Starting phenix.real_space_refine on Tue Dec 31 12:04:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9egy_48040/12_2024/9egy_48040.cif Found real_map, /net/cci-nas-00/data/ceres_data/9egy_48040/12_2024/9egy_48040.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9egy_48040/12_2024/9egy_48040.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9egy_48040/12_2024/9egy_48040.map" model { file = "/net/cci-nas-00/data/ceres_data/9egy_48040/12_2024/9egy_48040.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9egy_48040/12_2024/9egy_48040.cif" } resolution = 2.9 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= 0.002 sd= 0.015 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 332 5.49 5 Mg 1 5.21 5 S 259 5.16 5 C 40362 2.51 5 N 12221 2.21 5 O 13465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 66649 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 11210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1426, 11210 Classifications: {'peptide': 1426} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 71, 'TRANS': 1353} Chain breaks: 7 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'TPO:plan-1': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 8980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1122, 8980 Classifications: {'peptide': 1122} Link IDs: {'PTRANS': 52, 'TRANS': 1069} Chain breaks: 4 Chain: "C" Number of atoms: 2072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2072 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 15, 'TRANS': 242} Chain breaks: 1 Chain: "D" Number of atoms: 1004 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1004 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "E" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1720 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 11, 'TRANS': 197} Chain: "F" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 626 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "G" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1333 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "H" Number of atoms: 1197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1197 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 4, 'TRANS': 144} Chain: "I" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 942 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "J" Number of atoms: 524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 524 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "K" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 920 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "L" Number of atoms: 397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 397 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "M" Number of atoms: 4309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1002, 4309 Classifications: {'peptide': 1002} Incomplete info: {'backbone_only': 747, 'truncation_to_alanine': 161} Link IDs: {'PTRANS': 44, 'TRANS': 957} Chain breaks: 12 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 4067 Unresolved non-hydrogen angles: 5716 Unresolved non-hydrogen dihedrals: 2768 Unresolved non-hydrogen chiralities: 1012 Planarities with less than four sites: {'GLN:plan1': 49, 'HIS:plan': 25, 'TYR:plan': 40, 'ASN:plan1': 36, 'TRP:plan': 11, 'ASP:plan': 61, 'PHE:plan': 46, 'GLU:plan': 95, 'ARG:plan': 68} Unresolved non-hydrogen planarities: 2160 Chain: "N" Number of atoms: 3070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 3070 Classifications: {'DNA': 149} Link IDs: {'rna3p': 148} Chain breaks: 1 Chain: "O" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 656 Classifications: {'peptide': 132} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PTRANS': 7, 'TRANS': 124} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 407 Unresolved non-hydrogen angles: 508 Unresolved non-hydrogen dihedrals: 341 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 8, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 181 Chain: "P" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 432 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 5, 'rna3p_pur': 3, 'rna3p_pyr': 12} Link IDs: {'rna2p': 6, 'rna3p': 14} Chain: "Q" Number of atoms: 6427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 6427 Classifications: {'peptide': 890} Incomplete info: {'truncation_to_alanine': 230} Link IDs: {'CIS': 2, 'PTRANS': 19, 'TRANS': 868} Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 843 Unresolved non-hydrogen angles: 1069 Unresolved non-hydrogen dihedrals: 693 Unresolved non-hydrogen chiralities: 73 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 20, 'TYR:plan': 11, 'ASN:plan1': 15, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 8, 'GLU:plan': 18, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 458 Chain: "R" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1428 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 161} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 235} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 603 Unresolved non-hydrogen angles: 755 Unresolved non-hydrogen dihedrals: 500 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 12, 'ASP:plan': 8, 'TYR:plan': 3, 'ASN:plan1': 9, 'TRP:plan': 2, 'HIS:plan': 3, 'PHE:plan': 8, 'GLU:plan': 19, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 342 Chain: "S" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 657 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 148} Link IDs: {'PTRANS': 4, 'TRANS': 156} Chain breaks: 1 Unresolved non-hydrogen bonds: 628 Unresolved non-hydrogen angles: 894 Unresolved non-hydrogen dihedrals: 391 Unresolved non-hydrogen chiralities: 187 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 11, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 4, 'GLU:plan': 14, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 297 Chain: "T" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3264 Classifications: {'DNA': 160} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 159} Chain: "U" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 617 Classifications: {'peptide': 125} Incomplete info: {'truncation_to_alanine': 112} Link IDs: {'PTRANS': 6, 'TRANS': 118} Chain breaks: 3 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 426 Unresolved non-hydrogen angles: 542 Unresolved non-hydrogen dihedrals: 361 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 5, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 8, 'GLU:plan': 8, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 248 Chain: "V" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1378 Classifications: {'peptide': 244} Incomplete info: {'truncation_to_alanine': 181} Link IDs: {'CIS': 2, 'PTRANS': 14, 'TRANS': 227} Chain breaks: 4 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 697 Unresolved non-hydrogen angles: 889 Unresolved non-hydrogen dihedrals: 583 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 12, 'ASN:plan1': 9, 'TRP:plan': 2, 'ASP:plan': 17, 'PHE:plan': 7, 'GLU:plan': 23, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 425 Chain: "W" Number of atoms: 2333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2333 Classifications: {'peptide': 300} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 291} Chain: "X" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 353 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain: "Y" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "Z" Number of atoms: 4025 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4025 Classifications: {'peptide': 510} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 19, 'TRANS': 490} Chain breaks: 5 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'TPO:plan-1': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 23 Chain: "a" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 751 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} 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: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} 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: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} 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: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 755 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} 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 472 SG CYS A 71 82.440 158.620 168.121 1.00179.88 S ATOM 494 SG CYS A 74 86.216 158.674 168.995 1.00173.46 S ATOM 541 SG CYS A 81 84.677 161.557 166.952 1.00147.19 S ATOM 19760 SG CYS B1119 98.299 149.879 164.207 1.00166.94 S ATOM 19782 SG CYS B1122 96.202 148.873 161.168 1.00168.93 S ATOM 19897 SG CYS B1137 94.493 149.592 164.455 1.00163.85 S ATOM 19918 SG CYS B1140 96.580 146.431 163.898 1.00180.52 S ATOM 20884 SG CYS C 88 77.572 226.045 167.102 1.00177.91 S ATOM 20897 SG CYS C 90 75.492 226.061 168.756 1.00189.12 S ATOM 20954 SG CYS C 97 75.743 227.147 164.378 1.00135.87 S ATOM 28204 SG CYS I 17 61.390 139.807 78.714 1.00140.34 S ATOM 28228 SG CYS I 20 60.777 139.216 82.224 1.00127.57 S ATOM 28389 SG CYS I 39 63.730 138.153 82.118 1.00150.02 S ATOM 28766 SG CYS I 86 70.647 182.461 68.416 1.00138.36 S ATOM 28790 SG CYS I 89 67.501 184.442 67.696 1.00131.71 S ATOM 28994 SG CYS I 114 68.520 183.905 71.254 1.00102.61 S ATOM 29029 SG CYS I 119 67.302 180.899 69.130 1.00135.89 S ATOM 29139 SG CYS J 7 75.891 221.882 132.227 1.00105.80 S ATOM 29427 SG CYS J 44 78.683 223.585 129.696 1.00136.22 S ATOM 29433 SG CYS J 45 75.625 225.304 131.110 1.00117.55 S ATOM 55990 SG CYS Y 19 38.398 115.449 151.865 1.00 80.34 S Residues with excluded nonbonded symmetry interactions: 94 residue: pdb=" N ASN M1145 " occ=0.00 ... (2 atoms not shown) pdb=" O ASN M1145 " occ=0.00 residue: pdb=" N THR M1146 " occ=0.00 ... (2 atoms not shown) pdb=" O THR M1146 " occ=0.00 residue: pdb=" N GLU M1147 " occ=0.00 ... (2 atoms not shown) pdb=" O GLU M1147 " occ=0.00 residue: pdb=" N GLU M1148 " occ=0.00 ... (2 atoms not shown) pdb=" O GLU M1148 " occ=0.00 residue: pdb=" N ILE M1149 " occ=0.00 ... (2 atoms not shown) pdb=" O ILE M1149 " occ=0.00 residue: pdb=" N PHE M1150 " occ=0.00 ... (2 atoms not shown) pdb=" O PHE M1150 " occ=0.00 residue: pdb=" N ASN M1151 " occ=0.00 ... (2 atoms not shown) pdb=" O ASN M1151 " occ=0.00 residue: pdb=" N MET M1152 " occ=0.00 ... (2 atoms not shown) pdb=" O MET M1152 " occ=0.00 residue: pdb=" N LEU M1153 " occ=0.00 ... (2 atoms not shown) pdb=" O LEU M1153 " occ=0.00 residue: pdb=" N THR M1154 " occ=0.00 ... (2 atoms not shown) pdb=" O THR M1154 " occ=0.00 residue: pdb=" N LYS M1155 " occ=0.00 ... (2 atoms not shown) pdb=" O LYS M1155 " occ=0.00 residue: pdb=" N GLU M1156 " occ=0.00 ... (2 atoms not shown) pdb=" O GLU M1156 " occ=0.00 ... (remaining 82 not shown) Time building chain proxies: 30.14, per 1000 atoms: 0.45 Number of scatterers: 66649 At special positions: 0 Unit cell: (197.806, 318.687, 269.235, 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 259 16.00 P 332 15.00 Mg 1 11.99 O 13465 8.00 N 12221 7.00 C 40362 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.95 Conformation dependent library (CDL) restraints added in 6.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2001 " pdb="ZN ZN A2001 " - pdb=" NE2 HIS A 84 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 81 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 74 " pdb="ZN ZN A2001 " - pdb=" SG CYS A 71 " pdb=" ZN B1201 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1122 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1140 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1137 " pdb="ZN ZN B1201 " - pdb=" SG CYS B1119 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 90 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 88 " pdb=" ZN I 201 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 20 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 17 " pdb="ZN ZN I 201 " - pdb=" SG CYS I 39 " pdb=" ZN I 202 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 89 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 86 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 119 " pdb="ZN ZN I 202 " - pdb=" SG CYS I 114 " pdb=" ZN J 101 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 7 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 45 " pdb="ZN ZN J 101 " - pdb=" SG CYS J 44 " pdb=" ZN Y 201 " pdb="ZN ZN Y 201 " - pdb=" SG CYS Y 19 " Number of angles added : 15 16484 Ramachandran restraints generated. 