pdb=" O GLU G 148 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 120 through 122 removed outlier: 3.571A pdb=" N SER G 129 " --> pdb=" O ASN G 122 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 4 through 8 removed outlier: 7.550A pdb=" N ASP O 4 " --> pdb=" O ILE O 21 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N ILE O 21 " --> pdb=" O ASP O 4 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ASP O 6 " --> pdb=" O PHE O 19 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N PHE O 19 " --> pdb=" O ASP O 6 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE O 8 " --> pdb=" O GLY O 17 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY O 27 " --> pdb=" O ARG O 20 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'O' and resid 33 through 35 Processing sheet with id=AF7, first strand: chain 'O' and resid 52 through 55 removed outlier: 7.325A pdb=" N ASN O 69 " --> pdb=" O SER O 53 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 115 through 118 Processing sheet with id=AF9, first strand: chain 'O' and resid 142 through 145 removed outlier: 4.045A pdb=" N GLU O 171 " --> pdb=" O THR Q 627 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR Q 627 " --> pdb=" O GLU O 171 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG O 173 " --> pdb=" O SER Q 625 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER Q 625 " --> pdb=" O ARG O 173 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 243 through 244 removed outlier: 3.967A pdb=" N VAL O 243 " --> pdb=" O ILE O 261 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 243 through 244 removed outlier: 3.967A pdb=" N VAL O 243 " --> pdb=" O ILE O 261 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER O 265 " --> pdb=" O TYR O 262 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 282 through 289 Processing sheet with id=AG4, first strand: chain 'O' and resid 325 through 329 removed outlier: 3.693A pdb=" N THR O 326 " --> pdb=" O ALA O 351 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ALA O 351 " --> pdb=" O THR O 326 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL O 328 " --> pdb=" O TYR O 349 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N TYR O 349 " --> pdb=" O VAL O 328 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'O' and resid 384 through 388 Processing sheet with id=AG6, first strand: chain 'O' and resid 417 through 423 removed outlier: 6.897A pdb=" N VAL O 440 " --> pdb=" O SER O 418 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL O 420 " --> pdb=" O GLU O 438 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLU O 438 " --> pdb=" O VAL O 420 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE O 422 " --> pdb=" O ASP O 436 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP O 436 " --> pdb=" O ILE O 422 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU O 437 " --> pdb=" O ALA O 451 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ALA O 451 " --> pdb=" O LEU O 437 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL O 439 " --> pdb=" O THR O 449 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N THR O 449 " --> pdb=" O VAL O 439 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU O 441 " --> pdb=" O SER O 447 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N SER O 447 " --> pdb=" O LEU O 441 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Q' and resid 555 through 556 removed outlier: 3.927A pdb=" N THR Q 561 " --> pdb=" O ASP Q 556 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Q' and resid 716 through 720 removed outlier: 3.830A pdb=" N ILE Q 717 " --> pdb=" O PHE Q 707 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN Q 708 " --> pdb=" O THR Q 697 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR Q 697 " --> pdb=" O GLN Q 708 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL Q 698 " --> pdb=" O ASP Q 681 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP Q 681 " --> pdb=" O VAL Q 698 " (cutoff:3.500A) removed outlier: 9.875A pdb=" N GLN Q 682 " --> pdb=" O GLU Q 763 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N GLU Q 763 " --> pdb=" O GLN Q 682 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N ASP Q 757 " --> pdb=" O ASN Q 746 " (cutoff:3.500A) removed outlier: 10.686A pdb=" N ASN Q 746 " --> pdb=" O ASP Q 757 " (cutoff:3.500A) removed outlier: 10.893A pdb=" N GLN Q 759 " --> pdb=" O LEU Q 744 " (cutoff:3.500A) removed outlier: 11.379A pdb=" N LEU Q 744 " --> pdb=" O GLN Q 759 " (cutoff:3.500A) removed outlier: 10.856A pdb=" N TYR Q 761 " --> pdb=" O ILE Q 742 " (cutoff:3.500A) removed outlier: 11.914A pdb=" N ILE Q 742 " --> pdb=" O TYR Q 761 " (cutoff:3.500A) removed outlier: 11.423A pdb=" N GLU Q 763 " --> pdb=" O ILE Q 740 " (cutoff:3.500A) removed outlier: 11.536A pdb=" N ILE Q 740 " --> pdb=" O GLU Q 763 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL Q 739 " --> pdb=" O PHE Q 729 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N PHE Q 729 " --> pdb=" O VAL Q 739 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N HIS Q 741 " --> pdb=" O LEU Q 727 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU Q 727 " --> pdb=" O HIS Q 741 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N HIS Q 743 " --> pdb=" O LYS Q 725 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 834 through 836 Processing sheet with id=AH1, first strand: chain 'Q' and resid 898 through 899 removed outlier: 3.823A pdb=" N ILE Q 899 " --> pdb=" O MET Q 885 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AH3, first strand: chain 'b' and resid 97 through 98 Processing sheet with id=AH4, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AH5, first strand: chain 'c' and resid 101 through 102 removed outlier: 7.011A pdb=" N THR c 101 " --> pdb=" O TYR f 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'e' and resid 83 through 84 removed outlier: 7.763A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH6 Processing sheet with id=AH7, first strand: chain 'g' and resid 77 through 78 2026 hydrogen bonds defined for protein. 5688 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 323 hydrogen bonds 646 hydrogen bond angles 0 basepair planarities 127 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 42.30 Time building geometry restraints manager: 22.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 9114 1.33 - 1.45: 14300 1.45 - 1.57: 29010 1.57 - 1.69: 601 1.69 - 1.82: 357 Bond restraints: 53382 Sorted by residual: bond pdb=" CA ARG J 62 " pdb=" C ARG J 62 " ideal model delta sigma weight residual 1.523 1.577 -0.053 1.80e-02 3.09e+03 8.81e+00 bond pdb=" C SER Q 709 " pdb=" N PRO Q 710 " ideal model delta sigma weight residual 1.334 1.403 -0.069 2.34e-02 1.83e+03 8.73e+00 bond pdb=" CD ARG a 49 " pdb=" NE ARG a 49 " ideal model delta sigma weight residual 1.458 1.425 0.033 1.40e-02 5.10e+03 5.46e+00 bond pdb=" C3' DC T -63 " pdb=" O3' DC T -63 " ideal model delta sigma weight residual 1.422 1.490 -0.068 3.00e-02 1.11e+03 5.13e+00 bond pdb=" C3' DG N 21 " pdb=" O3' DG N 21 " ideal model delta sigma weight residual 1.422 1.487 -0.065 3.00e-02 1.11e+03 4.76e+00 ... (remaining 53377 not shown) Histogram of bond angle deviations from ideal: 97.77 - 105.05: 1935 105.05 - 112.33: 26340 112.33 - 119.61: 19418 119.61 - 126.89: 24463 126.89 - 134.17: 1198 Bond angle restraints: 73354 Sorted by residual: angle pdb=" C ARG O 104 " pdb=" N GLU O 105 " pdb=" CA GLU O 105 " ideal model delta sigma weight residual 121.70 131.50 -9.80 1.80e+00 3.09e-01 2.96e+01 angle pdb=" CA ARG B1129 " pdb=" CB ARG B1129 " pdb=" CG ARG B1129 " ideal model delta sigma weight residual 114.10 124.21 -10.11 2.00e+00 2.50e-01 2.55e+01 angle pdb=" N GLU b 63 " pdb=" CA GLU b 63 " pdb=" CB GLU b 63 " ideal model delta sigma weight residual 110.12 116.96 -6.84 1.47e+00 4.63e-01 2.16e+01 angle pdb=" CA PRO I 66 " pdb=" N PRO I 66 " pdb=" CD PRO I 66 " ideal model delta sigma weight residual 112.00 105.60 6.40 1.40e+00 5.10e-01 2.09e+01 angle pdb=" CA TRP Y 59 " pdb=" CB TRP Y 59 " pdb=" CG TRP Y 59 " ideal model delta sigma weight residual 113.60 122.23 -8.63 1.90e+00 2.77e-01 2.07e+01 ... (remaining 73349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.87: 29505 33.87 - 67.73: 2190 67.73 - 101.60: 139 101.60 - 135.47: 4 135.47 - 169.34: 7 Dihedral angle restraints: 31845 sinusoidal: 15211 harmonic: 16634 Sorted by residual: dihedral pdb=" CA VAL A 524 " pdb=" C VAL A 524 " pdb=" N GLN A 525 " pdb=" CA GLN A 525 " ideal model delta harmonic sigma weight residual -180.00 -137.78 -42.22 0 5.00e+00 4.00e-02 7.13e+01 dihedral pdb=" CA VAL Q 738 " pdb=" C VAL Q 738 " pdb=" N VAL Q 739 " pdb=" CA VAL Q 739 " ideal model delta harmonic sigma weight residual 180.00 -149.73 -30.27 0 5.00e+00 4.00e-02 3.66e+01 dihedral pdb=" CA ARG Z 808 " pdb=" C ARG Z 808 " pdb=" N SER Z 809 " pdb=" CA SER Z 809 " ideal model delta harmonic sigma weight residual 180.00 151.92 28.08 0 5.00e+00 4.00e-02 3.15e+01 ... (remaining 31842 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 6129 0.052 - 0.103: 1676 0.103 - 0.155: 393 0.155 - 0.206: 57 0.206 - 0.258: 6 Chirality restraints: 8261 Sorted by residual: chirality pdb=" CB VAL A1212 " pdb=" CA VAL A1212 " pdb=" CG1 VAL A1212 " pdb=" CG2 VAL A1212 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA GLU b 63 " pdb=" N GLU b 63 " pdb=" C GLU b 63 " pdb=" CB GLU b 63 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CB THR C 250 " pdb=" CA THR C 250 " pdb=" OG1 THR C 250 " pdb=" CG2 THR C 250 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.54e+00 ... (remaining 8258 not shown) Planarity restraints: 8409 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG a 49 " -0.803 9.50e-02 1.11e+02 3.60e-01 8.01e+01 pdb=" NE ARG a 49 " 0.041 2.00e-02 2.50e+03 pdb=" CZ ARG a 49 " 0.029 2.00e-02 2.50e+03 pdb=" NH1 ARG a 49 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG a 49 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR d 80 " -0.023 2.00e-02 2.50e+03 2.92e-02 1.71e+01 pdb=" CG TYR d 80 " 0.069 2.00e-02 2.50e+03 pdb=" CD1 TYR d 80 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR d 80 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR d 80 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR d 80 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR d 80 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR d 80 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 724 " -0.069 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO B 725 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO B 725 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO B 725 " -0.056 5.00e-02 4.00e+02 ... (remaining 8406 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 484 2.57 - 3.15: 42393 3.15 - 3.73: 84877 3.73 - 4.32: 116185 4.32 - 4.90: 186266 Nonbonded interactions: 430205 Sorted by model distance: nonbonded pdb=" OD1 ASP A 483 " pdb="MG MG A1803 " model vdw 1.982 2.170 nonbonded pdb=" OE1 GLU B1004 " pdb=" OH TYR B1064 " model vdw 1.985 2.440 nonbonded pdb=" OG SER B 493 " pdb=" OE2 GLU B 526 " model vdw 1.998 2.440 nonbonded pdb=" OG1 THR A 497 " pdb=" OE1 GLU B1149 " model vdw 2.016 2.440 nonbonded pdb=" OG1 THR h 87 " pdb=" OE1 GLU h 90 " model vdw 2.042 2.440 ... (remaining 430200 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'a' selection = (chain 'e' and resid 45 through 132) } ncs_group { reference = (chain 'b' and resid 25 through 102) selection = chain 'f' } ncs_group { reference = (chain 'c' and resid 16 through 110) selection = (chain 'g' and resid 16 through 110) } ncs_group { reference = (chain 'd' and resid 29 through 121) selection = chain 'h' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.950 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: 0.060 Extract box with map and model: 16.640 Check model and map are aligned: 0.750 Set scattering table: 0.490 Process input model: 173.760 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.350 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: 0.020 Load rotamer database and sin/cos tables:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 201.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 53382 Z= 0.372 Angle : 0.970 10.741 73354 Z= 0.526 Chirality : 0.050 0.258 8261 Planarity : 0.010 0.360 8409 Dihedral : 20.482 169.337 21081 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.02 % Allowed : 0.56 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.11), residues: 5648 helix: 0.96 (0.11), residues: 2070 sheet: -0.80 (0.17), residues: 834 loop : -0.84 (0.12), residues: 2744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP B 519 HIS 0.022 0.003 HIS B 984 PHE 0.052 0.003 PHE G 18 TYR 0.069 0.003 TYR d 80 ARG 0.026 0.002 ARG D 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11296 Ramachandran restraints generated. 5648 Oldfield, 0 Emsley, 5648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11296 Ramachandran restraints generated. 5648 Oldfield, 0 Emsley, 5648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 5028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 742 time to evaluate : 5.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 895 LYS cc_start: 0.8558 (mmtt) cc_final: 0.8325 (mmtt) REVERT: A 1218 GLN cc_start: 0.8694 (mt0) cc_final: 0.8473 (mt0) REVERT: A 1436 ILE cc_start: 0.7108 (mt) cc_final: 0.6867 (mt) REVERT: A 1454 MET cc_start: 0.4566 (mmm) cc_final: 0.4306 (mmt) REVERT: B 310 MET cc_start: 0.6643 (mmm) cc_final: 0.6138 (mmt) REVERT: B 313 MET cc_start: 0.7719 (tpp) cc_final: 0.7514 (tpt) REVERT: B 328 GLU cc_start: 0.8472 (tp30) cc_final: 0.8224 (tp30) REVERT: B 864 LYS cc_start: 0.7675 (ttpt) cc_final: 0.7199 (tmtt) REVERT: B 868 MET cc_start: 0.6074 (mpp) cc_final: 0.5760 (mpp) REVERT: B 1169 MET cc_start: 0.7609 (mtm) cc_final: 0.7336 (mtm) REVERT: C 29 MET cc_start: 0.8422 (ttm) cc_final: 0.8072 (ttm) REVERT: C 75 MET cc_start: 0.8132 (tpt) cc_final: 0.7840 (tpt) REVERT: C 199 LYS cc_start: 0.8207 (tmmt) cc_final: 0.7961 (pttp) REVERT: E 114 ASN cc_start: 0.7991 (m-40) cc_final: 0.7707 (m-40) REVERT: F 103 MET cc_start: 0.8231 (mtt) cc_final: 0.7875 (mtt) REVERT: F 147 SER cc_start: 0.8377 (m) cc_final: 0.7798 (t) REVERT: F 149 GLU cc_start: 0.7996 (pm20) cc_final: 0.7673 (pm20) REVERT: H 11 GLN cc_start: 0.7870 (tt0) cc_final: 0.7546 (tm-30) REVERT: H 22 LYS cc_start: 0.8402 (mttt) cc_final: 0.8191 (mttp) REVERT: I 26 LEU cc_start: 0.7441 (mt) cc_final: 0.7107 (pp) REVERT: I 81 ARG cc_start: 0.7217 (tpp80) cc_final: 0.6950 (tpp80) REVERT: J 58 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7182 (mm-30) REVERT: L 47 ARG cc_start: 0.7229 (mtp85) cc_final: 0.6599 (mmt90) REVERT: Z 823 ASN cc_start: 0.4115 (t0) cc_final: 0.3791 (t0) REVERT: G 58 ARG cc_start: 0.6351 (mtt-85) cc_final: 0.5848 (mmt90) REVERT: Q 798 ARG cc_start: 0.4271 (tmt170) cc_final: 0.3570 (tpp-160) REVERT: Q 885 MET cc_start: 0.0545 (tmm) cc_final: -0.0217 (ttp) REVERT: a 64 LYS cc_start: 0.8201 (mmmt) cc_final: 0.7984 (mmtt) REVERT: a 77 ASP cc_start: 0.8444 (m-30) cc_final: 0.8205 (m-30) REVERT: a 79 LYS cc_start: 0.8144 (tptm) cc_final: 0.7786 (tttp) REVERT: a 120 MET cc_start: 0.5903 (mmt) cc_final: 0.5701 (mmt) REVERT: a 128 ARG cc_start: 0.8183 (mmm-85) cc_final: 0.7792 (mmm160) REVERT: b 29 ILE cc_start: 0.8863 (mm) cc_final: 0.8630 (mm) REVERT: b 59 LYS cc_start: 0.8861 (tttp) cc_final: 0.8610 (tptm) REVERT: c 20 ARG cc_start: 0.6772 (mtt-85) cc_final: 0.6510 (mtt90) REVERT: c 64 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7432 (mm-30) REVERT: c 68 ASN cc_start: 0.8283 (m-40) cc_final: 0.7987 (m-40) REVERT: c 90 ASP cc_start: 0.7343 (t70) cc_final: 0.7031 (t0) REVERT: c 94 ASN cc_start: 0.8095 (t0) cc_final: 0.7888 (t0) REVERT: c 95 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8245 (mtpp) REVERT: d 65 ASP cc_start: 0.8266 (t70) cc_final: 0.8004 (t70) REVERT: d 108 VAL cc_start: 0.9099 (m) cc_final: 0.8865 (t) REVERT: d 117 LYS cc_start: 0.8953 (mtpt) cc_final: 0.8653 (mtmt) REVERT: e 54 TYR cc_start: 0.8638 (m-80) cc_final: 0.8369 (m-80) REVERT: e 55 GLN cc_start: 0.8417 (mt0) cc_final: 0.8216 (mt0) REVERT: e 103 LEU cc_start: 0.8577 (tp) cc_final: 0.8345 (tt) REVERT: e 120 MET cc_start: 0.7346 (mmt) cc_final: 0.7110 (mmt) REVERT: f 34 ILE cc_start: 0.8101 (mm) cc_final: 0.7794 (tt) REVERT: g 17 ARG cc_start: 0.7840 (mtt90) cc_final: 0.7540 (mtm-85) REVERT: g 20 ARG cc_start: 0.8556 (ttp-170) cc_final: 0.8006 (ttp-170) REVERT: g 39 TYR cc_start: 0.7242 (m-80) cc_final: 0.6914 (m-80) REVERT: g 64 GLU cc_start: 0.7987 (mt-10) cc_final: 0.7677 (mt-10) REVERT: g 75 LYS cc_start: 0.8721 (tttt) cc_final: 0.8372 (tttp) REVERT: g 81 ARG cc_start: 0.7224 (tpt170) cc_final: 0.6367 (tpt170) REVERT: g 104 GLN cc_start: 0.7756 (mp10) cc_final: 0.7313 (mp10) REVERT: h 39 TYR cc_start: 0.8055 (t80) cc_final: 0.7817 (t80) REVERT: h 54 LYS cc_start: 0.8191 (ttmm) cc_final: 0.7743 (tppt) REVERT: h 59 MET cc_start: 0.8251 (mmt) cc_final: 0.7941 (mmt) REVERT: h 76 ARG cc_start: 0.7775 (mtm180) cc_final: 0.7483 (mtm-85) REVERT: h 86 ILE cc_start: 0.7798 (mt) cc_final: 0.7456 (mt) REVERT: h 90 GLU cc_start: 0.8079 (mp0) cc_final: 0.7667 (mp0) REVERT: h 99 LEU cc_start: 0.8185 (mm) cc_final: 0.7974 (mm) REVERT: h 103 LEU cc_start: 0.8700 (mt) cc_final: 0.8486 (mm) REVERT: h 105 LYS cc_start: 0.8900 (mtpp) cc_final: 0.8584 (mtmm) outliers start: 1 outliers final: 0 residues processed: 743 average time/residue: 0.6948 time to fit residues: 831.0180 Evaluate side-chains 597 residues out of total 5028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 597 time to evaluate : 5.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 498 optimal weight: 7.9990 chunk 447 optimal weight: 7.9990 chunk 248 optimal weight: 4.9990 chunk 152 optimal weight: 2.9990 chunk 301 optimal weight: 7.9990 chunk 238 optimal weight: 0.7980 chunk 462 optimal weight: 8.9990 chunk 178 optimal weight: 0.6980 chunk 281 optimal weight: 4.9990 chunk 344 optimal weight: 3.9990 chunk 535 optimal weight: 0.5980 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 HIS A 488 ASN A 515 GLN ** A 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 ASN A 659 HIS ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 996 ASN A1078 GLN ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 255 GLN B 761 HIS B 763 GLN B 881 ASN B 887 HIS B 958 GLN B1084 GLN B1093 GLN B1117 GLN B1179 GLN ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 17 ASN F 100 GLN F 104 ASN ** H 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 11 ASN I 46 HIS ** I 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 HIS Q 682 GLN Q 938 GLN a 68 GLN b 64 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN g 31 HIS g 82 HIS ** g 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 79 HIS Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 53382 Z= 0.306 Angle : 0.671 10.383 73354 Z= 0.360 Chirality : 0.045 0.211 8261 Planarity : 0.005 0.098 8409 Dihedral : 20.878 178.814 9626 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.26 % Allowed : 10.34 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.11), residues: 5648 helix: 1.25 (0.11), residues: 2092 sheet: -0.56 (0.17), residues: 832 loop : -0.80 (0.12), residues: 2724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 519 HIS 0.009 0.001 HIS J 53 PHE 0.029 0.002 PHE L 67 TYR 0.051 0.002 TYR d 80 ARG 0.017 0.001 ARG g 35 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11296 Ramachandran restraints generated. 5648 Oldfield, 0 Emsley, 5648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11296 Ramachandran restraints generated. 5648 Oldfield, 0 Emsley, 5648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 5028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 655 time to evaluate : 5.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 ASP cc_start: 0.7065 (m-30) cc_final: 0.6752 (m-30) REVERT: A 456 MET cc_start: 0.7882 (mtt) cc_final: 0.7494 (mtp) REVERT: A 472 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8216 (tt) REVERT: A 547 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7397 (mp) REVERT: A 895 LYS cc_start: 0.8605 (mmtt) cc_final: 0.8366 (mmtt) REVERT: A 1209 MET cc_start: 0.7655 (tmm) cc_final: 0.7036 (tmm) REVERT: A 1218 GLN cc_start: 0.8771 (mt0) cc_final: 0.8403 (mt0) REVERT: A 1259 MET cc_start: 0.7509 (ptp) cc_final: 0.6972 (mpp) REVERT: A 1268 LEU cc_start: 0.8141 (tp) cc_final: 0.7864 (tp) REVERT: A 1436 ILE cc_start: 0.7359 (mt) cc_final: 0.7102 (mt) REVERT: B 841 MET cc_start: 0.8754 (ttm) cc_final: 0.8478 (ttm) REVERT: B 868 MET cc_start: 0.6239 (mpp) cc_final: 0.5945 (mpp) REVERT: B 956 THR cc_start: 0.7913 (p) cc_final: 0.7660 (p) REVERT: F 103 MET cc_start: 0.8241 (mtt) cc_final: 0.7975 (mtm) REVERT: F 119 ARG cc_start: 0.8311 (mmt-90) cc_final: 0.7903 (mmm-85) REVERT: H 22 LYS cc_start: 0.8383 (mttt) cc_final: 0.8132 (mttp) REVERT: H 93 TYR cc_start: 0.8018 (m-80) cc_final: 0.7648 (m-80) REVERT: I 26 LEU cc_start: 0.7438 (mt) cc_final: 0.7030 (pp) REVERT: J 55 ASP cc_start: 0.7694 (t70) cc_final: 0.6803 (t70) REVERT: J 58 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7296 (mm-30) REVERT: Z 808 ARG cc_start: 0.4670 (OUTLIER) cc_final: 0.2558 (tpm-80) REVERT: D 66 ARG cc_start: 0.6007 (ttm170) cc_final: 0.5794 (ttm110) REVERT: G 22 MET cc_start: 0.6549 (tpp) cc_final: 0.5971 (ttm) REVERT: O 172 MET cc_start: 0.5654 (tmm) cc_final: 0.5340 (ptt) REVERT: Q 589 TYR cc_start: 0.3582 (m-80) cc_final: 0.3015 (m-10) REVERT: Q 591 TYR cc_start: 0.3956 (m-80) cc_final: 0.3424 (t80) REVERT: Q 798 ARG cc_start: 0.4132 (tmt170) cc_final: 0.3465 (tpp-160) REVERT: a 93 GLN cc_start: 0.8519 (tt0) cc_final: 0.7973 (tp40) REVERT: b 29 ILE cc_start: 0.8773 (mm) cc_final: 0.8536 (mm) REVERT: b 59 LYS cc_start: 0.8748 (tttp) cc_final: 0.8464 (tptm) REVERT: b 93 GLN cc_start: 0.8216 (mm110) cc_final: 0.7982 (mm-40) REVERT: c 64 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7672 (mm-30) REVERT: d 44 GLN cc_start: 0.7452 (mm110) cc_final: 0.7215 (mm110) REVERT: d 56 MET cc_start: 0.8337 (tpp) cc_final: 0.8114 (tpp) REVERT: d 73 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7796 (mm-30) REVERT: d 80 TYR cc_start: 0.7148 (m-80) cc_final: 0.6856 (m-80) REVERT: d 117 LYS cc_start: 0.9014 (mtpt) cc_final: 0.8575 (mtmt) REVERT: f 53 GLU cc_start: 0.8325 (tp30) cc_final: 0.7992 (tp30) REVERT: g 17 ARG cc_start: 0.7940 (mtt90) cc_final: 0.7611 (mtm-85) REVERT: g 20 ARG cc_start: 0.8548 (ttp-170) cc_final: 0.8136 (ttp-170) REVERT: g 25 PHE cc_start: 0.8052 (m-80) cc_final: 0.7420 (m-80) REVERT: g 56 GLU cc_start: 0.7808 (tt0) cc_final: 0.7570 (tp30) REVERT: g 64 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7689 (tm-30) REVERT: g 73 ASN cc_start: 0.7734 (t0) cc_final: 0.7303 (m110) REVERT: g 75 LYS cc_start: 0.8953 (tttt) cc_final: 0.8519 (tttp) REVERT: g 81 ARG cc_start: 0.7186 (tpt170) cc_final: 0.6314 (tpt170) REVERT: g 104 GLN cc_start: 0.8019 (mp10) cc_final: 0.7354 (mp10) REVERT: h 54 LYS cc_start: 0.8100 (ttmm) cc_final: 0.7617 (tppt) REVERT: h 86 ILE cc_start: 0.7773 (mt) cc_final: 0.7551 (mt) REVERT: h 90 GLU cc_start: 0.8275 (mp0) cc_final: 0.7974 (mp0) REVERT: h 105 LYS cc_start: 0.8919 (mtpp) cc_final: 0.8598 (mtmm) outliers start: 63 outliers final: 34 residues processed: 687 average time/residue: 0.6720 time to fit residues: 752.3398 Evaluate side-chains 622 residues out of total 5028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 585 time to evaluate : 5.