8242 Oldfield, 0 Emsley, 8242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14042 Finding SS restraints... Secondary structure from input PDB file: 316 helices and 89 sheets defined 44.7% alpha, 11.3% beta 159 base pairs and 243 stacking pairs defined. Time for finding SS restraints: 19.11 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 123 through 133 removed outlier: 3.776A pdb=" N ILE A 129 " --> pdb=" O LYS A 125 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 148 removed outlier: 3.724A pdb=" N CYS A 148 " --> pdb=" O VAL A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.609A pdb=" N VAL A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE A 228 " --> pdb=" O ILE A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 235 removed outlier: 4.169A pdb=" N VAL A 235 " --> pdb=" O GLU A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 296 Processing helix chain 'A' and resid 301 through 319 removed outlier: 4.281A pdb=" N GLU A 305 " --> pdb=" O HIS A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 381 through 388 removed outlier: 3.744A pdb=" N ALA A 385 " --> pdb=" O PRO A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 409 Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 434 through 439 removed outlier: 3.625A pdb=" N LEU A 438 " --> pdb=" O LYS A 434 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS A 439 " --> pdb=" O PRO A 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 434 through 439' Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 488 through 493 removed outlier: 4.041A pdb=" N TYR A 492 " --> pdb=" O VAL A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 508 through 519 Processing helix chain 'A' and resid 521 through 524 Processing helix chain 'A' and resid 539 through 549 removed outlier: 3.781A pdb=" N THR A 543 " --> pdb=" O GLN A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 556 through 565 removed outlier: 3.619A pdb=" N MET A 565 " --> pdb=" O MET A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 596 removed outlier: 3.904A pdb=" N LEU A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE A 595 " --> pdb=" O ILE A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 646 Processing helix chain 'A' and resid 651 through 660 Processing helix chain 'A' and resid 661 through 684 removed outlier: 3.861A pdb=" N ASN A 678 " --> pdb=" O THR A 674 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE A 682 " --> pdb=" O ASN A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 692 Processing helix chain 'A' and resid 697 through 722 Processing helix chain 'A' and resid 732 through 759 Processing helix chain 'A' and resid 764 through 772 removed outlier: 3.535A pdb=" N SER A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 785 removed outlier: 3.550A pdb=" N ILE A 781 " --> pdb=" O SER A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 866 removed outlier: 4.547A pdb=" N GLY A 858 " --> pdb=" O THR A 854 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR A 859 " --> pdb=" O ALA A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 894 Processing helix chain 'A' and resid 912 through 918 Processing helix chain 'A' and resid 926 through 934 Processing helix chain 'A' and resid 935 through 945 removed outlier: 3.924A pdb=" N LYS A 940 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASP A 941 " --> pdb=" O ASP A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 970 removed outlier: 4.087A pdb=" N GLN A 949 " --> pdb=" O ASN A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 995 Processing helix chain 'A' and resid 1005 through 1020 Processing helix chain 'A' and resid 1027 through 1038 Processing helix chain 'A' and resid 1039 through 1049 Processing helix chain 'A' and resid 1061 through 1080 Processing helix chain 'A' and resid 1086 through 1097 removed outlier: 3.501A pdb=" N LEU A1090 " --> pdb=" O MET A1086 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1101 Processing helix chain 'A' and resid 1120 through 1129 Processing helix chain 'A' and resid 1145 through 1149 Processing helix chain 'A' and resid 1151 through 1161 removed outlier: 4.228A pdb=" N ASP A1156 " --> pdb=" O GLU A1152 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ILE A1157 " --> pdb=" O ARG A1153 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1169 Processing helix chain 'A' and resid 1190 through 1195 removed outlier: 3.933A pdb=" N ASN A1194 " --> pdb=" O GLN A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1225 removed outlier: 3.790A pdb=" N MET A1221 " --> pdb=" O ASP A1217 " (cutoff:3.500A) Processing helix chain 'A' and resid 1227 through 1239 removed outlier: 3.914A pdb=" N PHE A1239 " --> pdb=" O ILE A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1295 removed outlier: 3.947A pdb=" N LEU A1285 " --> pdb=" O ASP A1281 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG A1286 " --> pdb=" O ASP A1282 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP A1295 " --> pdb=" O ASN A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1343 through 1348 removed outlier: 3.606A pdb=" N SER A1348 " --> pdb=" O MET A1344 " (cutoff:3.500A) Processing helix chain 'A' and resid 1361 through 1367 removed outlier: 4.048A pdb=" N ILE A1365 " --> pdb=" O ASP A1361 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A1366 " --> pdb=" O ILE A1362 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR A1367 " --> pdb=" O VAL A1363 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1361 through 1367' Processing helix chain 'A' and resid 1370 through 1387 Processing helix chain 'A' and resid 1394 through 1406 removed outlier: 3.790A pdb=" N LEU A1398 " --> pdb=" O ASN A1394 " (cutoff:3.500A) Processing helix chain 'A' and resid 1415 through 1420 removed outlier: 3.670A pdb=" N ASN A1420 " --> pdb=" O ARG A1416 " (cutoff:3.500A) Processing helix chain 'A' and resid 1425 through 1433 removed outlier: 4.029A pdb=" N SER A1431 " --> pdb=" O LEU A1427 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N PHE A1432 " --> pdb=" O MET A1428 " (cutoff:3.500A) Processing helix chain 'A' and resid 1434 through 1446 Processing helix chain 'A' and resid 1453 through 1460 Processing helix chain 'A' and resid 1478 through 1482 removed outlier: 3.845A pdb=" N LYS A1481 " --> pdb=" O GLU A1478 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR A1482 " --> pdb=" O LYS A1479 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1478 through 1482' Processing helix chain 'B' and resid 24 through 37 removed outlier: 3.606A pdb=" N ILE B 28 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL B 29 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ILE B 30 " --> pdb=" O CYS B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 62 removed outlier: 3.503A pdb=" N LEU B 44 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N VAL B 55 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLN B 56 " --> pdb=" O GLN B 52 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA B 62 " --> pdb=" O ILE B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 117 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 268 through 276 Processing helix chain 'B' and resid 280 through 289 removed outlier: 3.512A pdb=" N ILE B 284 " --> pdb=" O SER B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 308 removed outlier: 3.619A pdb=" N MET B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 3.696A pdb=" N ALA B 308 " --> pdb=" O SER B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 324 removed outlier: 3.669A pdb=" N ALA B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG B 324 " --> pdb=" O PHE B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 331 through 343 removed outlier: 3.781A pdb=" N ARG B 335 " --> pdb=" O THR B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 377 Processing helix chain 'B' and resid 387 through 389 No H-bonds generated for 'chain 'B' and resid 387 through 389' Processing helix chain 'B' and resid 395 through 424 removed outlier: 3.705A pdb=" N LEU B 403 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY B 406 " --> pdb=" O PHE B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 435 Processing helix chain 'B' and resid 439 through 451 Processing helix chain 'B' and resid 458 through 462 Processing helix chain 'B' and resid 474 through 483 Processing helix chain 'B' and resid 538 through 548 removed outlier: 3.879A pdb=" N TRP B 548 " --> pdb=" O PHE B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 557 through 562 removed outlier: 4.027A pdb=" N ALA B 562 " --> pdb=" O ALA B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 594 removed outlier: 3.836A pdb=" N ASN B 585 " --> pdb=" O GLU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 645 Processing helix chain 'B' and resid 652 through 660 removed outlier: 3.740A pdb=" N LEU B 656 " --> pdb=" O SER B 652 " (cutoff:3.500A) Processing helix chain 'B' and resid 669 through 673 removed outlier: 3.791A pdb=" N VAL B 673 " --> pdb=" O GLU B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 684 removed outlier: 4.119A pdb=" N GLU B 684 " --> pdb=" O ASP B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 704 Processing helix chain 'B' and resid 713 through 717 Processing helix chain 'B' and resid 718 through 730 removed outlier: 4.224A pdb=" N LYS B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 768 removed outlier: 3.605A pdb=" N LEU B 767 " --> pdb=" O SER B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 803 Processing helix chain 'B' and resid 970 through 976 removed outlier: 4.163A pdb=" N SER B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG B 975 " --> pdb=" O ALA B 971 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 994 removed outlier: 3.848A pdb=" N LEU B 981 " --> pdb=" O THR B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 1007 through 1016 removed outlier: 3.864A pdb=" N ILE B1011 " --> pdb=" O ASN B1007 " (cutoff:3.500A) Processing helix chain 'B' and resid 1017 through 1019 No H-bonds generated for 'chain 'B' and resid 1017 through 1019' Processing helix chain 'B' and resid 1087 through 1098 Processing helix chain 'B' and resid 1099 through 1108 Processing helix chain 'B' and resid 1152 through 1164 Processing helix chain 'C' and resid 27 through 40 Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.918A pdb=" N ILE C 64 " --> pdb=" O HIS C 60 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 88 Processing helix chain 'C' and resid 94 through 98 removed outlier: 3.504A pdb=" N SER C 98 " --> pdb=" O PRO C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 120 No H-bonds generated for 'chain 'C' and resid 118 through 120' Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 240 through 270 Processing helix chain 'D' and resid 16 through 20 Processing helix chain 'D' and resid 23 through 28 removed outlier: 3.854A pdb=" N THR D 28 " --> pdb=" O LYS D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 50 removed outlier: 3.833A pdb=" N SER D 50 " --> pdb=" O GLN D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 69 Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.532A pdb=" N ILE D 80 " --> pdb=" O ASN D 76 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU D 87 " --> pdb=" O VAL D 83 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 104 removed outlier: 3.893A pdb=" N ALA D 98 " --> pdb=" O LYS D 94 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N CYS D 99 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU D 100 " --> pdb=" O GLU D 96 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N CYS D 104 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 115 Processing helix chain 'D' and resid 116 through 119 Processing helix chain 'D' and resid 123 through 138 removed outlier: 3.682A pdb=" N LEU D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE D 130 " --> pdb=" O GLU D 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 25 Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.551A pdb=" N ASP E 34 " --> pdb=" O GLN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 45 Processing helix chain 'E' and resid 84 through 95 Processing helix chain 'E' and resid 111 through 121 removed outlier: 3.696A pdb=" N LYS E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 138 through 142 Processing helix chain 'E' and resid 152 through 163 Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 177 through 184 Processing helix chain 'F' and resid 58 through 75 Processing helix chain 'F' and resid 88 through 100 Processing helix chain 'G' and resid 14 through 18 Processing helix chain 'G' and resid 21 through 32 Processing helix chain 'H' and resid 83 through 88 removed outlier: 3.660A pdb=" N GLN H 87 " --> pdb=" O ARG H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 68 removed outlier: 4.018A pdb=" N GLN I 67 " --> pdb=" O ASP I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 69 through 74 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 28 removed outlier: 3.743A pdb=" N GLU J 28 " --> pdb=" O LEU J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 39 removed outlier: 4.271A pdb=" N ASP J 36 " --> pdb=" O GLY J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 51 Processing helix chain 'J' and resid 55 through 62 removed outlier: 3.849A pdb=" N TYR J 62 " --> pdb=" O LYS J 58 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 10 removed outlier: 3.953A pdb=" N SER K 9 " --> pdb=" O ALA K 6 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE K 10 " --> pdb=" O PHE K 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 6 through 10' Processing helix chain 'K' and resid 40 through 53 removed outlier: 4.444A pdb=" N ILE K 45 " --> pdb=" O THR K 41 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ILE K 46 " --> pdb=" O LEU K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 113 Processing helix chain 'M' and resid 285 through 291 removed outlier: 3.717A pdb=" N ILE M 289 " --> pdb=" O GLN M 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 302 Processing helix chain 'M' and resid 309 through 323 removed outlier: 4.275A pdb=" N GLU M 314 " --> pdb=" O ASP M 310 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU M 315 " --> pdb=" O ASP M 311 " (cutoff:3.500A) Processing helix chain 'M' and resid 351 through 370 Processing helix chain 'M' and resid 372 through 379 Processing helix chain 'M' and resid 392 through 429 Processing helix chain 'M' and resid 445 through 453 removed outlier: 4.070A pdb=" N GLU M 449 " --> pdb=" O THR M 445 " (cutoff:3.500A) Processing helix chain 'M' and resid 456 through 472 Processing helix chain 'M' and resid 542 through 553 Processing helix chain 'M' and resid 565 through 570 Processing helix chain 'M' and resid 586 through 598 removed outlier: 3.582A pdb=" N TYR M 590 " --> pdb=" O GLU M 586 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N MET M 591 " --> pdb=" O GLY M 587 " (cutoff:3.500A) Processing helix chain 'M' and resid 599 through 607 Processing helix chain 'M' and resid 623 through 629 removed outlier: 3.686A pdb=" N ASP M 629 " --> pdb=" O ARG M 625 " (cutoff:3.500A) Processing helix chain 'M' and resid 632 through 637 removed outlier: 4.555A pdb=" N PHE M 637 " --> pdb=" O TYR M 633 " (cutoff:3.500A) Processing helix chain 'M' and resid 644 through 650 removed outlier: 3.780A pdb=" N LEU M 648 " --> pdb=" O PRO M 644 " (cutoff:3.500A) Processing helix chain 'M' and resid 651 through 662 removed outlier: 3.578A pdb=" N LYS M 655 " --> pdb=" O ASP M 651 " (cutoff:3.500A) Processing helix chain 'M' and resid 685 through 692 removed outlier: 4.183A pdb=" N ILE M 689 " --> pdb=" O TYR M 685 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS M 690 " --> pdb=" O PHE M 686 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN M 691 " --> pdb=" O GLU M 687 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE M 692 " --> pdb=" O GLU M 688 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 685 through 692' Processing helix chain 'M' and resid 700 through 721 Processing helix chain 'M' and resid 721 through 754 removed outlier: 3.771A pdb=" N ARG M 754 " --> pdb=" O TYR M 750 " (cutoff:3.500A) Processing helix chain 'M' and resid 759 through 763 removed outlier: 3.743A pdb=" N GLN M 763 " --> pdb=" O PRO M 760 " (cutoff:3.500A) Processing helix chain 'M' and resid 830 through 843 removed outlier: 3.703A pdb=" N LYS M 843 " --> pdb=" O PHE M 839 " (cutoff:3.500A) Processing helix chain 'M' and resid 854 through 871 Processing helix chain 'M' and resid 888 through 895 