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 307 ASP Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 1040 GLN Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 949 VAL Chi-restraints excluded: chain B residue 1189 ILE Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 133 ASN Chi-restraints excluded: chain I residue 111 THR Chi-restraints excluded: chain Z residue 808 ARG Chi-restraints excluded: chain Z residue 844 LYS Chi-restraints excluded: chain a residue 86 SER Chi-restraints excluded: chain a residue 96 SER Chi-restraints excluded: chain b residue 49 LEU Chi-restraints excluded: chain c residue 78 ILE Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 110 GLU Chi-restraints excluded: chain d residue 112 THR Chi-restraints excluded: chain e residue 77 ASP Chi-restraints excluded: chain e residue 105 GLU Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 49 VAL Chi-restraints excluded: chain g residue 79 ILE Chi-restraints excluded: chain h residue 33 SER Chi-restraints excluded: chain h residue 81 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 297 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 445 optimal weight: 20.0000 chunk 364 optimal weight: 0.6980 chunk 147 optimal weight: 2.9990 chunk 536 optimal weight: 1.9990 chunk 579 optimal weight: 4.9990 chunk 478 optimal weight: 9.9990 chunk 532 optimal weight: 5.9990 chunk 182 optimal weight: 1.9990 chunk 430 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 ASN ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 ASN ** A 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 HIS B 583 ASN B 587 HIS B 794 ASN B1176 ASN ** B1187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1195 HIS ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 GLN I 87 GLN ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 330 ASN Z 837 HIS G 10 ASN G 71 ASN O 279 HIS a 108 ASN c 68 ASN d 92 GLN e 108 ASN e 125 GLN ** g 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 79 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 53382 Z= 0.275 Angle : 0.616 10.942 73354 Z= 0.331 Chirality : 0.043 0.261 8261 Planarity : 0.005 0.091 8409 Dihedral : 20.830 179.652 9626 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.43 % Allowed : 14.23 % Favored : 83.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.11), residues: 5648 helix: 1.47 (0.11), residues: 2091 sheet: -0.45 (0.17), residues: 843 loop : -0.76 (0.12), residues: 2714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 519 HIS 0.010 0.001 HIS J 53 PHE 0.027 0.002 PHE K 58 TYR 0.029 0.002 TYR A 465 ARG 0.013 0.001 ARG I 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11296 Ramachandran restraints generated. 5648 Oldfield, 0 Emsley, 5648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11296 Ramachandran restraints generated. 5648 Oldfield, 0 Emsley, 5648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 5028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 631 time to evaluate : 6.413 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 547 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7299 (mp) REVERT: A 708 MET cc_start: 0.7855 (mtm) cc_final: 0.7629 (mtm) REVERT: A 895 LYS cc_start: 0.8588 (mmtt) cc_final: 0.8361 (mmtt) REVERT: A 961 ARG cc_start: 0.7331 (ptm160) cc_final: 0.7075 (ptp-110) REVERT: A 1133 LEU cc_start: 0.8428 (mm) cc_final: 0.8131 (mt) REVERT: A 1259 MET cc_start: 0.7586 (ptp) cc_final: 0.7103 (mpp) REVERT: A 1268 LEU cc_start: 0.8219 (tp) cc_final: 0.7950 (tp) REVERT: A 1436 ILE cc_start: 0.7349 (mt) cc_final: 0.7144 (mt) REVERT: B 597 MET cc_start: 0.8422 (tpp) cc_final: 0.8148 (tpt) REVERT: B 864 LYS cc_start: 0.7597 (ttpt) cc_final: 0.7288 (ttpt) REVERT: B 956 THR cc_start: 0.8430 (p) cc_final: 0.8191 (p) REVERT: C 104 PHE cc_start: 0.8215 (t80) cc_final: 0.7944 (t80) REVERT: E 67 GLU cc_start: 0.7253 (tm-30) cc_final: 0.7036 (tp30) REVERT: F 103 MET cc_start: 0.8303 (mtt) cc_final: 0.7971 (mtt) REVERT: F 119 ARG cc_start: 0.8382 (mmt-90) cc_final: 0.7983 (mmm-85) REVERT: H 22 LYS cc_start: 0.8468 (mttt) cc_final: 0.8207 (mttp) REVERT: H 93 TYR cc_start: 0.8063 (m-80) cc_final: 0.7687 (m-80) REVERT: I 26 LEU cc_start: 0.7482 (mt) cc_final: 0.7063 (pp) REVERT: J 1 MET cc_start: 0.7392 (mpp) cc_final: 0.6899 (mpp) REVERT: J 58 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7574 (mm-30) REVERT: L 37 LYS cc_start: 0.8304 (mtmm) cc_final: 0.8007 (ttmm) REVERT: Z 808 ARG cc_start: 0.4795 (OUTLIER) cc_final: 0.2636 (tpm-80) REVERT: G 62 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8248 (mm) REVERT: Q 538 TYR cc_start: -0.4175 (m-80) cc_final: -0.4824 (m-80) REVERT: Q 589 TYR cc_start: 0.3604 (m-80) cc_final: 0.3026 (m-10) REVERT: Q 591 TYR cc_start: 0.4015 (m-80) cc_final: 0.3495 (t80) REVERT: Q 798 ARG cc_start: 0.4154 (tmt170) cc_final: 0.3474 (tpp-160) REVERT: b 59 LYS cc_start: 0.8761 (tttp) cc_final: 0.8397 (tptm) REVERT: c 64 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7700 (mm-30) REVERT: d 44 GLN cc_start: 0.7446 (mm110) cc_final: 0.7154 (mm110) REVERT: d 56 MET cc_start: 0.8331 (tpp) cc_final: 0.8096 (tpp) REVERT: d 80 TYR cc_start: 0.7338 (m-80) cc_final: 0.7039 (m-80) REVERT: d 117 LYS cc_start: 0.9074 (mtpt) cc_final: 0.8640 (mtmt) REVERT: f 27 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7625 (tm-30) REVERT: f 53 GLU cc_start: 0.8421 (tp30) cc_final: 0.8182 (tp30) REVERT: f 79 LYS cc_start: 0.8161 (tptp) cc_final: 0.7791 (tptt) REVERT: f 92 ARG cc_start: 0.8392 (ttp80) cc_final: 0.8135 (ttp80) REVERT: g 25 PHE cc_start: 0.8092 (m-80) cc_final: 0.7625 (m-80) REVERT: g 64 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7594 (mt-10) REVERT: g 75 LYS cc_start: 0.8742 (tttt) cc_final: 0.8308 (tttp) REVERT: h 90 GLU cc_start: 0.8300 (mp0) cc_final: 0.8017 (mp0) REVERT: h 118 TYR cc_start: 0.8954 (t80) cc_final: 0.8572 (t80) outliers start: 122 outliers final: 66 residues processed: 699 average time/residue: 0.6594 time to fit residues: 763.3403 Evaluate side-chains 647 residues out of total 5028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 578 time to evaluate : 5.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 1040 GLN Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 568 ASP Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 572 HIS Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 949 VAL Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain I residue 108 HIS Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain Y residue 52 MET Chi-restraints excluded: chain Z residue 808 ARG Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain Q residue 578 TYR Chi-restraints excluded: chain Q residue 739 VAL Chi-restraints excluded: chain Q residue 932 THR Chi-restraints excluded: chain a residue 86 SER Chi-restraints excluded: chain a residue 107 THR Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 62 LEU Chi-restraints excluded: chain c residue 93 LEU Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 102 GLU Chi-restraints excluded: chain d residue 110 GLU Chi-restraints excluded: chain d residue 112 THR Chi-restraints excluded: chain e residue 59 GLU Chi-restraints excluded: chain e residue 74 ILE Chi-restraints excluded: chain e residue 77 ASP Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 94 ASN Chi-restraints excluded: chain g residue 107 VAL Chi-restraints excluded: chain h residue 81 ASN Chi-restraints excluded: chain h residue 116 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 530 optimal weight: 4.9990 chunk 403 optimal weight: 0.8980 chunk 278 optimal weight: 0.5980 chunk 59 optimal weight: 3.9990 chunk 256 optimal weight: 0.8980 chunk 360 optimal weight: 0.8980 chunk 538 optimal weight: 8.9990 chunk 570 optimal weight: 2.9990 chunk 281 optimal weight: 0.9990 chunk 510 optimal weight: 30.0000 chunk 153 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 ASN ** A 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 GLN ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1211 GLN B 572 HIS ** B1187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 83 GLN ** I 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 108 HIS ** K 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 815 GLN D 132 GLN G 10 ASN G 71 ASN O 296 HIS c 68 ASN d 92 GLN e 108 ASN e 125 GLN ** g 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 79 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 53382 Z= 0.189 Angle : 0.572 10.831 73354 Z= 0.307 Chirality : 0.041 0.195 8261 Planarity : 0.004 0.067 8409 Dihedral : 20.725 179.383 9626 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.19 % Allowed : 16.86 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.11), residues: 5648 helix: 1.69 (0.11), residues: 2089 sheet: -0.25 (0.18), residues: 817 loop : -0.73 (0.12), residues: 2742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 519 HIS 0.008 0.001 HIS J 53 PHE 0.026 0.001 PHE Q 878 TYR 0.018 0.001 TYR d 80 ARG 0.007 0.000 ARG a 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11296 Ramachandran restraints generated. 5648 Oldfield, 0 Emsley, 5648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11296 Ramachandran restraints generated. 5648 Oldfield, 0 Emsley, 5648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 5028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 617 time to evaluate : 5.973 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 57 ARG cc_start: 0.8287 (mtm110) cc_final: 0.7807 (mtm110) REVERT: A 576 GLN cc_start: 0.7518 (mt0) cc_final: 0.7232 (mt0) REVERT: A 895 LYS cc_start: 0.8564 (mmtt) cc_final: 0.8336 (mmtt) REVERT: A 961 ARG cc_start: 0.7269 (ptm160) cc_final: 0.7034 (ptp-110) REVERT: A 1133 LEU cc_start: 0.8397 (mm) cc_final: 0.8150 (mt) REVERT: A 1157 ASP cc_start: 0.7041 (p0) cc_final: 0.6620 (t70) REVERT: A 1214 GLU cc_start: 0.7656 (pp20) cc_final: 0.7182 (pp20) REVERT: A 1218 GLN cc_start: 0.8891 (mt0) cc_final: 0.8459 (mt0) REVERT: A 1259 MET cc_start: 0.7591 (ptp) cc_final: 0.7078 (mpp) REVERT: A 1268 LEU cc_start: 0.8245 (tp) cc_final: 0.7934 (tp) REVERT: A 1336 MET cc_start: 0.8165 (tmm) cc_final: 0.7886 (ttt) REVERT: A 1436 ILE cc_start: 0.7362 (mt) cc_final: 0.7145 (mt) REVERT: B 597 MET cc_start: 0.8436 (tpp) cc_final: 0.8117 (tpt) REVERT: B 841 MET cc_start: 0.8746 (ttm) cc_final: 0.8318 (ttm) REVERT: B 864 LYS cc_start: 0.7637 (ttpt) cc_final: 0.7178 (tmtt) REVERT: B 956 THR cc_start: 0.8553 (p) cc_final: 0.8319 (p) REVERT: C 61 GLU cc_start: 0.6925 (mm-30) cc_final: 0.6517 (mt-10) REVERT: F 103 MET cc_start: 0.8254 (mtt) cc_final: 0.7915 (mtt) REVERT: F 119 ARG cc_start: 0.8314 (mmt-90) cc_final: 0.7907 (mmm-85) REVERT: H 22 LYS cc_start: 0.8466 (mttt) cc_final: 0.8194 (mttp) REVERT: H 52 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8238 (mm-40) REVERT: H 93 TYR cc_start: 0.8009 (m-80) cc_final: 0.7637 (m-80) REVERT: H 97 MET cc_start: 0.7442 (mtm) cc_final: 0.7241 (mtm) REVERT: I 26 LEU cc_start: 0.7472 (mt) cc_final: 0.7057 (pp) REVERT: J 1 MET cc_start: 0.7408 (mpp) cc_final: 0.7083 (mpp) REVERT: J 58 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7518 (mm-30) REVERT: L 37 LYS cc_start: 0.8261 (mtmm) cc_final: 0.7905 (ttmm) REVERT: Z 808 ARG cc_start: 0.4524 (OUTLIER) cc_final: 0.2263 (tpm-80) REVERT: D 67 ARG cc_start: 0.5751 (mmm160) cc_final: 0.5232 (mmm160) REVERT: G 62 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8295 (mm) REVERT: Q 615 GLU cc_start: 0.2724 (tp30) cc_final: 0.2219 (tt0) REVERT: Q 798 ARG cc_start: 0.4184 (tmt170) cc_final: 0.3500 (tpp-160) REVERT: Q 885 MET cc_start: 0.0791 (tmm) cc_final: -0.0205 (ttp) REVERT: Q 898 HIS cc_start: -0.0875 (OUTLIER) cc_final: -0.3342 (m-70) REVERT: a 57 SER cc_start: 0.8717 (t) cc_final: 0.8427 (t) REVERT: a 93 GLN cc_start: 0.8469 (tt0) cc_final: 0.7891 (tp40) REVERT: b 59 LYS cc_start: 0.8939 (tttp) cc_final: 0.8559 (tptm) REVERT: c 64 GLU cc_start: 0.8090 (mt-10) cc_final: 0.7714 (mm-30) REVERT: d 80 TYR cc_start: 0.7363 (m-80) cc_final: 0.6968 (m-80) REVERT: d 117 LYS cc_start: 0.9044 (mtpt) cc_final: 0.8598 (mtmt) REVERT: e 97 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7181 (mm-30) REVERT: f 27 GLN cc_start: 0.7854 (tm-30) cc_final: 0.7395 (tm-30) REVERT: f 53 GLU cc_start: 0.8453 (tp30) cc_final: 0.8201 (tp30) REVERT: f 79 LYS cc_start: 0.8054 (tptp) cc_final: 0.7837 (tptt) REVERT: f 92 ARG cc_start: 0.8285 (ttp80) cc_final: 0.8057 (ttp80) REVERT: g 64 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7705 (tm-30) REVERT: g 73 ASN cc_start: 0.7627 (t0) cc_final: 0.7239 (m110) REVERT: h 54 LYS cc_start: 0.8246 (ttmm) cc_final: 0.7985 (tppt) REVERT: h 86 ILE cc_start: 0.7712 (mt) cc_final: 0.7316 (mt) REVERT: h 90 GLU cc_start: 0.8282 (mp0) cc_final: 0.7958 (mp0) REVERT: h 118 TYR cc_start: 0.8893 (t80) cc_final: 0.8544 (t80) outliers start: 110 outliers final: 54 residues processed: 689 average time/residue: 0.6433 time to fit residues: 734.3261 Evaluate side-chains 652 residues out of total 5028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 595 time to evaluate : 6.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1424 VAL Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 328 GLU Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 572 HIS Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 949 VAL Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain H residue 133 ASN Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 108 HIS Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain Y residue 52 MET Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Z residue 808 ARG Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain Q residue 739 VAL Chi-restraints excluded: chain Q residue 898 HIS Chi-restraints excluded: chain Q residue 932 THR Chi-restraints excluded: chain a residue 86 SER Chi-restraints excluded: chain a residue 117 VAL Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 60 VAL Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 102 GLU Chi-restraints excluded: chain d residue 110 GLU Chi-restraints excluded: chain e residue 77 ASP Chi-restraints excluded: chain e residue 108 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 474 optimal weight: 20.0000 chunk 323 optimal weight: 0.0010 chunk 8 optimal weight: 7.9990 chunk 424 optimal weight: 2.9990 chunk 235 optimal weight: 0.4980 chunk 486 optimal weight: 8.9990 chunk 394 optimal weight: 20.0000 chunk 0 optimal weight: 9.9990 chunk 291 optimal weight: 0.6980 chunk 511 optimal weight: 8.9990 chunk 143 optimal weight: 0.5980 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 ASN ** A 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 GLN ** A1128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1173 HIS B 572 HIS ** B1187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 96 ASN Q 682 GLN b 93 GLN c 68 ASN d 92 GLN e 76 GLN ** g 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 79 HIS h 81 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 53382 Z= 0.196 Angle : 0.560 10.616 73354 Z= 0.302 Chirality : 0.041 0.197 8261 Planarity : 0.004 0.060 8409 Dihedral : 20.675 178.939 9626 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.27 % Allowed : 17.64 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.11), residues: 5648 helix: 1.78 (0.11), residues: 2090 sheet: -0.23 (0.17), residues: 839 loop : -0.67 (0.12), residues: 2719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 201 HIS 0.011 0.001 HIS I 108 PHE 0.022 0.001 PHE C 219 TYR 0.021 0.001 TYR B 666 ARG 0.009 0.000 ARG f 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11296 Ramachandran restraints generated. 5648 Oldfield, 0 Emsley, 5648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11296 Ramachandran restraints generated. 5648 Oldfield, 0 Emsley, 5648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 5028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 618 time to evaluate : 5.650 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 57 ARG cc_start: 0.8317 (mtm110) cc_final: 0.7826 (mtm110) REVERT: A 547 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7423 (mp) REVERT: A 576 GLN cc_start: 0.7542 (mt0) cc_final: 0.7224 (mt0) REVERT: A 895 LYS cc_start: 0.8581 (mmtt) cc_final: 0.8347 (mmtt) REVERT: A 961 ARG cc_start: 0.7296 (ptm160) cc_final: 0.7062 (ptp-110) REVERT: A 1133 LEU cc_start: 0.8388 (mm) cc_final: 0.8149 (mt) REVERT: A 1157 ASP cc_start: 0.7142 (p0) cc_final: 0.6708 (t70) REVERT: A 1214 GLU cc_start: 0.7818 (pp20) cc_final: 0.7363 (pp20) REVERT: A 1218 GLN cc_start: 0.8934 (mt0) cc_final: 0.8509 (mt0) REVERT: A 1259 MET cc_start: 0.7613 (ptp) cc_final: 0.7107 (mpp) REVERT: A 1268 LEU cc_start: 0.8238 (tp) cc_final: 0.7930 (tp) REVERT: A 1336 MET cc_start: 0.8187 (tmm) cc_final: 0.7891 (ttt) REVERT: A 1436 ILE cc_start: 0.7365 (mt) cc_final: 0.7158 (mt) REVERT: B 310 MET cc_start: 0.7013 (mmm) cc_final: 0.6532 (mmt) REVERT: B 597 MET cc_start: 0.8442 (tpp) cc_final: 0.8122 (tpt) REVERT: B 864 LYS cc_start: 0.7646 (ttpt) cc_final: 0.7245 (tmtt) REVERT: B 868 MET cc_start: 0.6429 (mpp) cc_final: 0.6191 (mpp) REVERT: B 956 THR cc_start: 0.8602 (p) cc_final: 0.8369 (p) REVERT: C 61 GLU cc_start: 0.7012 (mm-30) cc_final: 0.6552 (mt-10) REVERT: E 101 GLN cc_start: 0.6911 (mm110) cc_final: 0.6698 (mm110) REVERT: F 103 MET cc_start: 0.8253 (mtt) cc_final: 0.7935 (mtt) REVERT: F 119 ARG cc_start: 0.8306 (mmt-90) cc_final: 0.7906 (mmm-85) REVERT: H 22 LYS cc_start: 0.8476 (mttt) cc_final: 0.8221 (mttp) REVERT: H 52 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8234 (mm-40) REVERT: H 93 TYR cc_start: 0.8050 (m-80) cc_final: 0.7693 (m-80) REVERT: H 97 MET cc_start: 0.7404 (mtm) cc_final: 0.7140 (mtt) REVERT: I 26 LEU cc_start: 0.7495 (mt) cc_final: 0.7127 (pp) REVERT: J 1 MET cc_start: 0.7445 (mpp) cc_final: 0.7119 (mpp) REVERT: J 58 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7522 (mm-30) REVERT: L 37 LYS cc_start: 0.8294 (mtmm) cc_final: 0.7804 (ttmm) REVERT: Z 349 CYS cc_start: 0.5863 (m) cc_final: 0.5327 (p) REVERT: Z 808 ARG cc_start: 0.4526 (OUTLIER) cc_final: 0.3744 (mtp85) REVERT: G 62 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8180 (mm) REVERT: Q 538 TYR cc_start: -0.4473 (m-80) cc_final: -0.4775 (m-80) REVERT: Q 615 GLU cc_start: 0.2758 (tp30) cc_final: 0.2297 (tt0) REVERT: Q 662 ASP cc_start: 0.2703 (p0) cc_final: 0.2004 (t70) REVERT: Q 798 ARG cc_start: 0.4072 (tmt170) cc_final: 0.3384 (tpp-160) REVERT: Q 885 MET cc_start: 0.0583 (tmm) cc_final: 0.0316 (tmm) REVERT: Q 898 HIS cc_start: -0.0638 (OUTLIER) cc_final: -0.3067 (m-70) REVERT: a 57 SER cc_start: 0.8786 (t) cc_final: 0.8477 (t) REVERT: a 93 GLN cc_start: 0.8459 (tt0) cc_final: 0.7862 (tp40) REVERT: c 64 GLU cc_start: 0.8082 (mt-10) cc_final: 0.7702 (mm-30) REVERT: d 56 MET cc_start: 0.8361 (tpp) cc_final: 0.8152 (tpp) REVERT: d 80 TYR cc_start: 0.7425 (m-10) cc_final: 0.7050 (m-80) REVERT: d 117 LYS cc_start: 0.9043 (mtpt) cc_final: 0.8628 (mtmt) REVERT: e 97 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7269 (mm-30) REVERT: f 27 GLN cc_start: 0.7912 (tm-30) cc_final: 0.7436 (tm-30) REVERT: f 36 ARG cc_start: 0.7342 (mtm110) cc_final: 0.6981 (mtp-110) REVERT: f 92 ARG cc_start: 0.8315 (ttp80) cc_final: 0.8085 (ttp80) REVERT: g 64 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7584 (mt-10) REVERT: g 73 ASN cc_start: 0.7578 (t0) cc_final: 0.7112 (m110) REVERT: h 54 LYS cc_start: 0.8274 (ttmm) cc_final: 0.7999 (tppt) REVERT: h 86 ILE cc_start: 0.7751 (mt) cc_final: 0.7203 (mt) REVERT: h 90 GLU cc_start: 0.8284 (mp0) cc_final: 0.7866 (mp0) REVERT: h 118 TYR cc_start: 0.8899 (t80) cc_final: 0.8505 (t80) outliers start: 114 outliers final: 70 residues processed: 690 average time/residue: 0.6484 time to fit residues: 741.2091 Evaluate side-chains 668 residues out of total 5028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 594 time to evaluate : 6.