removed outlier: 4.162A pdb=" N LEU M 892 " --> pdb=" O GLU M 888 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ASN M 895 " --> pdb=" O ILE M 891 " (cutoff:3.500A) Processing helix chain 'M' and resid 896 through 903 Processing helix chain 'M' and resid 907 through 920 Processing helix chain 'M' and resid 922 through 929 Processing helix chain 'M' and resid 936 through 940 removed outlier: 4.276A pdb=" N LEU M 940 " --> pdb=" O ASP M 936 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 936 through 940' Processing helix chain 'M' and resid 943 through 949 removed outlier: 4.178A pdb=" N GLU M 947 " --> pdb=" O HIS M 943 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N HIS M 948 " --> pdb=" O PRO M 944 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL M 949 " --> pdb=" O LEU M 945 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 943 through 949' Processing helix chain 'M' and resid 950 through 970 removed outlier: 3.975A pdb=" N LEU M 954 " --> pdb=" O VAL M 950 " (cutoff:3.500A) Processing helix chain 'M' and resid 974 through 979 removed outlier: 4.127A pdb=" N ALA M 978 " --> pdb=" O ASN M 974 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N HIS M 979 " --> pdb=" O ARG M 975 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 974 through 979' Processing helix chain 'M' and resid 993 through 1008 Processing helix chain 'M' and resid 1015 through 1020 Processing helix chain 'M' and resid 1024 through 1031 Processing helix chain 'M' and resid 1062 through 1075 Processing helix chain 'M' and resid 1086 through 1095 removed outlier: 3.788A pdb=" N ILE M1092 " --> pdb=" O ALA M1088 " (cutoff:3.500A) Processing helix chain 'M' and resid 1103 through 1114 Processing helix chain 'M' and resid 1121 through 1132 removed outlier: 4.191A pdb=" N ASP M1125 " --> pdb=" O ILE M1121 " (cutoff:3.500A) Processing helix chain 'M' and resid 1145 through 1154 Processing helix chain 'M' and resid 1241 through 1246 removed outlier: 3.736A pdb=" N LEU M1245 " --> pdb=" O PRO M1241 " (cutoff:3.500A) Processing helix chain 'M' and resid 1282 through 1287 removed outlier: 3.895A pdb=" N LEU M1286 " --> pdb=" O ARG M1282 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET M1287 " --> pdb=" O THR M1283 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1282 through 1287' Processing helix chain 'M' and resid 1342 through 1347 removed outlier: 3.543A pdb=" N MET M1347 " --> pdb=" O GLU M1344 " (cutoff:3.500A) Processing helix chain 'M' and resid 1402 through 1406 Processing helix chain 'M' and resid 1410 through 1416 Processing helix chain 'M' and resid 1416 through 1428 removed outlier: 3.594A pdb=" N LEU M1426 " --> pdb=" O PHE M1422 " (cutoff:3.500A) Processing helix chain 'M' and resid 1434 through 1439 removed outlier: 3.785A pdb=" N ASP M1439 " --> pdb=" O CYS M1435 " (cutoff:3.500A) Processing helix chain 'M' and resid 1441 through 1452 removed outlier: 4.367A pdb=" N GLU M1445 " --> pdb=" O LYS M1441 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU M1446 " --> pdb=" O LYS M1442 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU M1447 " --> pdb=" O LEU M1443 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE M1448 " --> pdb=" O GLU M1444 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS M1452 " --> pdb=" O ILE M1448 " (cutoff:3.500A) Processing helix chain 'M' and resid 1503 through 1512 removed outlier: 4.074A pdb=" N LEU M1507 " --> pdb=" O THR M1503 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE M1508 " --> pdb=" O VAL M1504 " (cutoff:3.500A) Processing helix chain 'O' and resid 555 through 580 Processing helix chain 'O' and resid 585 through 590 Processing helix chain 'O' and resid 590 through 599 removed outlier: 3.789A pdb=" N HIS O 597 " --> pdb=" O ALA O 593 " (cutoff:3.500A) Processing helix chain 'O' and resid 600 through 602 No H-bonds generated for 'chain 'O' and resid 600 through 602' Processing helix chain 'O' and resid 603 through 611 removed outlier: 3.707A pdb=" N GLY O 611 " --> pdb=" O PHE O 607 " (cutoff:3.500A) Processing helix chain 'O' and resid 611 through 621 Processing helix chain 'O' and resid 630 through 642 removed outlier: 3.771A pdb=" N GLU O 636 " --> pdb=" O LYS O 632 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS O 639 " --> pdb=" O GLU O 635 " (cutoff:3.500A) Processing helix chain 'O' and resid 648 through 656 removed outlier: 3.569A pdb=" N LEU O 652 " --> pdb=" O SER O 648 " (cutoff:3.500A) Processing helix chain 'O' and resid 656 through 666 Processing helix chain 'O' and resid 671 through 685 removed outlier: 3.757A pdb=" N LYS O 675 " --> pdb=" O SER O 671 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N MET O 677 " --> pdb=" O SER O 673 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 37 removed outlier: 4.069A pdb=" N ILE Q 31 " --> pdb=" O GLY Q 27 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER Q 32 " --> pdb=" O ASP Q 28 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU Q 37 " --> pdb=" O ILE Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 53 removed outlier: 4.144A pdb=" N TRP Q 44 " --> pdb=" O GLN Q 40 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE Q 45 " --> pdb=" O LEU Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 58 through 64 removed outlier: 3.968A pdb=" N LEU Q 64 " --> pdb=" O PHE Q 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 65 through 69 removed outlier: 3.869A pdb=" N ARG Q 68 " --> pdb=" O GLU Q 65 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE Q 69 " --> pdb=" O ALA Q 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 65 through 69' Processing helix chain 'Q' and resid 78 through 99 removed outlier: 3.631A pdb=" N GLN Q 82 " --> pdb=" O HIS Q 78 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR Q 88 " --> pdb=" O THR Q 84 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU Q 89 " --> pdb=" O CYS Q 85 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N TYR Q 93 " --> pdb=" O LEU Q 89 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N VAL Q 94 " --> pdb=" O ALA Q 90 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN Q 95 " --> pdb=" O ALA Q 91 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG Q 98 " --> pdb=" O VAL Q 94 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LYS Q 99 " --> pdb=" O GLN Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 105 through 121 removed outlier: 3.722A pdb=" N LEU Q 109 " --> pdb=" O ASN Q 105 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLN Q 112 " --> pdb=" O ASP Q 108 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU Q 116 " --> pdb=" O GLN Q 112 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR Q 117 " --> pdb=" O ALA Q 113 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR Q 118 " --> pdb=" O THR Q 114 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET Q 119 " --> pdb=" O LEU Q 115 " (cutoff:3.500A) Processing helix chain 'Q' and resid 129 through 137 Processing helix chain 'Q' and resid 144 through 159 removed outlier: 3.595A pdb=" N PHE Q 154 " --> pdb=" O ALA Q 150 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL Q 155 " --> pdb=" O GLN Q 151 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LEU Q 156 " --> pdb=" O PHE Q 152 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASN Q 157 " --> pdb=" O HIS Q 153 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER Q 159 " --> pdb=" O VAL Q 155 " (cutoff:3.500A) Processing helix chain 'Q' and resid 163 through 176 removed outlier: 3.866A pdb=" N GLY Q 168 " --> pdb=" O PRO Q 164 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LYS Q 169 " --> pdb=" O ALA Q 165 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ALA Q 170 " --> pdb=" O LEU Q 166 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS Q 171 " --> pdb=" O LEU Q 167 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE Q 172 " --> pdb=" O GLY Q 168 " (cutoff:3.500A) Processing helix chain 'Q' and resid 178 through 187 removed outlier: 3.501A pdb=" N ALA Q 182 " --> pdb=" O ASP Q 178 " (cutoff:3.500A) Processing helix chain 'Q' and resid 187 through 192 removed outlier: 3.784A pdb=" N ARG Q 191 " --> pdb=" O LYS Q 187 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N THR Q 192 " --> pdb=" O LYS Q 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 187 through 192' Processing helix chain 'Q' and resid 200 through 208 removed outlier: 3.988A pdb=" N MET Q 204 " --> pdb=" O VAL Q 200 " (cutoff:3.500A) Processing helix chain 'Q' and resid 213 through 228 removed outlier: 3.518A pdb=" N ARG Q 218 " --> pdb=" O LEU Q 214 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU Q 219 " --> pdb=" O GLU Q 215 " (cutoff:3.500A) Processing helix chain 'Q' and resid 232 through 243 removed outlier: 3.574A pdb=" N GLY Q 237 " --> pdb=" O GLY Q 233 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU Q 238 " --> pdb=" O ALA Q 234 " (cutoff:3.500A) Processing helix chain 'Q' and resid 249 through 255 removed outlier: 3.834A pdb=" N ASN Q 253 " --> pdb=" O ASP Q 249 " (cutoff:3.500A) Processing helix chain 'Q' and resid 258 through 265 Processing helix chain 'Q' and resid 268 through 282 removed outlier: 3.929A pdb=" N PHE Q 281 " --> pdb=" O ASN Q 277 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS Q 282 " --> pdb=" O HIS Q 278 " (cutoff:3.500A) Processing helix chain 'Q' and resid 284 through 295 removed outlier: 3.994A pdb=" N VAL Q 288 " --> pdb=" O ASP Q 284 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLN Q 289 " --> pdb=" O TYR Q 285 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N HIS Q 290 " --> pdb=" O SER Q 286 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU Q 293 " --> pdb=" O GLN Q 289 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS Q 294 " --> pdb=" O HIS Q 290 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 318 removed outlier: 3.965A pdb=" N GLN Q 305 " --> pdb=" O VAL Q 301 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA Q 306 " --> pdb=" O GLU Q 302 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU Q 307 " --> pdb=" O ALA Q 303 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL Q 318 " --> pdb=" O ARG Q 314 " (cutoff:3.500A) Processing helix chain 'Q' and resid 321 through 336 removed outlier: 3.865A pdb=" N ALA Q 325 " --> pdb=" O ASP Q 321 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN Q 327 " --> pdb=" O ASP Q 323 " (cutoff:3.500A) Processing helix chain 'Q' and resid 341 through 351 Processing helix chain 'Q' and resid 352 through 355 Processing helix chain 'Q' and resid 356 through 371 removed outlier: 3.840A pdb=" N ALA Q 360 " --> pdb=" O ASP Q 356 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LYS Q 366 " --> pdb=" O GLN Q 362 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL Q 367 " --> pdb=" O CYS Q 363 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU Q 368 " --> pdb=" O PHE Q 364 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS Q 369 " --> pdb=" O GLU Q 365 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA Q 370 " --> pdb=" O LYS Q 366 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR Q 371 " --> pdb=" O VAL Q 367 " (cutoff:3.500A) Processing helix chain 'Q' and resid 375 through 383 removed outlier: 3.712A pdb=" N LYS Q 379 " --> pdb=" O TYR Q 375 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE Q 380 " --> pdb=" O GLU Q 376 " (cutoff:3.500A) Processing helix chain 'Q' and resid 390 through 407 removed outlier: 3.578A pdb=" N ASP Q 395 " --> pdb=" O GLN Q 391 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILE Q 396 " --> pdb=" O GLU Q 392 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA Q 397 " --> pdb=" O LYS Q 393 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU Q 406 " --> pdb=" O LYS Q 402 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN Q 407 " --> pdb=" O LYS Q 403 " (cutoff:3.500A) Processing helix chain 'Q' and resid 413 through 423 removed outlier: 3.666A pdb=" N ILE Q 421 " --> pdb=" O GLU Q 417 " (cutoff:3.500A) Processing helix chain 'Q' and resid 426 through 440 removed outlier: 4.015A pdb=" N ALA Q 430 " --> pdb=" O ASP Q 426 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ARG Q 439 " --> pdb=" O GLY Q 435 " (cutoff:3.500A) Processing helix chain 'Q' and resid 450 through 463 removed outlier: 3.748A pdb=" N LEU Q 454 " --> pdb=" O PRO Q 450 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG Q 463 " --> pdb=" O ALA Q 459 " (cutoff:3.500A) Processing helix chain 'Q' and resid 466 through 483 Processing helix chain 'Q' and resid 491 through 510 Processing helix chain 'Q' and resid 512 through 527 removed outlier: 3.526A pdb=" N ALA Q 516 " --> pdb=" O GLU Q 512 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU Q 526 " --> pdb=" O ASN Q 522 " (cutoff:3.500A) Processing helix chain 'Q' and resid 531 through 545 removed outlier: 3.870A pdb=" N GLY Q 538 " --> pdb=" O TYR Q 534 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS Q 544 " --> pdb=" O MET Q 540 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY Q 545 " --> pdb=" O ALA Q 541 " (cutoff:3.500A) Processing helix chain 'Q' and resid 548 through 561 removed outlier: 4.058A pdb=" N ASP Q 552 " --> pdb=" O TYR Q 548 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS Q 555 " --> pdb=" O SER Q 551 " (cutoff:3.500A) Processing helix chain 'Q' and resid 564 through 575 removed outlier: 3.744A pdb=" N HIS Q 575 " --> pdb=" O ILE Q 571 " (cutoff:3.500A) Processing helix chain 'Q' and resid 584 through 590 removed outlier: 4.173A pdb=" N PHE Q 588 " --> pdb=" O GLY Q 584 " (cutoff:3.500A) Processing helix chain 'Q' and resid 600 through 613 Processing helix chain 'Q' and resid 619 through 623 Processing helix chain 'Q' and resid 624 through 642 Processing helix chain 'Q' and resid 646 through 660 removed outlier: 4.043A pdb=" N ALA Q 650 " --> pdb=" O ASN Q 646 " (cutoff:3.500A) Processing helix chain 'Q' and resid 665 through 677 removed outlier: 3.912A pdb=" N VAL Q 669 " --> pdb=" O GLU Q 665 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLN Q 672 " --> pdb=" O ASP Q 668 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL Q 673 " --> pdb=" O VAL Q 669 " (cutoff:3.500A) Processing helix chain 'Q' and resid 680 through 694 removed outlier: 3.854A pdb=" N TRP Q 684 " --> pdb=" O ILE Q 680 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU Q 685 " --> pdb=" O SER Q 681 " (cutoff:3.500A) Processing helix chain 'Q' and resid 700 through 708 removed