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 871 ASP Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1040 GLN Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 572 HIS Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 949 VAL Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain L residue 65 VAL Chi-restraints excluded: chain Y residue 52 MET Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Z residue 344 VAL Chi-restraints excluded: chain Z residue 808 ARG Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain Q residue 739 VAL Chi-restraints excluded: chain Q residue 887 PHE Chi-restraints excluded: chain Q residue 898 HIS Chi-restraints excluded: chain a residue 86 SER Chi-restraints excluded: chain a residue 107 THR Chi-restraints excluded: chain a residue 117 VAL Chi-restraints excluded: chain b residue 63 GLU Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 102 GLU Chi-restraints excluded: chain d residue 110 GLU Chi-restraints excluded: chain d residue 119 THR Chi-restraints excluded: chain e residue 77 ASP Chi-restraints excluded: chain f residue 37 LEU Chi-restraints excluded: chain f residue 95 ARG Chi-restraints excluded: chain g residue 101 THR Chi-restraints excluded: chain h residue 81 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 191 optimal weight: 0.9980 chunk 513 optimal weight: 20.0000 chunk 112 optimal weight: 0.6980 chunk 334 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 570 optimal weight: 3.9990 chunk 473 optimal weight: 7.9990 chunk 264 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 188 optimal weight: 0.0070 chunk 299 optimal weight: 2.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 HIS A 399 HIS ** A 447 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 654 ASN A 742 ASN ** A 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 GLN A1070 GLN A1173 HIS B 572 HIS ** B1187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 93 GLN c 68 ASN d 92 GLN e 108 ASN e 125 GLN ** g 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 81 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7290 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 53382 Z= 0.177 Angle : 0.553 10.825 73354 Z= 0.295 Chirality : 0.041 0.234 8261 Planarity : 0.004 0.052 8409 Dihedral : 20.635 178.996 9626 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.37 % Allowed : 18.57 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.11), residues: 5648 helix: 1.83 (0.11), residues: 2092 sheet: -0.12 (0.18), residues: 827 loop : -0.68 (0.12), residues: 2729 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 201 HIS 0.014 0.001 HIS B 572 PHE 0.021 0.001 PHE C 219 TYR 0.025 0.001 TYR A 465 ARG 0.008 0.000 ARG B1106 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11296 Ramachandran restraints generated. 5648 Oldfield, 0 Emsley, 5648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11296 Ramachandran restraints generated. 5648 Oldfield, 0 Emsley, 5648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 5028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 621 time to evaluate : 5.574 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 57 ARG cc_start: 0.8320 (mtm110) cc_final: 0.7819 (mtm110) REVERT: A 133 LYS cc_start: 0.8148 (mttp) cc_final: 0.7914 (mttp) REVERT: A 547 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7434 (mp) REVERT: A 895 LYS cc_start: 0.8571 (mmtt) cc_final: 0.8339 (mmtt) REVERT: A 961 ARG cc_start: 0.7250 (ptm160) cc_final: 0.7037 (ptp-110) REVERT: A 1133 LEU cc_start: 0.8376 (mm) cc_final: 0.8144 (mt) REVERT: A 1157 ASP cc_start: 0.7193 (p0) cc_final: 0.6734 (t70) REVERT: A 1214 GLU cc_start: 0.7787 (pp20) cc_final: 0.7375 (pp20) REVERT: A 1218 GLN cc_start: 0.8861 (mt0) cc_final: 0.8418 (mt0) REVERT: A 1259 MET cc_start: 0.7655 (ptp) cc_final: 0.7119 (mpp) REVERT: A 1268 LEU cc_start: 0.8247 (tp) cc_final: 0.8005 (tp) REVERT: B 310 MET cc_start: 0.6901 (mmm) cc_final: 0.6404 (mmt) REVERT: B 560 GLU cc_start: 0.7511 (mt-10) cc_final: 0.7268 (mt-10) REVERT: B 597 MET cc_start: 0.8444 (tpp) cc_final: 0.8103 (tpt) REVERT: B 603 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8386 (mp) REVERT: B 841 MET cc_start: 0.8726 (ttm) cc_final: 0.8338 (ttm) REVERT: B 864 LYS cc_start: 0.7615 (ttpt) cc_final: 0.7213 (tmtt) REVERT: B 868 MET cc_start: 0.6422 (OUTLIER) cc_final: 0.6220 (mpp) REVERT: B 956 THR cc_start: 0.8638 (p) cc_final: 0.8404 (p) REVERT: B 1208 MET cc_start: 0.8183 (mtm) cc_final: 0.7960 (mtp) REVERT: C 95 CYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8066 (p) REVERT: F 103 MET cc_start: 0.8261 (mtt) cc_final: 0.7877 (mtt) REVERT: F 119 ARG cc_start: 0.8301 (mmt-90) cc_final: 0.7898 (mmm-85) REVERT: F 138 LEU cc_start: 0.8361 (mm) cc_final: 0.8158 (mt) REVERT: H 22 LYS cc_start: 0.8443 (mttt) cc_final: 0.8190 (mttp) REVERT: H 52 GLN cc_start: 0.8511 (mm-40) cc_final: 0.8229 (mm-40) REVERT: H 77 ARG cc_start: 0.5541 (ptt180) cc_final: 0.5218 (ptt-90) REVERT: H 93 TYR cc_start: 0.8032 (m-80) cc_final: 0.7680 (m-80) REVERT: I 26 LEU cc_start: 0.7483 (mt) cc_final: 0.7102 (pp) REVERT: J 1 MET cc_start: 0.7429 (mpp) cc_final: 0.7138 (mpp) REVERT: L 37 LYS cc_start: 0.8269 (mtmm) cc_final: 0.7791 (ttmm) REVERT: Z 349 CYS cc_start: 0.5840 (m) cc_final: 0.5328 (p) REVERT: Z 808 ARG cc_start: 0.4468 (OUTLIER) cc_final: 0.2852 (ttm-80) REVERT: Z 818 ILE cc_start: 0.7675 (mp) cc_final: 0.7003 (mt) REVERT: G 62 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8170 (mm) REVERT: O 407 LYS cc_start: 0.5685 (mtpt) cc_final: 0.5303 (mmtt) REVERT: Q 538 TYR cc_start: -0.4594 (m-80) cc_final: -0.4817 (m-80) REVERT: Q 591 TYR cc_start: 0.3948 (m-80) cc_final: 0.3319 (t80) REVERT: Q 615 GLU cc_start: 0.2780 (tp30) cc_final: 0.2369 (tt0) REVERT: Q 662 ASP cc_start: 0.2196 (p0) cc_final: 0.1778 (t70) REVERT: Q 798 ARG cc_start: 0.4070 (tmt170) cc_final: 0.3378 (tpp-160) REVERT: Q 885 MET cc_start: 0.0105 (tmm) cc_final: -0.0471 (ttp) REVERT: Q 898 HIS cc_start: -0.0817 (OUTLIER) cc_final: -0.3172 (m-70) REVERT: a 93 GLN cc_start: 0.8443 (tt0) cc_final: 0.7976 (tp40) REVERT: c 64 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7766 (mm-30) REVERT: d 44 GLN cc_start: 0.7029 (mm110) cc_final: 0.6743 (mm110) REVERT: d 56 MET cc_start: 0.8343 (tpp) cc_final: 0.8131 (tpp) REVERT: d 80 TYR cc_start: 0.7419 (m-10) cc_final: 0.7128 (m-80) REVERT: d 117 LYS cc_start: 0.9061 (mtpt) cc_final: 0.8631 (mtmt) REVERT: e 97 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7326 (mm-30) REVERT: f 27 GLN cc_start: 0.8031 (tm-30) cc_final: 0.7541 (tm-30) REVERT: f 62 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7913 (mm) REVERT: f 92 ARG cc_start: 0.8255 (ttp80) cc_final: 0.7909 (ttp80) REVERT: g 64 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7569 (mt-10) REVERT: g 92 GLU cc_start: 0.7714 (tp30) cc_final: 0.7286 (tp30) REVERT: h 54 LYS cc_start: 0.8226 (ttmm) cc_final: 0.7941 (tppt) REVERT: h 86 ILE cc_start: 0.7844 (mt) cc_final: 0.7515 (mt) REVERT: h 90 GLU cc_start: 0.8270 (mp0) cc_final: 0.7977 (mp0) REVERT: h 118 TYR cc_start: 0.8890 (t80) cc_final: 0.8497 (t80) outliers start: 119 outliers final: 82 residues processed: 698 average time/residue: 0.6422 time to fit residues: 746.3818 Evaluate side-chains 688 residues out of total 5028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 598 time to evaluate : 5.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 871 ASP Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1040 GLN Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 572 HIS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 949 VAL Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain H residue 133 ASN Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain Y residue 52 MET Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Z residue 808 ARG Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain Q residue 738 VAL Chi-restraints excluded: chain Q residue 739 VAL Chi-restraints excluded: chain Q residue 887 PHE Chi-restraints excluded: chain Q residue 898 HIS Chi-restraints excluded: chain Q residue 932 THR Chi-restraints excluded: chain a residue 117 VAL Chi-restraints excluded: chain b residue 63 GLU Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain d residue 102 GLU Chi-restraints excluded: chain d residue 110 GLU Chi-restraints excluded: chain d residue 112 THR Chi-restraints excluded: chain d residue 119 THR Chi-restraints excluded: chain e residue 77 ASP Chi-restraints excluded: chain e residue 96 SER Chi-restraints excluded: chain e residue 108 ASN Chi-restraints excluded: chain f residue 37 LEU Chi-restraints excluded: chain f residue 62 LEU Chi-restraints excluded: chain g residue 93 LEU Chi-restraints excluded: chain g residue 101 THR Chi-restraints excluded: chain g residue 107 VAL Chi-restraints excluded: chain h residue 81 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 550 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 325 optimal weight: 0.5980 chunk 416 optimal weight: 0.9990 chunk 322 optimal weight: 1.9990 chunk 480 optimal weight: 5.9990 chunk 318 optimal weight: 0.5980 chunk 568 optimal weight: 0.9980 chunk 355 optimal weight: 0.9990 chunk 346 optimal weight: 2.9990 chunk 262 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 ASN ** A 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 GLN A 994 GLN A1173 HIS ** B 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1025 HIS ** B1187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 ASN e 108 ASN ** g 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 81 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 53382 Z= 0.184 Angle : 0.550 10.603 73354 Z= 0.294 Chirality : 0.040 0.209 8261 Planarity : 0.004 0.051 8409 Dihedral : 20.596 178.832 9626 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.59 % Allowed : 18.77 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.11), residues: 5648 helix: 1.89 (0.11), residues: 2083 sheet: -0.12 (0.18), residues: 829 loop : -0.65 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 201 HIS 0.009 0.001 HIS B 572 PHE 0.024 0.001 PHE C 219 TYR 0.024 0.001 TYR A 465 ARG 0.007 0.000 ARG B1106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11296 Ramachandran restraints generated. 5648 Oldfield, 0 Emsley, 5648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11296 Ramachandran restraints generated. 5648 Oldfield, 0 Emsley, 5648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 5028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 613 time to evaluate : 5.