outlier: 3.528A pdb=" N LEU Q 708 " --> pdb=" O TYR Q 704 " (cutoff:3.500A) Processing helix chain 'Q' and resid 716 through 724 removed outlier: 3.661A pdb=" N VAL Q 720 " --> pdb=" O ASN Q 716 " (cutoff:3.500A) Processing helix chain 'Q' and resid 729 through 732 Processing helix chain 'Q' and resid 733 through 747 removed outlier: 3.939A pdb=" N VAL Q 746 " --> pdb=" O LYS Q 742 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA Q 747 " --> pdb=" O ALA Q 743 " (cutoff:3.500A) Processing helix chain 'Q' and resid 750 through 770 removed outlier: 3.851A pdb=" N MET Q 754 " --> pdb=" O ASP Q 750 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA Q 758 " --> pdb=" O MET Q 754 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS Q 770 " --> pdb=" O THR Q 766 " (cutoff:3.500A) Processing helix chain 'Q' and resid 775 through 797 removed outlier: 3.707A pdb=" N VAL Q 779 " --> pdb=" O ASN Q 775 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL Q 783 " --> pdb=" O VAL Q 779 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS Q 784 " --> pdb=" O LEU Q 780 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER Q 797 " --> pdb=" O PHE Q 793 " (cutoff:3.500A) Processing helix chain 'Q' and resid 807 through 809 No H-bonds generated for 'chain 'Q' and resid 807 through 809' Processing helix chain 'Q' and resid 810 through 892 removed outlier: 4.380A pdb=" N ALA Q 829 " --> pdb=" O GLN Q 825 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ARG Q 830 " --> pdb=" O TYR Q 826 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU Q 848 " --> pdb=" O LYS Q 844 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLU Q 883 " --> pdb=" O ALA Q 879 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS Q 886 " --> pdb=" O VAL Q 882 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN Q 887 " --> pdb=" O GLU Q 883 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N THR Q 892 " --> pdb=" O ILE Q 888 " (cutoff:3.500A) Processing helix chain 'R' and resid 355 through 360 removed outlier: 3.637A pdb=" N LEU R 359 " --> pdb=" O LEU R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 361 through 363 No H-bonds generated for 'chain 'R' and resid 361 through 363' Processing helix chain 'R' and resid 368 through 372 removed outlier: 3.625A pdb=" N TRP R 372 " --> pdb=" O LEU R 369 " (cutoff:3.500A) Processing helix chain 'R' and resid 377 through 382 removed outlier: 3.617A pdb=" N VAL R 382 " --> pdb=" O PHE R 378 " (cutoff:3.500A) Processing helix chain 'R' and resid 448 through 463 Processing helix chain 'R' and resid 468 through 484 removed outlier: 4.154A pdb=" N LEU R 477 " --> pdb=" O ASN R 473 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N SER R 478 " --> pdb=" O LYS R 474 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ILE R 479 " --> pdb=" O LYS R 475 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS R 480 " --> pdb=" O GLU R 476 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASN R 484 " --> pdb=" O LYS R 480 " (cutoff:3.500A) Processing helix chain 'R' and resid 491 through 503 removed outlier: 3.814A pdb=" N PHE R 502 " --> pdb=" O GLU R 498 " (cutoff:3.500A) Processing helix chain 'R' and resid 510 through 525 Processing helix chain 'R' and resid 527 through 553 removed outlier: 3.525A pdb=" N LYS R 531 " --> pdb=" O GLY R 527 " (cutoff:3.500A) Processing helix chain 'R' and resid 556 through 585 removed outlier: 3.766A pdb=" N SER R 561 " --> pdb=" O ILE R 557 " (cutoff:3.500A) Processing helix chain 'S' and resid 138 through 153 Processing helix chain 'S' and resid 156 through 162 removed outlier: 3.644A pdb=" N ALA S 160 " --> pdb=" O ASP S 156 " (cutoff:3.500A) Processing helix chain 'S' and resid 164 through 181 Processing helix chain 'S' and resid 184 through 199 Processing helix chain 'S' and resid 203 through 212 removed outlier: 4.297A pdb=" N ARG S 207 " --> pdb=" O ASN S 203 " (cutoff:3.500A) Processing helix chain 'S' and resid 216 through 223 Processing helix chain 'S' and resid 224 through 229 Processing helix chain 'S' and resid 230 through 249 removed outlier: 3.557A pdb=" N GLN S 249 " --> pdb=" O ILE S 245 " (cutoff:3.500A) Processing helix chain 'U' and resid 379 through 383 Processing helix chain 'U' and resid 411 through 415 Processing helix chain 'V' and resid 63 through 68 Processing helix chain 'V' and resid 101 through 106 Processing helix chain 'V' and resid 122 through 126 removed outlier: 3.503A pdb=" N LYS V 126 " --> pdb=" O GLN V 123 " (cutoff:3.500A) Processing helix chain 'V' and resid 172 through 186 removed outlier: 3.833A pdb=" N THR V 177 " --> pdb=" O ASP V 173 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA V 186 " --> pdb=" O THR V 182 " (cutoff:3.500A) Processing helix chain 'X' and resid 219 through 226 removed outlier: 3.514A pdb=" N ILE X 224 " --> pdb=" O VAL X 220 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER X 226 " --> pdb=" O ARG X 222 " (cutoff:3.500A) Processing helix chain 'X' and resid 233 through 239 removed outlier: 3.609A pdb=" N LEU X 238 " --> pdb=" O ARG X 234 " (cutoff:3.500A) Processing helix chain 'X' and resid 246 through 260 removed outlier: 3.753A pdb=" N ALA X 251 " --> pdb=" O LYS X 247 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N ILE X 252 " --> pdb=" O ASN X 248 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS X 257 " --> pdb=" O LEU X 253 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU X 260 " --> pdb=" O VAL X 256 " (cutoff:3.500A) Processing helix chain 'Y' and resid 25 through 31 Processing helix chain 'Y' and resid 46 through 53 Processing helix chain 'Y' and resid 65 through 68 Processing helix chain 'Y' and resid 69 through 76 Processing helix chain 'Y' and resid 97 through 104 removed outlier: 3.757A pdb=" N LEU Y 101 " --> pdb=" O ILE Y 97 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS Y 102 " --> pdb=" O VAL Y 98 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER Y 103 " --> pdb=" O ARG Y 99 " (cutoff:3.500A) Processing helix chain 'Z' and resid 189 through 203 Processing helix chain 'Z' and resid 231 through 239 removed outlier: 4.054A pdb=" N VAL Z 235 " --> pdb=" O LYS Z 231 " (cutoff:3.500A) Processing helix chain 'Z' and resid 246 through 250 removed outlier: 3.601A pdb=" N TYR Z 249 " --> pdb=" O ARG Z 246 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N TRP Z 250 " --> pdb=" O LEU Z 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 246 through 250' Processing helix chain 'Z' and resid 256 through 261 removed outlier: 4.211A pdb=" N THR Z 261 " --> pdb=" O LYS Z 258 " (cutoff:3.500A) Processing helix chain 'Z' and resid 379 through 381 No H-bonds generated for 'chain 'Z' and resid 379 through 381' Processing helix chain 'Z' and resid 389 through 396 Processing helix chain 'Z' and resid 630 through 634 Processing helix chain 'a' and resid 44 through 57 Processing helix chain 'a' and resid 63 through 79 removed outlier: 3.562A pdb=" N PHE a 67 " --> pdb=" O ARG a 63 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 Processing helix chain 'a' and resid 120 through 132 Processing helix chain 'b' and resid 24 through 29 Processing helix chain 'b' and resid 30 through 41 Processing helix chain 'b' and resid 49 through 76 removed outlier: 3.618A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 93 Processing helix chain 'c' and resid 26 through 37 Processing helix chain 'c' and resid 45 through 73 removed outlier: 4.323A pdb=" N VAL c 49 " --> pdb=" O ALA c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 90 removed outlier: 3.570A pdb=" N LEU c 83 " --> pdb=" O ILE c 79 " (cutoff:3.500A) 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 Processing helix chain 'd' and resid 100 through 121 Processing helix chain 'e' and resid 44 through 57 removed outlier: 3.711A pdb=" N LEU e 48 " --> pdb=" O GLY e 44 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER e 57 " --> pdb=" O ARG e 53 " (cutoff:3.500A) Processing helix chain 'e' and resid 63 through 77 removed outlier: 3.647A pdb=" N PHE e 67 " --> pdb=" O ARG e 63 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASP e 77 " --> pdb=" O GLU e 73 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 114 Processing helix chain 'e' and resid 120 through 132 Processing helix chain 'f' and resid 25 through 29 Processing helix chain 'f' and resid 30 through 42 Processing helix chain 'f' and resid 49 through 76 Processing helix chain 'f' and resid 82 through 93 Processing helix chain 'g' and resid 16 through 21 Processing helix chain 'g' and resid 26 through 36 Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.288A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU g 65 " --> pdb=" O GLU g 61 " (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 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 21 through 22 removed outlier: 3.664A pdb=" N VAL A 21 " --> pdb=" O ASP A1449 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 192 through 193 removed outlier: 3.513A pdb=" N TYR A 199 " --> pdb=" O ARG A 192 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.658A pdb=" N LYS A 357 " --> pdb=" O PHE B1086 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 364 through 365 removed outlier: 4.159A pdb=" N THR A 365 " --> pdb=" O MET A 501 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET A 501 " --> pdb=" O THR A 365 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET A 470 " --> pdb=" O PHE A 458 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 367 through 369 removed outlier: 3.825A pdb=" N LEU A 484 " --> pdb=" O THR A 368 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 393 removed outlier: 4.251A pdb=" N TYR A 418 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N HIS A 449 " --> pdb=" O ALA A 416 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ALA A 416 " --> pdb=" O HIS A 449 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 526 through 527 removed outlier: 3.501A pdb=" N THR A 527 " --> pdb=" O ARG A 532 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG A 532 " --> pdb=" O THR A 527 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 554 through 555 Processing sheet with id=AA9, first strand: chain 'A' and resid 602 through 604 removed outlier: 6.429A pdb=" N VAL A 629 " --> pdb=" O ILE A 636 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 872 through 874 removed outlier: 3.906A pdb=" N THR A 878 " --> pdb=" O LYS A 874 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 902 through 904 Processing sheet with id=AB3, first strand: chain 'A' and resid 1211 through 1216 removed outlier: 3.527A pdb=" N ASN A1172 " --> pdb=" O GLU A1215 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N TYR I 54 " --> pdb=" O ILE A1175 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1243 through 1245 removed outlier: 3.596A pdb=" N ARG A1260 " --> pdb=" O ASN A1244 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1308 through 1310 removed outlier: 3.666A pdb=" N GLU A1337 " --> pdb=" O TYR A1308 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ILE A1335 " --> pdb=" O HIS A1310 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1471 through 1475 removed outlier: 3.605A pdb=" N ASP A1472 " --> pdb=" O ARG F 107 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 83 through 84 removed outlier: 3.515A pdb=" N ARG B 83 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLN B 90 " --> pdb=" O ASP B 127 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR B 129 " --> pdb=" O PHE B 88 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N PHE B 88 " --> pdb=" O THR B 129 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 83 through 84 removed outlier: 3.515A pdb=" N ARG B 83 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ALA B 122 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N LYS B 151 " --> pdb=" O ALA B 122 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU B 124 " --> pdb=" O ILE B 149 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE B 128 " --> pdb=" O GLN B 145 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N GLN B 145 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N LYS B 130 " --> pdb=" O GLN B 143 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLN B 143 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N VAL B 132 " --> pdb=" O GLN B 141 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN B 141 " --> pdb=" O VAL B 132 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N LYS B 134 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLN B 139 " --> pdb=" O LYS B 134 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 185 through 187 Processing sheet with id=AC1, first strand: chain 'B' and resid 391 through 394 removed outlier: 3.525A pdb=" N ASN B 486 " --> pdb=" O ALA B 196 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU B 198 " --> pdb=" O ASN B 486 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 524 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 205 through 208 Processing sheet with id=AC3, first strand: chain 'B' and resid 205 through 208 removed outlier: 6.962A pdb=" N MET B 239 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR B 218 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL B 237 " --> pdb=" O THR B 218 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC5, first strand: chain 'B' and resid 531 through 532 Processing sheet with id=AC6, first strand: chain 'B' and resid 572 through 577 removed outlier: 4.607A pdb=" N ILE B 567 " --> pdb=" O VAL B 574 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ILE B 576 " --> pdb=" O THR B 565 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N THR B 565 " --> pdb=" O ILE B 576 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LYS B 566 " --> pdb=" O ILE B 612 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ILE B 614 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N PHE B 568 " --> pdb=" O ILE B 614 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLU B 611 " --> pdb=" O ASP B 606 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG B 613 " --> pdb=" O ILE B 604 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 602 " --> pdb=" O TYR B 615 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 749 through 751 removed outlier: 4.008A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 749 through 751 removed outlier: 4.008A pdb=" N SER B 808 " --> pdb=" O ARG B 927 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG B 922 " --> pdb=" O GLN B 906 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N GLN B 906 " --> pdb=" O ARG B 922 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ARG B 924 " --> pdb=" O VAL B 904 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N VAL B 904 " --> pdb=" O ARG B 924 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET L 44 " --> pdb=" O VAL B 909 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 759 through 760 Processing sheet with id=AD1, first strand: chain 'B' and resid 776 through 782 removed outlier: 4.095A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA B 936 " --> pdb=" O GLN B1049 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N VAL B 794 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLN B 948 " --> pdb=" O VAL B 794 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N MET B 796 " --> pdb=" O GLN B 948 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 776 through 782 removed outlier: 4.095A pdb=" N PHE B1042 " --> pdb=" O ILE B 782 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 826 through 829 removed outlier: 4.085A pdb=" N GLU B 826 " --> pdb=" O THR B 872 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1115 through 1119 removed outlier: 3.547A pdb=" N SER B1147 " --> pdb=" O VAL B1118 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 8 through 14 removed outlier: 6.581A pdb=" N LYS C 20 " --> pdb=" O THR C 12 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 99 through 100 Processing sheet with id=AD7, first strand: chain 'C' and resid 99 through 100 removed outlier: 7.206A pdb=" N ARG C 162 " --> pdb=" O ILE C 52 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N ILE C 52 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N TYR C 164 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N VAL C 50 " --> pdb=" O TYR C 164 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N LYS C 166 " --> pdb=" O ASP C 48 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ASP C 48 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N GLY C 168 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ALA C 46 " --> pdb=" O GLY C 168 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 113 through 116 removed outlier: 6.412A pdb=" N ARG C 113 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N LYS C 152 " --> pdb=" O ARG C 113 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL C 115 " --> pdb=" O ILE C 150 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 62 through 63 removed outlier: 3.777A pdb=" N VAL E 62 " --> pdb=" O MET E 72 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG E 101 " --> pdb=" O GLN E 71 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE E 73 " --> pdb=" O ARG E 101 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLU E 128 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 147 through 150 removed outlier: 3.721A pdb=" N GLU E 147 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE E 194 " --> pdb=" O GLU E 147 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.508A pdb=" N ALA G 74 " --> pdb=" O ILE G 5 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE G 11 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N ASP G 52 " --> pdb=" O PRO G 69 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N LYS G 71 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N THR G 50 " --> pdb=" O LYS G 71 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N LYS G 73 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N VAL G 48 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE G 75 " --> pdb=" O ILE G 46 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE G 46 " --> pdb=" O ILE G 75 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 2 through 13 removed outlier: 3.508A pdb=" N ALA G 74 " --> pdb=" O ILE G 5 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE G 11 " --> pdb=" O TYR G 68 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL G 66 " --> pdb=" O LEU G 13 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU G 67 " --> pdb=" O VAL G 58 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 107 through 109 removed outlier: 7.132A pdb=" N GLY G 96 " --> pdb=" O VAL G 92 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N VAL G 92 " --> pdb=" O GLY G 96 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N PHE G 98 " --> pdb=" O THR G 90 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N VAL G 88 " --> pdb=" O GLU G 100 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL G 85 " --> pdb=" O LEU G 145 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 128 through 129 Processing sheet with id=AE6, first strand: chain 'H' and resid 38 through 44 removed outlier: 3.604A pdb=" N LEU H 41 " --> pdb=" O LEU H 28 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL H 43 " --> pdb=" O SER H 26 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER H 26 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LYS H 55 " --> pdb=" O LEU H 148 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'H' and resid 121 through 128 removed outlier: 3.808A pdb=" N ALA H 114 " --> pdb=" O LEU H 125 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N SER H 117 " --> pdb=" O VAL H 96 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N VAL H 96 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER H 139 " --> pdb=" O VAL H 96 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 24 through 29 Processing sheet with id=AE9, first strand: chain 'I' and resid 80 through 81 Processing sheet with id=AF1, first strand: chain 'K' and resid 19 through 23 Processing sheet with id=AF2, first strand: chain 'M' and resid 804 through 809 removed outlier: 4.257A pdb=" N GLU M 804 " --> pdb=" O ASN M 800 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N LEU M 798 " --> pdb=" O THR M 806 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHE M 808 " --> pdb=" O CYS M 796 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N CYS M 796 " --> pdb=" O PHE M 808 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N VAL M 848 " --> pdb=" O GLU M 883 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'M' and resid 971 through 972 removed outlier: 5.965A pdb=" N VAL M 971 " --> pdb=" O LYS M1036 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'M' and resid 1237 through 1240 removed outlier: 3.709A pdb=" N CYS M1265 " --> pdb=" O ILE M1167 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG M1266 " --> pdb=" O THR M1280 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'M' and resid 1355 through 1359 removed outlier: 3.781A pdb=" N LEU M1367 " --> pdb=" O VAL M1383 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TRP M1371 " --> pdb=" O GLN M1379 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLN M1379 " --> pdb=" O TRP M1371 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'M' and resid 1461 through 1464 removed outlier: 4.194A pdb=" N PHE M1461 " --> pdb=" O GLY M1475 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY M1475 " --> pdb=" O PHE M1461 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Q' and resid 5 through 7 removed outlier: 4.400A pdb=" N ILE Q 6 " --> pdb=" O LEU Q 19 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU Q 19 " --> pdb=" O ILE Q 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'R' and resid 386 through 387 removed outlier: 3.962A pdb=" N VAL R 387 " --> pdb=" O ALA R 403 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALA R 403 " --> pdb=" O VAL R 387 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU R 428 " --> pdb=" O ARG R 435 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG R 435 " --> pdb=" O LEU R 428 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASP R 433 " --> pdb=" O HIS R 430 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'R' and resid 410 through 417 removed outlier: 8.138A pdb=" N LYS R 413 " --> pdb=" O LYS R 424 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LYS R 424 " --> pdb=" O LYS R 413 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N TYR R 415 " --> pdb=" O THR R 422 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR R 420 " --> pdb=" O LEU R 417 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'S' and resid 256 through 258 Processing sheet with id=AG2, first strand: chain 'U' and resid 376 through 377 removed outlier: 3.620A pdb=" N PHE V 312 " --> pdb=" O VAL U 376 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'U' and resid 494 through 495 removed outlier: 3.868A pdb=" N HIS U 494 " --> pdb=" O TYR U 460 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR U 460 " --> pdb=" O HIS U 494 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET U 448 " --> pdb=" O VAL U 459 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N HIS U 451 " --> pdb=" O ARG U 439 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARG U 439 " --> pdb=" O HIS U 451 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ILE U 440 " --> pdb=" O VAL V 204 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N VAL V 204 " --> pdb=" O ILE U 440 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LYS U 442 " --> pdb=" O VAL V 202 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'V' and resid 221 through 222 removed outlier: 3.617A pdb=" N ARG V 331 " --> pdb=" O LYS V 292 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER V 333 " --> pdb=" O LYS V 290 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS V 290 " --> pdb=" O SER V 333 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'V' and resid 250 through 251 removed outlier: 3.931A pdb=" N GLN V 250 " --> pdb=" O VAL V 261 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'W' and resid 6 through 11 removed outlier: 6.503A pdb=" N ILE W 300 " --> pdb=" O LEU W 8 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS W 10 " --> pdb=" O ILE W 298 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE W 298 " --> pdb=" O LYS W 10 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY W 279 " --> pdb=" O VAL W 292 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'W' and resid 19 through 24 removed outlier: 3.556A pdb=" N SER W 21 " --> pdb=" O GLY W 38 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS W 45 " --> pdb=" O THR W 37 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL W 44 " --> pdb=" O SER W 59 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER W 59 " --> pdb=" O VAL W 44 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N VAL W 46 " --> pdb=" O GLN W 57 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'W' and resid 67 through 72 removed outlier: 7.193A pdb=" N SER W 82 " --> pdb=" O VAL W 68 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N VAL W 70 " --> pdb=" O ALA W 80 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ALA W 80 " --> pdb=" O VAL W 70 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ILE W 72 " --> pdb=" O ILE W 78 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE W 78 " --> pdb=" O ILE W 72 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS W 100 " --> pdb=" O LEU W 90 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ASP W 92 " --> pdb=" O GLN W 98 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLN W 98 " --> pdb=" O ASP W 92 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'W' and resid 112 through 114 removed outlier: 3.683A pdb=" N VAL W 130 " --> pdb=" O LEU W 144 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR W 142 " --> pdb=" O ILE W 132 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLY W 134 " --> pdb=" O LYS W 140 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LYS W 140 " --> pdb=" O GLY W 134 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'W' and resid 151 through 156 removed outlier: 6.079A pdb=" N GLY W 166 " --> pdb=" O LEU W 152 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ILE W 154 " --> pdb=" O ALA W 164 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N ALA W 164 " --> pdb=" O ILE W 154 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'W' and resid 172 through 175 Processing sheet with id=AH3, first strand: chain 'W' and resid 195 through 198 removed outlier: 3.717A pdb=" N SER W 195 " --> pdb=" O ALA W 208 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N THR W 197 " --> pdb=" O VAL W 206 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL W 206 " --> pdb=" O THR W 197 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR W 207 " --> pdb=" O LYS W 215 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS W 215 " --> pdb=" O THR W 207 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY W 226 " --> pdb=" O ILE W 216 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ASP W 218 " --> pdb=" O LEU W 224 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU W 224 " --> pdb=" O ASP W 218 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'W' and resid 237 through 240 removed outlier: 3.538A pdb=" N LYS W 257 " --> pdb=" O SER W 249 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS W 268 " --> pdb=" O VAL W 258 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASP W 260 " --> pdb=" O CYS W 266 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N CYS W 266 " --> pdb=" O ASP W 260 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Y' and resid 13 through 15 removed outlier: 3.529A pdb=" N LYS Y 23 " --> pdb=" O ARG Y 14 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Y' and resid 57 through 58 removed outlier: 3.653A pdb=" N SER Y 88 " --> pdb=" O ASP Y 58 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Y' and resid 83 through 85 removed outlier: 4.087A pdb=" N ILE Y 60 " --> pdb=" O ALA Z 217 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'Z' and resid 224 through 228 removed outlier: 3.813A pdb=" N GLN Z 253 " --> pdb=" O THR Z 181 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'Z' and resid 278 through 280 Processing sheet with id=AI1, first strand: chain 'Z' and resid 302 through 303 Processing sheet with id=AI2, first strand: chain 'Z' and resid 367 through 368 Processing sheet with id=AI3, first strand: chain 'Z' and resid 438 through 439 Processing sheet with id=AI4, first strand: chain 'Z' and resid 477 through 479 removed outlier: 3.730A pdb=" N LEU Z 491 " --> pdb=" O PHE Z 503 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE Z 503 " --> pdb=" O LEU Z 491 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ILE Z 501 " --> pdb=" O VAL Z 493 