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 MET cc_start: 0.4556 (OUTLIER) cc_final: 0.4331 (tpt) REVERT: A 57 ARG cc_start: 0.8325 (mtm110) cc_final: 0.7839 (mtm110) REVERT: A 175 ARG cc_start: 0.7692 (mtp-110) cc_final: 0.7365 (ttp80) REVERT: A 264 PHE cc_start: 0.8187 (t80) cc_final: 0.7970 (t80) REVERT: A 277 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7784 (tt0) REVERT: A 320 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7865 (ptm160) REVERT: A 547 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7455 (mp) REVERT: A 576 GLN cc_start: 0.7538 (mt0) cc_final: 0.7203 (mt0) REVERT: A 895 LYS cc_start: 0.8571 (mmtt) cc_final: 0.8343 (mmtt) REVERT: A 961 ARG cc_start: 0.7275 (ptm160) cc_final: 0.7049 (ptp-110) REVERT: A 1133 LEU cc_start: 0.8376 (mm) cc_final: 0.8148 (mt) REVERT: A 1157 ASP cc_start: 0.7225 (p0) cc_final: 0.6745 (t70) REVERT: A 1209 MET cc_start: 0.7683 (OUTLIER) cc_final: 0.7287 (tmm) REVERT: A 1214 GLU cc_start: 0.7755 (pp20) cc_final: 0.7367 (pp20) REVERT: A 1218 GLN cc_start: 0.8912 (mt0) cc_final: 0.8485 (mt0) REVERT: A 1259 MET cc_start: 0.7660 (ptp) cc_final: 0.7135 (mpp) REVERT: A 1268 LEU cc_start: 0.8263 (tp) cc_final: 0.8007 (tp) REVERT: A 1336 MET cc_start: 0.8155 (tmm) cc_final: 0.7881 (ttt) REVERT: B 310 MET cc_start: 0.6936 (mmm) cc_final: 0.6439 (mmt) REVERT: B 597 MET cc_start: 0.8449 (tpp) cc_final: 0.8085 (tpt) REVERT: B 603 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8361 (mp) REVERT: B 789 MET cc_start: 0.8430 (mmm) cc_final: 0.7914 (mmt) REVERT: B 864 LYS cc_start: 0.7620 (ttpt) cc_final: 0.7210 (tmtt) REVERT: B 868 MET cc_start: 0.6458 (OUTLIER) cc_final: 0.6235 (mpp) REVERT: B 956 THR cc_start: 0.8665 (p) cc_final: 0.8432 (p) REVERT: B 1208 MET cc_start: 0.8159 (mtm) cc_final: 0.7936 (mtp) REVERT: C 95 CYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8046 (p) REVERT: E 101 GLN cc_start: 0.6810 (mm110) cc_final: 0.6603 (mm110) REVERT: F 103 MET cc_start: 0.8262 (mtt) cc_final: 0.7902 (mtt) REVERT: F 119 ARG cc_start: 0.8318 (mmt-90) cc_final: 0.7908 (mmm-85) REVERT: H 22 LYS cc_start: 0.8464 (mttt) cc_final: 0.8196 (mttp) REVERT: H 52 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8199 (mm-40) REVERT: H 77 ARG cc_start: 0.5543 (ptt180) cc_final: 0.5242 (ptt-90) REVERT: H 93 TYR cc_start: 0.8050 (m-80) cc_final: 0.7671 (m-80) REVERT: I 26 LEU cc_start: 0.7494 (mt) cc_final: 0.7144 (pp) REVERT: J 1 MET cc_start: 0.7435 (mpp) cc_final: 0.7149 (mpp) REVERT: L 37 LYS cc_start: 0.8302 (mtmm) cc_final: 0.7804 (ttmm) REVERT: Y 4 GLU cc_start: 0.5092 (mm-30) cc_final: 0.4888 (mm-30) REVERT: Z 808 ARG cc_start: 0.4514 (OUTLIER) cc_final: 0.2908 (ttm-80) REVERT: Z 818 ILE cc_start: 0.7630 (mp) cc_final: 0.6985 (mt) REVERT: G 62 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8197 (mm) REVERT: O 407 LYS cc_start: 0.5680 (mtpt) cc_final: 0.5294 (mmtt) REVERT: Q 591 TYR cc_start: 0.3700 (m-80) cc_final: 0.3339 (t80) REVERT: Q 615 GLU cc_start: 0.2823 (tp30) cc_final: 0.2405 (tt0) REVERT: Q 662 ASP cc_start: 0.2235 (p0) cc_final: 0.1784 (t70) REVERT: Q 798 ARG cc_start: 0.4047 (tmt170) cc_final: 0.3348 (tpp-160) REVERT: Q 885 MET cc_start: 0.0096 (tmm) cc_final: -0.0363 (ttp) REVERT: Q 898 HIS cc_start: -0.0728 (OUTLIER) cc_final: -0.3082 (m-70) REVERT: a 93 GLN cc_start: 0.8354 (tt0) cc_final: 0.8153 (tp40) REVERT: c 64 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7750 (mm-30) REVERT: d 44 GLN cc_start: 0.6985 (mm110) cc_final: 0.6768 (mm110) REVERT: d 80 TYR cc_start: 0.7436 (m-10) cc_final: 0.7210 (m-80) REVERT: d 117 LYS cc_start: 0.9068 (mtpt) cc_final: 0.8640 (mtmt) REVERT: e 125 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8195 (mm110) REVERT: f 27 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7411 (tm-30) REVERT: f 36 ARG cc_start: 0.7300 (mtm110) cc_final: 0.6950 (mtm110) REVERT: f 58 LEU cc_start: 0.9154 (tp) cc_final: 0.8948 (tp) REVERT: f 62 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7835 (mm) REVERT: h 33 SER cc_start: 0.8496 (OUTLIER) cc_final: 0.8226 (m) REVERT: h 54 LYS cc_start: 0.8227 (ttmm) cc_final: 0.7929 (tppt) REVERT: h 86 ILE cc_start: 0.7897 (mt) cc_final: 0.7616 (mt) REVERT: h 90 GLU cc_start: 0.8260 (mp0) cc_final: 0.7958 (mp0) REVERT: h 118 TYR cc_start: 0.8896 (t80) cc_final: 0.8528 (t80) outliers start: 130 outliers final: 88 residues processed: 696 average time/residue: 0.6349 time to fit residues: 736.1100 Evaluate side-chains 679 residues out of total 5028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 578 time to evaluate : 4.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 853 ASP Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 871 ASP Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1040 GLN Chi-restraints excluded: chain A residue 1209 MET Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 949 VAL Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain F residue 150 GLU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 21 ASN Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain L residue 57 LEU Chi-restraints excluded: chain Y residue 52 MET Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Z residue 808 ARG Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain Q residue 738 VAL Chi-restraints excluded: chain Q residue 739 VAL Chi-restraints excluded: chain Q residue 887 PHE Chi-restraints excluded: chain Q residue 898 HIS Chi-restraints excluded: chain Q residue 932 THR Chi-restraints excluded: chain a residue 117 VAL Chi-restraints excluded: chain b residue 63 GLU Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain d residue 102 GLU Chi-restraints excluded: chain d residue 110 GLU Chi-restraints excluded: chain d residue 112 THR Chi-restraints excluded: chain d residue 119 THR Chi-restraints excluded: chain e residue 77 ASP Chi-restraints excluded: chain e residue 100 LEU Chi-restraints excluded: chain e residue 108 ASN Chi-restraints excluded: chain f residue 37 LEU Chi-restraints excluded: chain f residue 62 LEU Chi-restraints excluded: chain g residue 101 THR Chi-restraints excluded: chain g residue 107 VAL Chi-restraints excluded: chain h residue 33 SER Chi-restraints excluded: chain h residue 81 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 351 optimal weight: 2.9990 chunk 227 optimal weight: 0.8980 chunk 339 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 361 optimal weight: 0.4980 chunk 387 optimal weight: 5.9990 chunk 281 optimal weight: 0.8980 chunk 52 optimal weight: 8.9990 chunk 446 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 HIS ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 ASN ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1173 HIS B 572 HIS ** B1187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 815 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN ** G 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 ASN d 81 ASN d 92 GLN e 76 GLN ** g 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 79 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 53382 Z= 0.242 Angle : 0.580 11.403 73354 Z= 0.309 Chirality : 0.041 0.273 8261 Planarity : 0.004 0.051 8409 Dihedral : 20.612 178.306 9626 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.47 % Allowed : 19.41 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.11), residues: 5648 helix: 1.80 (0.11), residues: 2085 sheet: -0.12 (0.18), residues: 843 loop : -0.65 (0.12), residues: 2720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1228 HIS 0.009 0.001 HIS C 167 PHE 0.024 0.002 PHE C 219 TYR 0.025 0.001 TYR A 465 ARG 0.012 0.000 ARG B 904 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11296 Ramachandran restraints generated. 5648 Oldfield, 0 Emsley, 5648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11296 Ramachandran restraints generated. 5648 Oldfield, 0 Emsley, 5648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 5028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 594 time to evaluate : 5.881 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 41 MET cc_start: 0.4807 (OUTLIER) cc_final: 0.4552 (tpt) REVERT: A 57 ARG cc_start: 0.8363 (mtm110) cc_final: 0.7839 (mtm110) REVERT: A 133 LYS cc_start: 0.8151 (mttp) cc_final: 0.7927 (mttp) REVERT: A 264 PHE cc_start: 0.8196 (t80) cc_final: 0.7968 (t80) REVERT: A 277 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7779 (tt0) REVERT: A 547 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7464 (mp) REVERT: A 576 GLN cc_start: 0.7652 (mt0) cc_final: 0.7345 (mt0) REVERT: A 895 LYS cc_start: 0.8595 (mmtt) cc_final: 0.8371 (mmtt) REVERT: A 929 LEU cc_start: 0.8209 (mm) cc_final: 0.7919 (mp) REVERT: A 961 ARG cc_start: 0.7392 (ptm160) cc_final: 0.7157 (ptp-110) REVERT: A 1157 ASP cc_start: 0.7302 (p0) cc_final: 0.6843 (t70) REVERT: A 1209 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7457 (tmm) REVERT: A 1214 GLU cc_start: 0.7822 (pp20) cc_final: 0.7427 (pp20) REVERT: A 1218 GLN cc_start: 0.8938 (mt0) cc_final: 0.8564 (mt0) REVERT: A 1259 MET cc_start: 0.7672 (ptp) cc_final: 0.7164 (mpp) REVERT: A 1268 LEU cc_start: 0.8239 (tp) cc_final: 0.7962 (tp) REVERT: A 1336 MET cc_start: 0.8184 (tmm) cc_final: 0.7903 (ttt) REVERT: B 310 MET cc_start: 0.7034 (mmm) cc_final: 0.6532 (mmt) REVERT: B 473 MET cc_start: 0.7418 (mmm) cc_final: 0.6624 (mmm) REVERT: B 597 MET cc_start: 0.8466 (tpp) cc_final: 0.8168 (tpt) REVERT: B 603 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8354 (mp) REVERT: B 789 MET cc_start: 0.8466 (mmm) cc_final: 0.7966 (mmt) REVERT: B 841 MET cc_start: 0.8768 (ttm) cc_final: 0.8419 (ttm) REVERT: B 864 LYS cc_start: 0.7669 (ttpt) cc_final: 0.7305 (tmtt) REVERT: B 868 MET cc_start: 0.6443 (OUTLIER) cc_final: 0.6182 (mpp) REVERT: B 1181 GLU cc_start: 0.7558 (tp30) cc_final: 0.7336 (tp30) REVERT: B 1208 MET cc_start: 0.8266 (mtp) cc_final: 0.8061 (mtp) REVERT: C 95 CYS cc_start: 0.8333 (OUTLIER) cc_final: 0.8011 (p) REVERT: F 103 MET cc_start: 0.8270 (mtt) cc_final: 0.7888 (mtt) REVERT: F 119 ARG cc_start: 0.8384 (mmt-90) cc_final: 0.7976 (mmm-85) REVERT: H 22 LYS cc_start: 0.8477 (mttt) cc_final: 0.8143 (mttp) REVERT: H 52 GLN cc_start: 0.8518 (mm-40) cc_final: 0.8157 (mm-40) REVERT: H 77 ARG cc_start: 0.5651 (ptt180) cc_final: 0.5348 (ptt-90) REVERT: I 26 LEU cc_start: 0.7468 (mt) cc_final: 0.7052 (pp) REVERT: J 1 MET cc_start: 0.7404 (mpp) cc_final: 0.7126 (mpp) REVERT: J 58 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7518 (mm-30) REVERT: K 54 ARG cc_start: 0.7547 (tpm170) cc_final: 0.7319 (tpt90) REVERT: L 37 LYS cc_start: 0.8382 (mtmm) cc_final: 0.7892 (ttmm) REVERT: Y 73 MET cc_start: 0.3164 (tpt) cc_final: 0.2957 (tpt) REVERT: Z 349 CYS cc_start: 0.5953 (m) cc_final: 0.5398 (p) REVERT: Z 808 ARG cc_start: 0.4555 (OUTLIER) cc_final: 0.2182 (tpm-80) REVERT: Z 818 ILE cc_start: 0.7630 (mp) cc_final: 0.6984 (mt) REVERT: G 62 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8173 (mm) REVERT: O 389 LYS cc_start: 0.5309 (mmtt) cc_final: 0.4289 (mmmt) REVERT: Q 615 GLU cc_start: 0.2757 (tp30) cc_final: 0.2401 (tt0) REVERT: Q 798 ARG cc_start: 0.4043 (tmt170) cc_final: 0.3331 (tpp-160) REVERT: a 93 GLN cc_start: 0.8387 (tt0) cc_final: 0.8035 (tp40) REVERT: c 64 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7785 (mm-30) REVERT: c 99 ARG cc_start: 0.6764 (mmp-170) cc_final: 0.6557 (mmp-170) REVERT: d 44 GLN cc_start: 0.6975 (mm110) cc_final: 0.6723 (mm110) REVERT: d 117 LYS cc_start: 0.9080 (mtpt) cc_final: 0.8670 (mtmt) REVERT: e 76 GLN cc_start: 0.7934 (mt0) cc_final: 0.7583 (pt0) REVERT: e 97 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7080 (mm-30) REVERT: e 125 GLN cc_start: 0.8741 (mm-40) cc_final: 0.8093 (mm110) REVERT: f 27 GLN cc_start: 0.8084 (tm-30) cc_final: 0.7452 (tm-30) REVERT: f 36 ARG cc_start: 0.7318 (mtm110) cc_final: 0.6865 (mtp-110) REVERT: f 53 GLU cc_start: 0.8463 (tp30) cc_final: 0.8247 (tp30) REVERT: f 62 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7915 (mm) REVERT: f 77 LYS cc_start: 0.8402 (mtmt) cc_final: 0.7999 (mtmm) REVERT: g 61 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7593 (mm-30) REVERT: g 79 ILE cc_start: 0.8107 (pt) cc_final: 0.7820 (mm) REVERT: h 33 SER cc_start: 0.8405 (OUTLIER) cc_final: 0.8127 (m) REVERT: h 54 LYS cc_start: 0.8228 (ttmm) cc_final: 0.7922 (tppt) REVERT: h 61 SER cc_start: 0.7804 (t) cc_final: 0.7516 (p) REVERT: h 86 ILE cc_start: 0.7924 (mt) cc_final: 0.7635 (mt) REVERT: h 90 GLU cc_start: 0.8273 (mp0) cc_final: 0.7948 (mp0) REVERT: h 105 LYS cc_start: 0.8993 (ttpp) cc_final: 0.8751 (ptmm) outliers start: 124 outliers final: 95 residues processed: 673 average time/residue: 0.6337 time to fit residues: 707.5704 Evaluate side-chains 689 residues out of total 5028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 583 time to evaluate : 6.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 41 MET Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 557 ASP Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 853 ASP Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 871 ASP Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1040 GLN Chi-restraints excluded: chain A residue 1124 HIS Chi-restraints excluded: chain A residue 1209 MET Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 572 HIS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 949 VAL Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain H residue 133 ASN Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain Y residue 52 MET Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Z residue 808 ARG Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain Q residue 738 VAL Chi-restraints excluded: chain Q residue 739 VAL Chi-restraints excluded: chain Q residue 749 LEU Chi-restraints excluded: chain Q residue 887 PHE Chi-restraints excluded: chain Q residue 932 THR Chi-restraints excluded: chain a residue 117 VAL Chi-restraints excluded: chain b residue 63 GLU Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 102 GLU Chi-restraints excluded: chain d residue 112 THR Chi-restraints excluded: chain d residue 119 THR Chi-restraints excluded: chain e residue 77 ASP Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain e residue 96 SER Chi-restraints excluded: chain e residue 100 LEU Chi-restraints excluded: chain e residue 107 THR Chi-restraints excluded: chain f residue 37 LEU Chi-restraints excluded: chain f residue 62 LEU Chi-restraints excluded: chain g residue 107 VAL Chi-restraints excluded: chain h residue 33 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 517 optimal weight: 30.0000 chunk 544 optimal weight: 6.9990 chunk 497 optimal weight: 0.8980 chunk 529 optimal weight: 0.0970 chunk 318 optimal weight: 2.9990 chunk 230 optimal weight: 3.9990 chunk 416 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 478 optimal weight: 40.0000 chunk 501 optimal weight: 20.0000 chunk 528 optimal weight: 0.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 ASN ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1173 HIS B 572 HIS ** B1187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN ** G 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 898 HIS ** a 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 68 ASN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 79 HIS h 81 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 53382 Z= 0.215 Angle : 0.575 12.740 73354 Z= 0.306 Chirality : 0.041 0.279 8261 Planarity : 0.004 0.052 8409 Dihedral : 20.602 178.460 9626 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 2.47 % Allowed : 19.69 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.11), residues: 5648 helix: 1.81 (0.11), residues: 2089 sheet: -0.14 (0.18), residues: 845 loop : -0.64 (0.12), residues: 2714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 519 HIS 0.021 0.001 HIS B 572 PHE 0.024 0.001 PHE C 219 TYR 0.023 0.001 TYR A 465 ARG 0.008 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11296 Ramachandran restraints generated. 5648 Oldfield, 0 Emsley, 5648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11296 Ramachandran restraints generated. 5648 Oldfield, 0 Emsley, 5648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 5028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 602 time to evaluate : 5.254 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 57 ARG cc_start: 0.8348 (mtm110) cc_final: 0.7849 (mtm110) REVERT: A 63 ARG cc_start: 0.7443 (tmm160) cc_final: 0.7216 (ttp80) REVERT: A 175 ARG cc_start: 0.7883 (ttp80) cc_final: 0.7599 (ttp80) REVERT: A 264 PHE cc_start: 0.8209 (t80) cc_final: 0.7980 (t80) REVERT: A 277 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: A 547 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7452 (mp) REVERT: A 576 GLN cc_start: 0.7605 (mt0) cc_final: 0.7217 (mt0) REVERT: A 895 LYS cc_start: 0.8583 (mmtt) cc_final: 0.8357 (mmtt) REVERT: A 961 ARG cc_start: 0.7374 (ptm160) cc_final: 0.7152 (ptp-110) REVERT: A 1157 ASP cc_start: 0.7298 (p0) cc_final: 0.6908 (t70) REVERT: A 1214 GLU cc_start: 0.7770 (pp20) cc_final: 0.7379 (pp20) REVERT: A 1218 GLN cc_start: 0.8965 (mt0) cc_final: 0.8631 (mt0) REVERT: A 1259 MET cc_start: 0.7678 (ptp) cc_final: 0.7164 (mpp) REVERT: A 1336 MET cc_start: 0.8173 (tmm) cc_final: 0.7902 (ttt) REVERT: B 310 MET cc_start: 0.6985 (mmm) cc_final: 0.6559 (mmt) REVERT: B 473 MET cc_start: 0.7381 (mmm) cc_final: 0.6678 (mmm) REVERT: B 597 MET cc_start: 0.8468 (tpp) cc_final: 0.8140 (tpt) REVERT: B 603 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8300 (mp) REVERT: B 789 MET cc_start: 0.8435 (mmm) cc_final: 0.7941 (mmt) REVERT: B 864 LYS cc_start: 0.7670 (ttpt) cc_final: 0.7297 (tmtt) REVERT: B 868 MET cc_start: 0.6474 (OUTLIER) cc_final: 0.6220 (mpp) REVERT: B 1181 GLU cc_start: 0.7588 (tp30) cc_final: 0.7373 (tp30) REVERT: C 95 CYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7985 (p) REVERT: F 103 MET cc_start: 0.8283 (mtt) cc_final: 0.7937 (mtt) REVERT: F 119 ARG cc_start: 0.8329 (mmt-90) cc_final: 0.7919 (mmm-85) REVERT: H 22 LYS cc_start: 0.8356 (mttt) cc_final: 0.8132 (mttp) REVERT: H 52 GLN cc_start: 0.8520 (mm-40) cc_final: 0.8169 (mm-40) REVERT: H 77 ARG cc_start: 0.5668 (ptt180) cc_final: 0.5393 (ptt-90) REVERT: I 26 LEU cc_start: 0.7488 (mt) cc_final: 0.7072 (pp) REVERT: J 1 MET cc_start: 0.7392 (mpp) cc_final: 0.7124 (mpp) REVERT: K 54 ARG cc_start: 0.7585 (tpm170) cc_final: 0.7248 (tpt90) REVERT: Z 349 CYS cc_start: 0.6223 (m) cc_final: 0.5606 (p) REVERT: Z 808 ARG cc_start: 0.4487 (OUTLIER) cc_final: 0.2939 (ttm-80) REVERT: Z 818 ILE cc_start: 0.7612 (mp) cc_final: 0.6953 (mt) REVERT: G 58 ARG cc_start: 0.6862 (mtt-85) cc_final: 0.6537 (mmt90) REVERT: G 62 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8157 (mm) REVERT: O 389 LYS cc_start: 0.5407 (mmtt) cc_final: 0.4445 (mmmt) REVERT: Q 615 GLU cc_start: 0.2706 (tp30) cc_final: 0.2400 (tt0) REVERT: Q 798 ARG cc_start: 0.3890 (tmt170) cc_final: 0.3167 (tpp-160) REVERT: a 93 GLN cc_start: 0.8345 (tt0) cc_final: 0.8047 (tp40) REVERT: b 63 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7515 (pt0) REVERT: c 20 ARG cc_start: 0.6666 (mtt-85) cc_final: 0.6393 (mtt90) REVERT: c 64 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7807 (mm-30) REVERT: c 73 ASN cc_start: 0.7956 (t0) cc_final: 0.7700 (t0) REVERT: c 99 ARG cc_start: 0.6723 (mmp-170) cc_final: 0.6515 (mmp-170) REVERT: d 117 LYS cc_start: 0.9073 (mtpt) cc_final: 0.8665 (mtmt) REVERT: e 76 GLN cc_start: 0.7884 (mt0) cc_final: 0.7573 (pt0) REVERT: e 125 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8082 (mm110) REVERT: f 27 GLN cc_start: 0.8015 (tm-30) cc_final: 0.7501 (tm-30) REVERT: f 36 ARG cc_start: 0.7330 (mtm110) cc_final: 0.6905 (mtp-110) REVERT: f 53 GLU cc_start: 0.8425 (tp30) cc_final: 0.8154 (tp30) REVERT: f 62 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7866 (mm) REVERT: f 79 LYS cc_start: 0.7446 (tptt) cc_final: 0.7012 (tptt) REVERT: g 64 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7657 (mt-10) REVERT: g 79 ILE cc_start: 0.8098 (pt) cc_final: 0.7813 (mm) REVERT: h 33 SER cc_start: 0.8332 (OUTLIER) cc_final: 0.8080 (m) REVERT: h 54 LYS cc_start: 0.8239 (ttmm) cc_final: 0.7937 (tppt) REVERT: h 56 MET cc_start: 0.7730 (tpp) cc_final: 0.7403 (tpp) REVERT: h 86 ILE cc_start: 0.7917 (mt) cc_final: 0.7423 (mt) REVERT: h 90 GLU cc_start: 0.8281 (mp0) cc_final: 0.7867 (mp0) REVERT: h 105 LYS cc_start: 0.9002 (ttpp) cc_final: 0.8756 (ptmm) REVERT: h 118 TYR cc_start: 0.8962 (t80) cc_final: 0.8483 (t80) outliers start: 124 outliers final: 102 residues processed: 679 average time/residue: 0.6324 time to fit residues: 713.6989 Evaluate side-chains 700 residues out of total 5028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 588 time to evaluate : 5.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 853 ASP Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 871 ASP Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1040 GLN Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 572 HIS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 805 THR Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 949 VAL Chi-restraints excluded: chain B residue 1169 MET Chi-restraints excluded: chain B residue 1210 MET Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 156 THR Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 178 ILE Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 77 ASP Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain H residue 133 ASN Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain L residue 30 ILE Chi-restraints excluded: chain Y residue 52 MET Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Z residue 808 ARG Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain Q residue 738 VAL Chi-restraints excluded: chain Q residue 739 VAL Chi-restraints excluded: chain Q residue 749 LEU Chi-restraints excluded: chain Q residue 932 THR Chi-restraints excluded: chain a residue 117 VAL Chi-restraints excluded: chain b residue 63 GLU Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 102 GLU Chi-restraints excluded: chain d residue 110 GLU Chi-restraints excluded: chain d residue 119 THR Chi-restraints excluded: chain e residue 77 ASP Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain e residue 96 SER Chi-restraints excluded: chain e residue 100 LEU Chi-restraints excluded: chain e residue 108 ASN Chi-restraints excluded: chain f residue 37 LEU Chi-restraints excluded: chain f residue 62 LEU Chi-restraints excluded: chain g residue 107 VAL Chi-restraints excluded: chain h residue 33 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 347 optimal weight: 4.9990 chunk 560 optimal weight: 1.9990 chunk 342 optimal weight: 0.0770 chunk 265 optimal weight: 0.7980 chunk 389 optimal weight: 0.0570 chunk 587 optimal weight: 0.9980 chunk 540 optimal weight: 0.9990 chunk 468 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 361 optimal weight: 0.4980 chunk 287 optimal weight: 2.9990 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 ASN ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 881 GLN ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1173 HIS B 572 HIS ** B1187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN ** G 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 92 GLN e 108 ASN ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 53382 Z= 0.169 Angle : 0.568 13.900 73354 Z= 0.300 Chirality : 0.041 0.288 8261 Planarity : 0.004 0.052 8409 Dihedral : 20.561 178.984 9626 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.15 % Allowed : 20.23 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.11), residues: 5648 helix: 1.88 (0.12), residues: 2085 sheet: -0.02 (0.18), residues: 828 loop : -0.64 (0.12), residues: 2735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 519 HIS 0.033 0.001 HIS B 572 PHE 0.024 0.001 PHE C 219 TYR 0.030 0.001 TYR B 666 ARG 0.009 0.000 ARG D 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11296 Ramachandran restraints generated. 