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Z' and resid 567 through 571 removed outlier: 7.638A pdb=" N THR Z 557 " --> pdb=" O LEU Z 553 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU Z 553 " --> pdb=" O THR Z 557 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N GLN Z 559 " --> pdb=" O VAL Z 551 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL Z 551 " --> pdb=" O GLN Z 559 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN Z 541 " --> pdb=" O THR Z 576 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR Z 576 " --> pdb=" O GLN Z 541 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Z' and resid 622 through 625 removed outlier: 6.961A pdb=" N PHE Z 623 " --> pdb=" O ARG Z 615 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLY Z 612 " --> pdb=" O VAL Z 600 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL Z 600 " --> pdb=" O GLY Z 612 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'Z' and resid 742 through 746 removed outlier: 3.578A pdb=" N ASP Z 726 " --> pdb=" O ARG Z 733 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLU Z 735 " --> pdb=" O VAL Z 724 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N VAL Z 724 " --> pdb=" O GLU Z 735 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.737A pdb=" N ARG a 83 " --> pdb=" O VAL b 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI8 Processing sheet with id=AI9, first strand: chain 'a' and resid 118 through 119 Processing sheet with id=AJ1, first strand: chain 'b' and resid 96 through 98 Processing sheet with id=AJ2, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.571A pdb=" N ARG c 42 " --> pdb=" O ILE d 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ2 Processing sheet with id=AJ3, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AJ4, first strand: chain 'c' and resid 100 through 102 Processing sheet with id=AJ5, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.535A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ5 Processing sheet with id=AJ6, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AJ7, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.171A pdb=" N ARG g 42 " --> pdb=" O ILE h 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ7 Processing sheet with id=AJ8, first strand: chain 'g' and resid 77 through 78 2687 hydrogen bonds defined for protein. 7689 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 406 hydrogen bonds 808 hydrogen bond angles 0 basepair planarities 159 basepair parallelities 243 stacking parallelities Total time for adding SS restraints: 42.17 Time building geometry restraints manager: 15.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 19249 1.33 - 1.45: 12484 1.45 - 1.58: 35590 1.58 - 1.70: 665 1.70 - 1.82: 411 Bond restraints: 68399 Sorted by residual: bond pdb=" OG1 TPO A1525 " pdb=" P TPO A1525 " ideal model delta sigma weight residual 1.717 1.611 0.106 2.00e-02 2.50e+03 2.82e+01 bond pdb=" OG1 TPO Z 775 " pdb=" P TPO Z 775 " ideal model delta sigma weight residual 1.717 1.614 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" O2P TPO A1525 " pdb=" P TPO A1525 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" O3P TPO Z 775 " pdb=" P TPO Z 775 " ideal model delta sigma weight residual 1.528 1.610 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" O3P TPO A1525 " pdb=" P TPO A1525 " ideal model delta sigma weight residual 1.528 1.609 -0.081 2.00e-02 2.50e+03 1.64e+01 ... (remaining 68394 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 92984 2.53 - 5.05: 607 5.05 - 7.58: 46 7.58 - 10.10: 5 10.10 - 12.63: 8 Bond angle restraints: 93650 Sorted by residual: angle pdb=" C GLU Q 772 " pdb=" N LYS Q 773 " pdb=" CA LYS Q 773 " ideal model delta sigma weight residual 121.70 134.33 -12.63 1.80e+00 3.09e-01 4.92e+01 angle pdb=" C TYR V 61 " pdb=" N LYS V 62 " pdb=" CA LYS V 62 " ideal model delta sigma weight residual 121.70 131.85 -10.15 1.80e+00 3.09e-01 3.18e+01 angle pdb=" CB TPO A1525 " pdb=" OG1 TPO A1525 " pdb=" P TPO A1525 " ideal model delta sigma weight residual 119.31 107.23 12.08 3.00e+00 1.11e-01 1.62e+01 angle pdb=" OG1 TPO Z 775 " pdb=" P TPO Z 775 " pdb=" O1P TPO Z 775 " ideal model delta sigma weight residual 100.43 111.71 -11.28 3.00e+00 1.11e-01 1.41e+01 angle pdb=" OP1 DA N 146 " pdb=" P DA N 146 " pdb=" OP2 DA N 146 " ideal model delta sigma weight residual 120.00 109.58 10.42 3.00e+00 1.11e-01 1.21e+01 ... (remaining 93645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 38109 35.90 - 71.80: 1282 71.80 - 107.70: 24 107.70 - 143.60: 2 143.60 - 179.50: 7 Dihedral angle restraints: 39424 sinusoidal: 16838 harmonic: 22586 Sorted by residual: dihedral pdb=" CA GLU I 105 " pdb=" C GLU I 105 " pdb=" N ASP I 106 " pdb=" CA ASP I 106 " ideal model delta harmonic sigma weight residual 180.00 159.37 20.63 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ASP A 120 " pdb=" C ASP A 120 " pdb=" N SER A 121 " pdb=" CA SER A 121 " ideal model delta harmonic sigma weight residual -180.00 -159.48 -20.52 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" O4' U P 13 " pdb=" C1' U P 13 " pdb=" N1 U P 13 " pdb=" C2 U P 13 " ideal model delta sinusoidal sigma weight residual -160.00 -108.07 -51.93 1 1.50e+01 4.44e-03 1.64e+01 ... (remaining 39421 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 9497 0.083 - 0.167: 642 0.167 - 0.250: 6 0.250 - 0.333: 0 0.333 - 0.416: 3 Chirality restraints: 10148 Sorted by residual: chirality pdb=" P DA N 146 " pdb=" OP1 DA N 146 " pdb=" OP2 DA N 146 " pdb=" O5' DA N 146 " both_signs ideal model delta sigma weight residual True 2.35 -2.76 -0.42 2.00e-01 2.50e+01 4.33e+00 chirality pdb=" P DG N 153 " pdb=" OP1 DG N 153 " pdb=" OP2 DG N 153 " pdb=" O5' DG N 153 " both_signs ideal model delta sigma weight residual True 2.35 -2.73 -0.38 2.00e-01 2.50e+01 3.65e+00 chirality pdb=" P DA T-145 " pdb=" OP1 DA T-145 " pdb=" OP2 DA T-145 " pdb=" O5' DA T-145 " both_signs ideal model delta sigma weight residual True 2.35 -2.72 -0.37 2.00e-01 2.50e+01 3.49e+00 ... (remaining 10145 not shown) Planarity restraints: 11378 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TRP Q 684 " 0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C TRP Q 684 " -0.073 2.00e-02 2.50e+03 pdb=" O TRP Q 684 " 0.027 2.00e-02 2.50e+03 pdb=" N LEU Q 685 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU Q 452 " 0.012 2.00e-02 2.50e+03 2.40e-02 5.76e+00 pdb=" C GLU Q 452 " -0.042 2.00e-02 2.50e+03 pdb=" O GLU Q 452 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE Q 453 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL e 117 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.58e+00 pdb=" C VAL e 117 " 0.041 2.00e-02 2.50e+03 pdb=" O VAL e 117 " -0.015 2.00e-02 2.50e+03 pdb=" N THR e 118 " -0.014 2.00e-02 2.50e+03 ... (remaining 11375 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 524 2.58 - 3.16: 56158 3.16 - 3.74: 104168 3.74 - 4.32: 137987 4.32 - 4.90: 223004 Nonbonded interactions: 521841 Sorted by model distance: nonbonded pdb=" O3' C P 26 " pdb="MG MG A2003 " model vdw 2.001 2.170 nonbonded pdb=" OH TYR Q 371 " pdb=" NE2 GLN V 69 " model vdw 2.065 3.120 nonbonded pdb=" O ASN D 76 " pdb=" OG1 THR D 79 " model vdw 2.111 3.040 nonbonded pdb=" O VAL Y 49 " pdb=" OG1 THR Y 53 " model vdw 2.113 3.040 nonbonded pdb=" N CYS J 45 " pdb="ZN ZN J 101 " model vdw 2.127 2.310 ... (remaining 521836 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'a' selection = (chain 'e' and resid 43 through 134) } ncs_group { reference = (chain 'b' and resid 25 through 102) selection = chain 'f' } ncs_group { reference = (chain 'c' and resid 16 through 111) selection = (chain 'g' and resid 16 through 111) } 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=0.00 max=1.00 mean=0.99 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: 9.670 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: 0.090 Extract box with map and model: 2.080 Check model and map are aligned: 0.380 Set scattering table: 0.450 Process input model: 156.710 Find NCS groups from input model: 1.460 Set up NCS constraints: 0.310 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:11.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 182.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5593 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 68399 Z= 0.179 Angle : 0.549 12.628 93650 Z= 0.288 Chirality : 0.042 0.416 10148 Planarity : 0.003 0.054 11378 Dihedral : 14.414 179.495 25382 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.79 % Favored : 93.13 % Rotamer: Outliers : 1.01 % Allowed : 3.65 % Favored : 95.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.09), residues: 8242 helix: 1.24 (0.10), residues: 3249 sheet: -2.93 (0.17), residues: 772 loop : -2.16 (0.09), residues: 4221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Q 568 HIS 0.003 0.001 HIS A 449 PHE 0.014 0.001 PHE B 185 TYR 0.017 0.001 TYR E 90 ARG 0.008 0.001 ARG Q 763 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16484 Ramachandran restraints generated. 8242 Oldfield, 0 Emsley, 8242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16484 Ramachandran restraints generated. 8242 Oldfield, 0 Emsley, 8242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 7356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 690 time to evaluate : 5.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.8523 (m-10) cc_final: 0.8282 (m-80) REVERT: A 359 VAL cc_start: 0.9153 (m) cc_final: 0.8807 (t) REVERT: A 467 MET cc_start: 0.8318 (mmt) cc_final: 0.7915 (mmp) REVERT: A 501 MET cc_start: 0.8031 (mtp) cc_final: 0.7736 (mtp) REVERT: A 1026 ASP cc_start: 0.8923 (m-30) cc_final: 0.8386 (t0) REVERT: A 1086 MET cc_start: 0.9057 (mmm) cc_final: 0.8838 (mpp) REVERT: A 1134 PRO cc_start: 0.8723 (Cg_endo) cc_final: 0.8121 (Cg_exo) REVERT: A 1344 MET cc_start: 0.8214 (tpp) cc_final: 0.7925 (tpt) REVERT: A 1428 MET cc_start: 0.8693 (ttt) cc_final: 0.8010 (tmm) REVERT: B 109 MET cc_start: 0.8783 (mmm) cc_final: 0.8525 (mmm) REVERT: B 764 MET cc_start: 0.8906 (ptp) cc_final: 0.8372 (ptm) REVERT: B 1054 MET cc_start: 0.8326 (mmt) cc_final: 0.8072 (mmm) REVERT: B 1075 MET cc_start: 0.7947 (mmm) cc_final: 0.7676 (mpt) REVERT: B 1151 MET cc_start: 0.8114 (ptp) cc_final: 0.7870 (ptm) REVERT: E 72 MET cc_start: 0.8579 (ptm) cc_final: 0.8119 (ptm) REVERT: H 12 VAL cc_start: 0.9170 (t) cc_final: 0.8727 (p) REVERT: H 33 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7565 (mt-10) REVERT: J 1 MET cc_start: 0.7511 (mtm) cc_final: 0.7263 (mtm) REVERT: J 48 MET cc_start: 0.7740 (mmt) cc_final: 0.6910 (mmt) REVERT: L 27 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7241 (mm-30) REVERT: L 38 GLU cc_start: 0.7743 (pm20) cc_final: 0.7506 (pp20) REVERT: Q 779 VAL cc_start: 0.4899 (OUTLIER) cc_final: 0.4615 (t) REVERT: R 503 ARG cc_start: -0.0007 (tmm160) cc_final: -0.0878 (ttm-80) REVERT: R 567 ASN cc_start: 0.0387 (m-40) cc_final: -0.0590 (t0) REVERT: R 586 MET cc_start: -0.1433 (ptt) cc_final: -0.2238 (mtt) REVERT: V 58 PHE cc_start: 0.4089 (p90) cc_final: 0.3061 (t80) REVERT: Z 378 MET cc_start: 0.1168 (tpt) cc_final: 0.0727 (ptp) REVERT: Z 635 MET cc_start: 0.0751 (ttt) cc_final: -0.0285 (tmt) REVERT: d 109 SER cc_start: 0.8363 (OUTLIER) cc_final: 0.8148 (t) outliers start: 56 outliers final: 8 residues processed: 732 average time/residue: 1.5994 time to fit residues: 1503.4410 Evaluate side-chains 369 residues out of total 7356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 359 time to evaluate : 5.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1095 LEU Chi-restraints excluded: chain A residue 1440 MET Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain Q residue 664 ARG Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 779 VAL Chi-restraints excluded: chain Z residue 429 CYS Chi-restraints excluded: chain d residue 77 LEU Chi-restraints excluded: chain d residue 109 SER Chi-restraints excluded: chain g residue 75 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 723 optimal weight: 6.9990 chunk 649 optimal weight: 3.9990 chunk 360 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 438 optimal weight: 0.0570 chunk 347 optimal weight: 0.7980 chunk 671 optimal weight: 6.9990 chunk 259 optimal weight: 0.0000 chunk 408 optimal weight: 50.0000 chunk 499 optimal weight: 0.6980 chunk 778 optimal weight: 40.0000 overall best weight: 0.7104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 96 HIS A 122 ASN A 288 ASN A 301 HIS A 320 ASN A 387 ASN A 529 GLN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 GLN A 790 GLN ** A 804 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 809 HIS A 991 GLN A1036 ASN A1044 HIS A1129 ASN A1332 GLN A1457 ASN A1462 GLN B 98 HIS B 197 GLN B 227 ASN B 319 ASN B 725 GLN ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 GLN H 29 HIS I 56 ASN I 91 HIS ** I 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 26 GLN K 2 ASN Q 273 ASN Q 305 GLN Q 527 HIS Q 616 HIS Q 628 HIS R 564 ASN ** R 567 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 56 ASN V 69 GLN V 72 HIS W 27 ASN W 173 ASN W 273 HIS Y 12 HIS a 108 ASN b 93 GLN c 73 ASN d 64 ASN e 108 ASN ** g 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 60 ASN h 64 ASN h 106 HIS Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5643 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 68399 Z= 0.179 Angle : 0.549 10.117 93650 Z= 0.289 Chirality : 0.041 0.218 10148 Planarity : 0.004 0.057 11378 Dihedral : 17.320 174.506 12702 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.49 % Favored : 95.46 % Rotamer: Outliers : 1.41 % Allowed : 9.63 % Favored : 88.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.06 % 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: -0.89 (0.10), residues: 8242 helix: 1.38 (0.10), residues: 3349 sheet: -2.56 (0.17), residues: 805 loop : -1.94 (0.09), residues: 4088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1192 HIS 0.009 0.001 HIS I 100 PHE 0.016 0.001 PHE A 496 TYR 0.018 0.001 TYR C 208 ARG 0.010 0.001 ARG Q 866 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16484 Ramachandran restraints generated. 8242 Oldfield, 0 Emsley, 8242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16484 Ramachandran restraints generated. 8242 Oldfield, 0 Emsley, 8242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 7356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 392 time to evaluate : 5.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 TYR cc_start: 0.8642 (m-10) cc_final: 0.8407 (m-80) REVERT: A 51 ARG cc_start: 0.8730 (mtm-85) cc_final: 0.8308 (pmt170) REVERT: A 78 MET cc_start: 0.8984 (tpp) cc_final: 0.8573 (tpp) REVERT: A 501 MET cc_start: 0.8076 (mtp) cc_final: 0.7873 (mtp) REVERT: A 1086 MET cc_start: 0.9007 (mmm) cc_final: 0.8805 (mpp) REVERT: A 1102 MET cc_start: 0.8967 (ptm) cc_final: 0.8767 (ptp) REVERT: A 1210 TRP cc_start: 0.6465 (p90) cc_final: 0.6214 (p90) REVERT: A 1344 MET cc_start: 0.7892 (tpp) cc_final: 0.7631 (tpp) REVERT: A 1428 MET cc_start: 0.8699 (ttt) cc_final: 0.8265 (tmt) REVERT: B 109 MET cc_start: 0.8758 (mmm) cc_final: 0.8527 (mmm) REVERT: B 1075 MET cc_start: 0.8024 (mmm) cc_final: 0.7659 (mpt) REVERT: B 1151 MET cc_start: 0.8032 (ptp) cc_final: 0.7783 (ptm) REVERT: E 72 MET cc_start: 0.8145 (ptm) cc_final: 0.7723 (ptm) REVERT: E 121 MET cc_start: 0.6737 (OUTLIER) cc_final: 0.6462 (mtt) REVERT: F 80 MET cc_start: 0.8137 (mmm) cc_final: 0.7841 (mmm) REVERT: F 88 ASP cc_start: 0.7388 (t0) cc_final: 0.6829 (t0) REVERT: H 13 LYS cc_start: 0.8146 (mmmm) cc_final: 0.7882 (mmmm) REVERT: H 145 MET cc_start: 0.7438 (ttp) cc_final: 0.7234 (ttp) REVERT: J 1 MET cc_start: 0.7535 (mtm) cc_final: 0.7290 (mtm) REVERT: K 68 GLU cc_start: 0.8285 (tm-30) cc_final: 0.8068 (tm-30) REVERT: L 38 GLU cc_start: 0.7832 (pm20) cc_final: 0.6655 (pm20) REVERT: L 47 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8637 (ttpp) REVERT: Q 602 TYR cc_start: 0.5650 (OUTLIER) cc_final: 0.5412 (m-80) REVERT: R 503 ARG cc_start: -0.0022 (tmm160) cc_final: -0.0523 (ttm110) REVERT: R 567 ASN cc_start: 0.0820 (m-40) cc_final: -0.0222 (t0) REVERT: R 582 GLU cc_start: -0.1725 (pt0) cc_final: -0.3359 (pp20) REVERT: R 586 MET cc_start: -0.1414 (ptt) cc_final: -0.2239 (mtt) REVERT: R 596 ARG cc_start: 0.0060 (mmp-170) cc_final: -0.0479 (tpm170) REVERT: R 597 ARG cc_start: -0.1808 (ptt-90) cc_final: -0.2861 (ptt180) REVERT: V 58 PHE cc_start: 0.4607 (p90) cc_final: 0.2585 (t80) REVERT: W 191 MET cc_start: 0.2277 (mpp) cc_final: 0.2072 (mpp) REVERT: W 234 TRP cc_start: 0.6711 (OUTLIER) cc_final: 0.6411 (m-90) REVERT: W 250 SER cc_start: 0.4590 (OUTLIER) cc_final: 0.4351 (p) REVERT: Z 378 MET cc_start: 0.1088 (tpt) cc_final: 0.0651 (ptp) REVERT: d 68 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7580 (tp30) REVERT: d 109 SER cc_start: 0.8467 (OUTLIER) cc_final: 0.8136 (t) REVERT: f 63 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7268 (tm-30) REVERT: h 48 ASP cc_start: 0.6131 (p0) cc_final: 0.5777 (p0) outliers start: 78 outliers final: 27 residues processed: 438 average time/residue: 1.4862 time to fit residues: 857.4212 Evaluate side-chains 366 residues out of total 7356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 332 time to evaluate : 5.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain L residue 47 LYS Chi-restraints excluded: chain Q residue 531 VAL Chi-restraints excluded: chain Q residue 602 TYR Chi-restraints excluded: chain Q residue 664 ARG Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 714 HIS Chi-restraints excluded: chain Q residue 779 VAL Chi-restraints excluded: chain Q residue 817 CYS Chi-restraints excluded: chain Q residue 837 GLU Chi-restraints excluded: chain V residue 42 ILE Chi-restraints excluded: chain W residue 234 TRP Chi-restraints excluded: chain W residue 250 SER Chi-restraints excluded: chain Y residue 97 ILE Chi-restraints excluded: chain Z residue 429 CYS Chi-restraints excluded: chain b residue 21 VAL Chi-restraints excluded: chain b residue 66 ILE Chi-restraints excluded: chain b residue 77 LYS Chi-restraints excluded: chain c residue 71 ARG Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 109 SER Chi-restraints excluded: chain d residue 115 VAL Chi-restraints excluded: chain d residue 117 LYS Chi-restraints excluded: chain e residue 117 VAL Chi-restraints excluded: chain f residue 63 GLU Chi-restraints excluded: chain g residue 75 LYS Chi-restraints excluded: chain g residue 107 VAL Chi-restraints excluded: chain h residue 84 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 432 optimal weight: 10.0000 chunk 241 optimal weight: 6.9990 chunk 647 optimal weight: 4.9990 chunk 529 optimal weight: 50.0000 chunk 214 optimal weight: 0.9990 chunk 779 optimal weight: 10.0000 chunk 842 optimal weight: 40.0000 chunk 694 optimal weight: 5.9990 chunk 773 optimal weight: 50.0000 chunk 265 optimal weight: 2.9990 chunk 625 optimal weight: 30.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 423 ASN ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 GLN A 791 GLN A 982 ASN A 995 HIS A1036 ASN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 GLN B 471 ASN B 582 GLN B 631 GLN B 789 ASN B1071 ASN B1094 GLN B1101 GLN ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 60 HIS C 66 HIS I 22 ASN I 91 HIS ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 289 GLN ** Q 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 598 GLN Q 775 ASN Q 860 GLN R 571 ASN V 69 GLN Y 27 GLN Z 337 GLN Z 446 ASN Z 616 HIS ** b 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 112 GLN ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 108 ASN g 24 GLN g 31 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5948 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.176 68399 Z= 0.482 Angle : 0.761 22.022 93650 Z= 0.403 Chirality : 0.048 0.363 10148 Planarity : 0.006 0.223 11378 Dihedral : 17.986 175.523 12695 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.98 % Favored : 93.96 % Rotamer: Outliers : 2.30 % Allowed : 10.75 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.06 % Twisted Proline : 0.29 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.09), residues: 8242 helix: 0.95 (0.09), residues: 3361 sheet: -2.33 (0.17), residues: 803 loop : -1.93 (0.09), residues: 4078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 27 HIS 0.029 0.002 HIS Z 572 PHE 0.037 0.003 PHE H 10 TYR 0.030 0.003 TYR d 39 ARG 0.033 0.001 ARG e 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16484 Ramachandran restraints generated. 8242 Oldfield, 0 Emsley, 8242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16484 Ramachandran restraints generated. 8242 Oldfield, 0 Emsley, 8242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 7356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 367 time to evaluate : 5.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 MET cc_start: 0.8999 (tpp) cc_final: 0.8622 (tpp) REVERT: A 136 GLN cc_start: 0.8058 (mp10) cc_final: 0.7857 (mp10) REVERT: A 501 MET cc_start: 0.8281 (mtp) cc_final: 0.7796 (mmm) REVERT: A 524 MET cc_start: 0.8552 (mtp) cc_final: 0.8323 (mtp) REVERT: A 868 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.7332 (ptp) REVERT: A 1228 MET cc_start: 0.8545 (mmm) cc_final: 0.8302 (mmm) REVERT: A 1344 MET cc_start: 0.8213 (tpp) cc_final: 0.7916 (tpp) REVERT: A 1428 MET cc_start: 0.8786 (ttt) cc_final: 0.8203 (tmm) REVERT: B 298 MET cc_start: 0.9203 (ttm) cc_final: 0.8861 (ttm) REVERT: B 744 MET cc_start: 0.8591 (mmm) cc_final: 0.8287 (mtm) REVERT: B 1054 MET cc_start: 0.8477 (mmm) cc_final: 0.8227 (mmm) REVERT: B 1071 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7940 (p0) REVERT: D 74 PHE cc_start: 0.5659 (OUTLIER) cc_final: 0.5300 (p90) REVERT: F 80 MET cc_start: 0.8161 (mmm) cc_final: 0.7707 (mmm) REVERT: F 88 ASP cc_start: 0.8173 (t0) cc_final: 0.7844 (t0) REVERT: H 51 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8149 (p0) REVERT: H 84 ARG cc_start: 0.8314 (OUTLIER) cc_final: 0.7934 (ptm160) REVERT: I 92 LYS cc_start: 0.8917 (pptt) cc_final: 0.8643 (tmmt) REVERT: J 1 MET cc_start: 0.7919 (mtm) cc_final: 0.7695 (mtm) REVERT: L 30 SER cc_start: 0.8993 (m) cc_final: 0.8457 (p) REVERT: L 38 GLU cc_start: 0.7851 (pm20) cc_final: 0.6831 (pm20) REVERT: L 44 MET cc_start: 0.7915 (ptp) cc_final: 0.7584 (ttp) REVERT: Q 736 CYS cc_start: 0.6846 (OUTLIER) cc_final: 0.6428 (t) REVERT: R 493 GLU cc_start: 0.4578 (OUTLIER) cc_final: 0.4235 (mm-30) REVERT: R 498 GLU cc_start: 0.5914 (OUTLIER) cc_final: 0.5505 (pt0) REVERT: R 503 ARG cc_start: 0.0652 (tmm160) cc_final: -0.1173 (ttm170) REVERT: R 563 ILE cc_start: -0.2131 (OUTLIER) cc_final: -0.2355 (tp) REVERT: R 567 ASN cc_start: 0.0158 (m-40) cc_final: -0.0772 (t0) REVERT: R 582 GLU cc_start: -0.1485 (pt0) cc_final: -0.3634 (pp20) REVERT: R 596 ARG cc_start: 0.0390 (mmp-170) cc_final: 0.0105 (mmp-170) REVERT: R 597 ARG cc_start: -0.1851 (ptt-90) cc_final: -0.2168 (ptt180) REVERT: W 234 TRP cc_start: 0.7334 (OUTLIER) cc_final: 0.6550 (m-90) REVERT: W 250 SER cc_start: 0.5064 (OUTLIER) cc_final: 0.4840 (p) REVERT: Z 635 MET cc_start: 0.0458 (OUTLIER) cc_final: 0.0070 (tmt) REVERT: d 46 HIS cc_start: 0.6872 (OUTLIER) cc_final: 0.6602 (m-70) REVERT: d 68 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8369 (tp30) outliers start: 127 outliers final: 39 residues processed: 456 average time/residue: 1.4557 time to fit residues: 879.8635 Evaluate side-chains 377 residues out of total 7356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 325 time to evaluate : 5.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 1440 MET Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 440 ILE Chi-restraints excluded: chain B residue 1071 ASN Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain Q residue 374 ASN Chi-restraints excluded: chain Q residue 531 VAL Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 714 HIS Chi-restraints excluded: chain Q residue 717 THR Chi-restraints excluded: chain Q residue 736 CYS Chi-restraints excluded: chain Q residue 779 VAL Chi-restraints excluded: chain Q residue 837 GLU Chi-restraints excluded: chain Q residue 889 LEU Chi-restraints excluded: chain R residue 493 GLU Chi-restraints excluded: chain R residue 498 GLU Chi-restraints excluded: chain R residue 563 ILE Chi-restraints excluded: chain V residue 69 GLN Chi-restraints excluded: chain W residue 234 TRP Chi-restraints excluded: chain W residue 250 SER Chi-restraints excluded: chain X residue 234 ARG Chi-restraints excluded: chain X residue 243 LYS Chi-restraints excluded: chain Y residue 97 ILE Chi-restraints excluded: chain Z residue 222 LYS Chi-restraints excluded: chain Z residue 635 MET Chi-restraints excluded: chain b residue 81 VAL Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 46 HIS Chi-restraints excluded: chain d residue 61 SER Chi-restraints excluded: chain d residue 87 THR Chi-restraints excluded: chain d residue 95 VAL Chi-restraints excluded: chain d residue 115 VAL Chi-restraints excluded: chain d residue 122 LYS Chi-restraints excluded: chain e residue 117 VAL Chi-restraints excluded: chain g residue 75 LYS Chi-restraints excluded: chain g residue 107 VAL Chi-restraints excluded: chain h residue 84 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 770 optimal weight: 9.9990 chunk 586 optimal weight: 9.9990 chunk 404 optimal weight: 50.0000 chunk 86 optimal weight: 0.1980 chunk 372 optimal weight: 0.7980 chunk 523 optimal weight: 9.9990 chunk 782 optimal weight: 5.9990 chunk 828 optimal weight: 2.9990 chunk 408 optimal weight: 50.0000 chunk 741 optimal weight: 50.0000 chunk 223 optimal weight: 0.4980 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 980 HIS B1071 ASN B1094 GLN ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 289 GLN Q 311 GLN Q 502 ASN ** Q 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 706 ASN a 125 GLN ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 113 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5905 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 68399 Z= 0.239 Angle : 0.566 12.335 93650 Z= 0.300 Chirality : 0.041 0.184 10148 Planarity : 0.004 0.056 11378 Dihedral : 18.111 174.339 12689 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.49 % Favored : 95.47 % Rotamer: Outliers : 1.61 % Allowed : 12.61 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.06 % Twisted Proline : 0.29 % 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: -0.71 (0.09), residues: 8242 helix: 1.31 (0.09), residues: 3366 sheet: -1.94 (0.18), residues: 759 loop : -1.77 (0.09), residues: 4117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1210 HIS 0.009 0.001 HIS a 113 PHE 0.014 0.001 PHE B 918 TYR 0.021 0.001 TYR H 118 ARG 0.013 0.000 ARG X 234 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16484 Ramachandran restraints generated. 8242 Oldfield, 0 Emsley, 8242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16484 Ramachandran restraints generated. 8242 Oldfield, 0 Emsley, 8242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 7356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 346 time to evaluate : 5.448 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 136 GLN cc_start: 0.8005 (mp10) cc_final: 0.7797 (mp10) REVERT: A 501 MET cc_start: 0.8256 (mtp) cc_final: 0.7858 (mmm) REVERT: A 868 MET cc_start: 0.8525 (mtp) cc_final: 0.7314 (ptp) REVERT: A 1133 LYS cc_start: 0.9045 (tptt) cc_final: 0.8833 (tptt) REVERT: A 1228 MET cc_start: 0.8529 (mmm) cc_final: 0.8303 (mmm) REVERT: A 1344 MET cc_start: 0.8061 (tpp) cc_final: 0.7778 (tpp) REVERT: A 1428 MET cc_start: 0.8773 (ttt) cc_final: 0.8241 (tmm) REVERT: B 239 MET cc_start: 0.7969 (ptm) cc_final: 0.7766 (ptm) REVERT: B 298 MET cc_start: 0.9143 (ttm) cc_final: 0.8719 (ttm) REVERT: B 508 MET cc_start: 0.9017 (mpt) cc_final: 0.8545 (mtt) REVERT: B 744 MET cc_start: 0.8574 (mmm) cc_final: 0.8112 (mtm) REVERT: B 1054 MET cc_start: 0.8394 (mmm) cc_final: 0.8136 (mmm) REVERT: B 1075 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8202 (mpp) REVERT: B 1106 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7610 (mpt180) REVERT: B 1172 MET cc_start: 0.8768 (mpt) cc_final: 0.8544 (mpt) REVERT: D 74 PHE cc_start: 0.6149 (OUTLIER) cc_final: 0.5906 (p90) REVERT: E 72 MET cc_start: 0.8660 (ttp) cc_final: 0.7920 (ptm) REVERT: F 80 MET cc_start: 0.8089 (mmm) cc_final: 0.7604 (mmt) REVERT: F 88 ASP cc_start: 0.8042 (t0) cc_final: 0.7615 (t0) REVERT: H 51 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.8331 (p0) REVERT: H 87 GLN cc_start: 0.9076 (pm20) cc_final: 0.8702 (mp10) REVERT: I 92 LYS cc_start: 0.8949 (pptt) cc_final: 0.8671 (tmmt) REVERT: L 37 ARG cc_start: 0.8614 (mmm160) cc_final: 0.8052 (mmp80) REVERT: L 38 GLU cc_start: 0.7774 (pm20) cc_final: 0.7340 (pm20) REVERT: Q 310 TYR cc_start: 0.5080 (OUTLIER) cc_final: 0.4704 (t80) REVERT: Q 736 CYS cc_start: 0.6734 (t) cc_final: 0.6283 (t) REVERT: R 493 GLU cc_start: 0.4419 (mm-30) cc_final: 0.3928 (mm-30) REVERT: R 498 GLU cc_start: 0.6293 (OUTLIER) cc_final: 0.5885 (pt0) REVERT: R 503 ARG cc_start: 0.0524 (tmm160) cc_final: -0.1218 (ttm170) REVERT: R 567 ASN cc_start: 0.0449 (m-40) cc_final: -0.0539 (t0) REVERT: R 582 GLU cc_start: -0.1611 (pt0) cc_final: -0.3047 (pp20) REVERT: W 234 TRP cc_start: 0.7290 (OUTLIER) cc_final: 0.6440 (m-90) REVERT: Y 97 ILE cc_start: 0.1219 (OUTLIER) cc_final: 0.0964 (pt) REVERT: Z 508 MET cc_start: 0.0475 (mmm) cc_final: 0.0143 (mmm) REVERT: d 46 HIS cc_start: 0.6557 (OUTLIER) cc_final: 0.6225 (m-70) REVERT: d 68 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8302 (tp30) REVERT: e 107 THR cc_start: 0.8887 (p) cc_final: 0.8551 (t) REVERT: f 63 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7541 (tm-30) outliers start: 89 outliers final: 22 residues processed: 410 average time/residue: 1.4279 time to fit residues: 775.3790 Evaluate side-chains 351 residues out of total 7356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 319 time to evaluate : 5.