5648 Oldfield, 0 Emsley, 5648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11296 Ramachandran restraints generated. 5648 Oldfield, 0 Emsley, 5648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 5028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 607 time to evaluate : 5.479 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 57 ARG cc_start: 0.8328 (mtm110) cc_final: 0.7861 (mtm110) REVERT: A 175 ARG cc_start: 0.7860 (ttp80) cc_final: 0.7611 (ttp80) REVERT: A 264 PHE cc_start: 0.8211 (t80) cc_final: 0.7946 (t80) REVERT: A 277 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: A 547 LEU cc_start: 0.7850 (OUTLIER) cc_final: 0.7445 (mp) REVERT: A 895 LYS cc_start: 0.8569 (mmtt) cc_final: 0.8341 (mmtt) REVERT: A 1157 ASP cc_start: 0.7282 (p0) cc_final: 0.6899 (t70) REVERT: A 1214 GLU cc_start: 0.7765 (pp20) cc_final: 0.7428 (pp20) REVERT: A 1218 GLN cc_start: 0.8977 (mt0) cc_final: 0.8627 (mt0) REVERT: A 1259 MET cc_start: 0.7680 (ptp) cc_final: 0.7155 (mpp) REVERT: A 1285 MET cc_start: 0.6506 (mtt) cc_final: 0.6222 (mtt) REVERT: A 1336 MET cc_start: 0.8157 (tmm) cc_final: 0.7891 (ttt) REVERT: B 310 MET cc_start: 0.6899 (mmm) cc_final: 0.6515 (mmt) REVERT: B 473 MET cc_start: 0.7325 (mmm) cc_final: 0.6698 (mmm) REVERT: B 597 MET cc_start: 0.8463 (tpp) cc_final: 0.8090 (tpt) REVERT: B 603 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8254 (mp) REVERT: B 705 MET cc_start: 0.8341 (tpt) cc_final: 0.7764 (tpt) REVERT: B 789 MET cc_start: 0.8403 (mmm) cc_final: 0.7918 (mmt) REVERT: B 841 MET cc_start: 0.8704 (ttm) cc_final: 0.8357 (ttm) REVERT: B 864 LYS cc_start: 0.7654 (ttpt) cc_final: 0.7279 (tmtt) REVERT: B 868 MET cc_start: 0.6441 (OUTLIER) cc_final: 0.6240 (mpp) REVERT: B 1128 LEU cc_start: 0.8367 (mm) cc_final: 0.8128 (mp) REVERT: B 1181 GLU cc_start: 0.7552 (tp30) cc_final: 0.7331 (tp30) REVERT: C 95 CYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8079 (p) REVERT: E 121 MET cc_start: 0.7512 (ppp) cc_final: 0.7202 (ppp) REVERT: F 103 MET cc_start: 0.8212 (mtt) cc_final: 0.7872 (mtt) REVERT: F 119 ARG cc_start: 0.8301 (mmt-90) cc_final: 0.7885 (mmm-85) REVERT: H 22 LYS cc_start: 0.8327 (mttt) cc_final: 0.8123 (mttp) REVERT: H 52 GLN cc_start: 0.8501 (mm-40) cc_final: 0.8156 (mm-40) REVERT: H 77 ARG cc_start: 0.5600 (ptt180) cc_final: 0.5338 (ptt-90) REVERT: H 93 TYR cc_start: 0.7888 (m-80) cc_final: 0.7564 (m-80) REVERT: I 26 LEU cc_start: 0.7498 (mt) cc_final: 0.7079 (pp) REVERT: J 1 MET cc_start: 0.7310 (mpp) cc_final: 0.7080 (mpp) REVERT: K 54 ARG cc_start: 0.7507 (tpm170) cc_final: 0.7241 (tpt170) REVERT: L 37 LYS cc_start: 0.8217 (mtmm) cc_final: 0.7827 (ttmm) REVERT: Y 52 MET cc_start: 0.3664 (OUTLIER) cc_final: 0.3126 (tmm) REVERT: Z 349 CYS cc_start: 0.6216 (m) cc_final: 0.5606 (p) REVERT: Z 808 ARG cc_start: 0.4477 (OUTLIER) cc_final: 0.3950 (mtp85) REVERT: Z 818 ILE cc_start: 0.7633 (mp) cc_final: 0.7008 (mt) REVERT: G 58 ARG cc_start: 0.6737 (mtt-85) cc_final: 0.6491 (mmt90) REVERT: G 62 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8152 (mm) REVERT: G 115 MET cc_start: 0.0387 (mmm) cc_final: 0.0033 (mpp) REVERT: O 389 LYS cc_start: 0.5383 (mmtt) cc_final: 0.4436 (mmmt) REVERT: O 449 THR cc_start: 0.7266 (OUTLIER) cc_final: 0.7048 (m) REVERT: Q 578 TYR cc_start: -0.0331 (m-80) cc_final: -0.0571 (m-80) REVERT: Q 615 GLU cc_start: 0.2671 (tp30) cc_final: 0.2407 (tt0) REVERT: Q 798 ARG cc_start: 0.3913 (tmt170) cc_final: 0.3201 (tpp-160) REVERT: a 93 GLN cc_start: 0.8325 (tt0) cc_final: 0.8036 (tp40) REVERT: b 63 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7576 (pt0) REVERT: c 64 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7697 (mm-30) REVERT: c 73 ASN cc_start: 0.7935 (t0) cc_final: 0.7692 (t0) REVERT: c 99 ARG cc_start: 0.6713 (mmp-170) cc_final: 0.6502 (mmp-170) REVERT: d 117 LYS cc_start: 0.9064 (mtpt) cc_final: 0.8651 (mtmt) REVERT: e 76 GLN cc_start: 0.7867 (mt0) cc_final: 0.7613 (pt0) REVERT: e 97 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7014 (mm-30) REVERT: e 125 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8081 (mm110) REVERT: f 27 GLN cc_start: 0.7949 (tm-30) cc_final: 0.7467 (tm-30) REVERT: f 36 ARG cc_start: 0.7277 (mtm110) cc_final: 0.6836 (mtp-110) REVERT: f 53 GLU cc_start: 0.8416 (tp30) cc_final: 0.8136 (tp30) REVERT: g 64 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7503 (mt-10) REVERT: g 104 GLN cc_start: 0.7841 (mp10) cc_final: 0.6933 (pm20) REVERT: h 33 SER cc_start: 0.8313 (OUTLIER) cc_final: 0.8073 (m) REVERT: h 54 LYS cc_start: 0.8239 (ttmm) cc_final: 0.7927 (tppt) REVERT: h 56 MET cc_start: 0.7752 (tpp) cc_final: 0.7453 (tpp) REVERT: h 86 ILE cc_start: 0.7906 (mt) cc_final: 0.7399 (mt) REVERT: h 90 GLU cc_start: 0.8257 (mp0) cc_final: 0.7868 (mp0) REVERT: h 105 LYS cc_start: 0.9014 (ttpp) cc_final: 0.8768 (ptmm) REVERT: h 118 TYR cc_start: 0.8968 (t80) cc_final: 0.8533 (t80) outliers start: 108 outliers final: 87 residues processed: 678 average time/residue: 0.6321 time to fit residues: 709.2661 Evaluate side-chains 692 residues out of total 5028 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 594 time to evaluate : 5.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 PHE Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 140 THR Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 247 ARG Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 320 ARG Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 455 MET Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 746 MET Chi-restraints excluded: chain A residue 853 ASP Chi-restraints excluded: chain A residue 867 ILE Chi-restraints excluded: chain A residue 871 ASP Chi-restraints excluded: chain A residue 886 ILE Chi-restraints excluded: chain A residue 948 VAL Chi-restraints excluded: chain A residue 999 VAL Chi-restraints excluded: chain A residue 1040 GLN Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain B residue 44 VAL Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 547 VAL Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 572 HIS Chi-restraints excluded: chain B residue 603 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 797 TYR Chi-restraints excluded: chain B residue 868 MET Chi-restraints excluded: chain B residue 871 THR Chi-restraints excluded: chain B residue 910 VAL Chi-restraints excluded: chain B residue 949 VAL Chi-restraints excluded: chain C residue 16 ASP Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 95 CYS Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 155 LEU Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain C residue 240 VAL Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain E residue 5 ASN Chi-restraints excluded: chain E residue 69 ILE Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 204 THR Chi-restraints excluded: chain F residue 93 ILE Chi-restraints excluded: chain F residue 130 ILE Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 39 THR Chi-restraints excluded: chain H residue 54 SER Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 128 ASN Chi-restraints excluded: chain H residue 133 ASN Chi-restraints excluded: chain I residue 50 THR Chi-restraints excluded: chain J residue 5 VAL Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain Y residue 52 MET Chi-restraints excluded: chain Y residue 66 VAL Chi-restraints excluded: chain Z residue 808 ARG Chi-restraints excluded: chain G residue 10 ASN Chi-restraints excluded: chain G residue 62 LEU Chi-restraints excluded: chain G residue 137 ILE Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain O residue 243 VAL Chi-restraints excluded: chain O residue 316 LEU Chi-restraints excluded: chain O residue 449 THR Chi-restraints excluded: chain Q residue 738 VAL Chi-restraints excluded: chain Q residue 739 VAL Chi-restraints excluded: chain Q residue 749 LEU Chi-restraints excluded: chain Q residue 932 THR Chi-restraints excluded: chain a residue 117 VAL Chi-restraints excluded: chain b residue 63 GLU Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain c residue 51 LEU Chi-restraints excluded: chain d residue 119 THR Chi-restraints excluded: chain e residue 77 ASP Chi-restraints excluded: chain e residue 92 LEU Chi-restraints excluded: chain e residue 108 ASN Chi-restraints excluded: chain f residue 37 LEU Chi-restraints excluded: chain g residue 107 VAL Chi-restraints excluded: chain h residue 33 SER Chi-restraints excluded: chain h residue 81 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 590 random chunks: chunk 371 optimal weight: 3.9990 chunk 498 optimal weight: 0.4980 chunk 143 optimal weight: 3.9990 chunk 431 optimal weight: 20.0000 chunk 69 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 468 optimal weight: 7.9990 chunk 196 optimal weight: 6.9990 chunk 481 optimal weight: 0.3980 chunk 59 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 576 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 742 ASN ** A 851 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 959 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 GLN A1173 HIS B 572 HIS ** B1187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN ** a 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 92 GLN e 108 ASN ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 79 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.135963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.100283 restraints weight = 123550.364| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.98 r_work: 0.3406 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 53382 Z= 0.262 Angle : 0.591 14.003 73354 Z= 0.313 Chirality : 0.042 0.218 8261 Planarity : 0.004 0.052 8409 Dihedral : 20.556 179.607 9626 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.21 % Allowed : 20.37 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.55 % Cis-general : 0.04 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.11), residues: 5648 helix: 1.79 (0.12), residues: 2083 sheet: -0.12 (0.18), residues: 849 loop : -0.65 (0.12), residues: 2716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1228 HIS 0.008 0.001 HIS f 75 PHE 0.023 0.002 PHE C 219 TYR 0.022 0.001 TYR A 465 ARG 0.008 0.000 ARG D 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14015.96 seconds wall clock time: 252 minutes 12.09 seconds (15132.09 seconds total)