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1106 ARG Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 70 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain Q residue 310 TYR Chi-restraints excluded: chain Q residue 374 ASN Chi-restraints excluded: chain Q residue 466 ASN Chi-restraints excluded: chain Q residue 531 VAL Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 714 HIS Chi-restraints excluded: chain Q residue 837 GLU Chi-restraints excluded: chain Q residue 881 TYR Chi-restraints excluded: chain R residue 498 GLU Chi-restraints excluded: chain W residue 234 TRP Chi-restraints excluded: chain Y residue 97 ILE Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 118 LYS Chi-restraints excluded: chain d residue 46 HIS Chi-restraints excluded: chain d residue 115 VAL Chi-restraints excluded: chain f residue 63 GLU Chi-restraints excluded: chain g residue 36 LYS Chi-restraints excluded: chain g residue 107 VAL Chi-restraints excluded: chain h residue 84 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 689 optimal weight: 50.0000 chunk 470 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 616 optimal weight: 50.0000 chunk 341 optimal weight: 6.9990 chunk 706 optimal weight: 5.9990 chunk 572 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 422 optimal weight: 0.9980 chunk 743 optimal weight: 0.0570 chunk 209 optimal weight: 0.0170 overall best weight: 2.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 504 HIS A 673 GLN ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1303 GLN A1313 GLN B 56 GLN B 731 GLN B 789 ASN ** B1097 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 407 GLN Q 428 GLN ** Q 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 98 GLN Z 234 HIS ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5980 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 68399 Z= 0.317 Angle : 0.614 11.854 93650 Z= 0.325 Chirality : 0.043 0.184 10148 Planarity : 0.004 0.091 11378 Dihedral : 18.267 174.100 12684 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.36 % Favored : 94.59 % Rotamer: Outliers : 2.17 % Allowed : 12.88 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.06 % Twisted Proline : 0.29 % 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: -0.67 (0.09), residues: 8242 helix: 1.26 (0.09), residues: 3386 sheet: -1.85 (0.18), residues: 790 loop : -1.67 (0.09), residues: 4066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1210 HIS 0.011 0.001 HIS b 75 PHE 0.021 0.002 PHE Q 335 TYR 0.028 0.002 TYR B 766 ARG 0.026 0.001 ARG e 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16484 Ramachandran restraints generated. 8242 Oldfield, 0 Emsley, 8242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16484 Ramachandran restraints generated. 8242 Oldfield, 0 Emsley, 8242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 7356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 335 time to evaluate : 5.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 GLN cc_start: 0.8035 (mp10) cc_final: 0.7789 (mp10) REVERT: A 501 MET cc_start: 0.8308 (mtp) cc_final: 0.8022 (mmm) REVERT: A 868 MET cc_start: 0.8480 (mtp) cc_final: 0.7323 (ptp) REVERT: A 1210 TRP cc_start: 0.6282 (p90) cc_final: 0.6012 (p90) REVERT: A 1228 MET cc_start: 0.8639 (mmm) cc_final: 0.8312 (mmt) REVERT: A 1344 MET cc_start: 0.8185 (tpp) cc_final: 0.7932 (tpp) REVERT: A 1428 MET cc_start: 0.8725 (ttt) cc_final: 0.8208 (tmm) REVERT: A 1451 MET cc_start: 0.8844 (tpp) cc_final: 0.8547 (mmm) REVERT: B 239 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7909 (ptm) REVERT: B 298 MET cc_start: 0.9226 (ttm) cc_final: 0.8793 (ttm) REVERT: B 508 MET cc_start: 0.9072 (mpt) cc_final: 0.8560 (mtt) REVERT: B 744 MET cc_start: 0.8670 (mmm) cc_final: 0.8119 (mtm) REVERT: B 1054 MET cc_start: 0.8282 (mmm) cc_final: 0.7990 (mmm) REVERT: B 1075 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8261 (mpp) REVERT: B 1106 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7633 (mpt180) REVERT: D 74 PHE cc_start: 0.6164 (OUTLIER) cc_final: 0.5941 (p90) REVERT: F 80 MET cc_start: 0.8004 (mmm) cc_final: 0.7523 (mmt) REVERT: F 88 ASP cc_start: 0.8218 (t0) cc_final: 0.7870 (t0) REVERT: G 84 VAL cc_start: 0.7587 (OUTLIER) cc_final: 0.7376 (p) REVERT: G 131 MET cc_start: 0.3418 (tmm) cc_final: 0.2672 (tpt) REVERT: H 87 GLN cc_start: 0.9075 (OUTLIER) cc_final: 0.8697 (mp10) REVERT: I 92 LYS cc_start: 0.8949 (pptt) cc_final: 0.8729 (pptt) REVERT: L 15 MET cc_start: 0.7148 (tpp) cc_final: 0.6715 (tpp) REVERT: L 37 ARG cc_start: 0.8674 (mmm160) cc_final: 0.8382 (mmp80) REVERT: L 38 GLU cc_start: 0.7747 (pm20) cc_final: 0.7425 (pm20) REVERT: Q 310 TYR cc_start: 0.5024 (OUTLIER) cc_final: 0.4635 (t80) REVERT: Q 736 CYS cc_start: 0.7095 (t) cc_final: 0.6667 (t) REVERT: Q 865 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8923 (tm) REVERT: R 498 GLU cc_start: 0.6159 (OUTLIER) cc_final: 0.5531 (pt0) REVERT: R 503 ARG cc_start: 0.0384 (tmm160) cc_final: -0.1477 (ttm170) REVERT: R 567 ASN cc_start: 0.0323 (m-40) cc_final: -0.0567 (t0) REVERT: R 582 GLU cc_start: -0.1700 (pt0) cc_final: -0.2973 (pp20) REVERT: W 234 TRP cc_start: 0.7530 (OUTLIER) cc_final: 0.6678 (m-90) REVERT: Y 48 MET cc_start: 0.1600 (OUTLIER) cc_final: 0.1363 (ppp) REVERT: Y 64 MET cc_start: 0.3610 (ppp) cc_final: 0.3380 (ppp) REVERT: Y 97 ILE cc_start: 0.1197 (OUTLIER) cc_final: 0.0954 (pt) REVERT: Z 307 MET cc_start: -0.0038 (pmt) cc_final: -0.0364 (pmm) REVERT: Z 378 MET cc_start: 0.1832 (OUTLIER) cc_final: 0.0715 (ptp) REVERT: c 79 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8791 (tt) REVERT: d 46 HIS cc_start: 0.6656 (OUTLIER) cc_final: 0.6284 (m-70) outliers start: 120 outliers final: 42 residues processed: 428 average time/residue: 1.4178 time to fit residues: 804.4951 Evaluate side-chains 366 residues out of total 7356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 309 time to evaluate : 5.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 928 ILE Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1106 ARG Chi-restraints excluded: chain B residue 1163 MET Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain Q residue 310 TYR Chi-restraints excluded: chain Q residue 340 PHE Chi-restraints excluded: chain Q residue 466 ASN Chi-restraints excluded: chain Q residue 531 VAL Chi-restraints excluded: chain Q residue 669 VAL Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 714 HIS Chi-restraints excluded: chain Q residue 837 GLU Chi-restraints excluded: chain Q residue 865 LEU Chi-restraints excluded: chain R residue 493 GLU Chi-restraints excluded: chain R residue 496 VAL Chi-restraints excluded: chain R residue 498 GLU Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain W residue 234 TRP Chi-restraints excluded: chain X residue 234 ARG Chi-restraints excluded: chain Y residue 36 CYS Chi-restraints excluded: chain Y residue 48 MET Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 97 ILE Chi-restraints excluded: chain Z residue 378 MET Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain b residue 92 ARG Chi-restraints excluded: chain c residue 62 ILE Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 46 HIS Chi-restraints excluded: chain d residue 49 THR Chi-restraints excluded: chain d residue 115 VAL Chi-restraints excluded: chain g residue 107 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 278 optimal weight: 4.9990 chunk 745 optimal weight: 0.0980 chunk 163 optimal weight: 6.9990 chunk 486 optimal weight: 3.9990 chunk 204 optimal weight: 4.9990 chunk 829 optimal weight: 0.7980 chunk 688 optimal weight: 0.0570 chunk 383 optimal weight: 30.0000 chunk 68 optimal weight: 0.7980 chunk 274 optimal weight: 5.9990 chunk 435 optimal weight: 40.0000 overall best weight: 1.1500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1299 GLN B1101 GLN ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 169 GLN ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 762 GLN Q 877 GLN V 56 ASN ** V 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5930 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 68399 Z= 0.181 Angle : 0.546 9.951 93650 Z= 0.288 Chirality : 0.040 0.196 10148 Planarity : 0.004 0.069 11378 Dihedral : 18.280 174.449 12684 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.05 % Favored : 95.91 % Rotamer: Outliers : 1.74 % Allowed : 13.68 % Favored : 84.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.06 % Twisted Proline : 0.29 % 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: -0.40 (0.09), residues: 8242 helix: 1.47 (0.09), residues: 3386 sheet: -1.66 (0.18), residues: 766 loop : -1.54 (0.09), residues: 4090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 176 HIS 0.010 0.001 HIS b 75 PHE 0.022 0.001 PHE Q 335 TYR 0.032 0.001 TYR B 766 ARG 0.016 0.000 ARG X 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16484 Ramachandran restraints generated. 8242 Oldfield, 0 Emsley, 8242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16484 Ramachandran restraints generated. 8242 Oldfield, 0 Emsley, 8242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 7356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 330 time to evaluate : 5.453 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 266 MET cc_start: 0.2169 (OUTLIER) cc_final: 0.1796 (tmm) REVERT: A 470 MET cc_start: 0.8533 (mtm) cc_final: 0.8198 (mtp) REVERT: A 868 MET cc_start: 0.8470 (mtp) cc_final: 0.7387 (ptp) REVERT: A 1228 MET cc_start: 0.8656 (mmm) cc_final: 0.8235 (mpp) REVERT: A 1344 MET cc_start: 0.8036 (tpp) cc_final: 0.7757 (tpp) REVERT: A 1428 MET cc_start: 0.8691 (ttt) cc_final: 0.8168 (tmm) REVERT: A 1459 MET cc_start: 0.8465 (mtm) cc_final: 0.8139 (mtm) REVERT: B 239 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7992 (ptm) REVERT: B 298 MET cc_start: 0.9202 (ttm) cc_final: 0.8757 (ttm) REVERT: B 300 MET cc_start: 0.8648 (tpp) cc_final: 0.8271 (tpp) REVERT: B 422 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7751 (t80) REVERT: B 508 MET cc_start: 0.9008 (mpt) cc_final: 0.8587 (mtt) REVERT: B 744 MET cc_start: 0.8621 (mmm) cc_final: 0.8049 (mtm) REVERT: B 1075 MET cc_start: 0.8668 (OUTLIER) cc_final: 0.8259 (mpp) REVERT: B 1106 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7831 (mpt180) REVERT: B 1172 MET cc_start: 0.8825 (mpt) cc_final: 0.8489 (mpp) REVERT: F 80 MET cc_start: 0.8054 (mmm) cc_final: 0.7523 (mmt) REVERT: F 88 ASP cc_start: 0.8065 (t0) cc_final: 0.7645 (t0) REVERT: H 13 LYS cc_start: 0.8898 (mmmm) cc_final: 0.8542 (mmmm) REVERT: H 75 TYR cc_start: 0.8431 (t80) cc_final: 0.8202 (t80) REVERT: H 87 GLN cc_start: 0.9019 (OUTLIER) cc_final: 0.8675 (mp10) REVERT: I 92 LYS cc_start: 0.8901 (pptt) cc_final: 0.8665 (pptt) REVERT: L 15 MET cc_start: 0.6997 (tpp) cc_final: 0.6606 (tpp) REVERT: L 38 GLU cc_start: 0.7581 (pm20) cc_final: 0.6928 (pm20) REVERT: Q 270 MET cc_start: 0.7648 (tmt) cc_final: 0.6832 (mmm) REVERT: Q 310 TYR cc_start: 0.4833 (OUTLIER) cc_final: 0.4345 (t80) REVERT: Q 350 MET cc_start: 0.5567 (mtp) cc_final: 0.5293 (mtp) REVERT: Q 736 CYS cc_start: 0.6973 (t) cc_final: 0.6659 (t) REVERT: Q 865 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8912 (tm) REVERT: R 493 GLU cc_start: 0.4157 (OUTLIER) cc_final: 0.3730 (mm-30) REVERT: R 498 GLU cc_start: 0.6077 (OUTLIER) cc_final: 0.5480 (pt0) REVERT: R 503 ARG cc_start: 0.0378 (tmm160) cc_final: -0.1465 (ttm170) REVERT: R 557 ILE cc_start: -0.4053 (mt) cc_final: -0.4539 (mt) REVERT: R 567 ASN cc_start: 0.0440 (m-40) cc_final: -0.0335 (t0) REVERT: R 582 GLU cc_start: -0.1831 (pt0) cc_final: -0.3008 (pp20) REVERT: W 234 TRP cc_start: 0.7326 (OUTLIER) cc_final: 0.6439 (m-10) REVERT: Y 42 MET cc_start: 0.2204 (pmm) cc_final: 0.1989 (pmm) REVERT: Y 64 MET cc_start: 0.3466 (ppp) cc_final: 0.3239 (ppp) REVERT: Z 222 LYS cc_start: 0.3776 (OUTLIER) cc_final: 0.3411 (mmtt) REVERT: Z 307 MET cc_start: -0.0039 (pmt) cc_final: -0.0341 (pmm) REVERT: Z 378 MET cc_start: 0.1798 (OUTLIER) cc_final: 0.0675 (ptp) REVERT: Z 460 MET cc_start: 0.1588 (tpp) cc_final: 0.0993 (tpp) REVERT: Z 508 MET cc_start: 0.0230 (mmm) cc_final: -0.0079 (mmm) REVERT: b 92 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8103 (tpp80) REVERT: d 46 HIS cc_start: 0.6544 (OUTLIER) cc_final: 0.6201 (m-70) REVERT: e 134 ARG cc_start: 0.7472 (ttp80) cc_final: 0.6907 (ttp80) outliers start: 96 outliers final: 31 residues processed: 401 average time/residue: 1.3818 time to fit residues: 738.2724 Evaluate side-chains 358 residues out of total 7356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 312 time to evaluate : 5.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain B residue 84 TYR Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 239 MET Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1106 ARG Chi-restraints excluded: chain B residue 1163 MET Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain Q residue 310 TYR Chi-restraints excluded: chain Q residue 466 ASN Chi-restraints excluded: chain Q residue 531 VAL Chi-restraints excluded: chain Q residue 669 VAL Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 714 HIS Chi-restraints excluded: chain Q residue 837 GLU Chi-restraints excluded: chain Q residue 865 LEU Chi-restraints excluded: chain R residue 493 GLU Chi-restraints excluded: chain R residue 498 GLU Chi-restraints excluded: chain V residue 66 LEU Chi-restraints excluded: chain W residue 234 TRP Chi-restraints excluded: chain W residue 241 CYS Chi-restraints excluded: chain X residue 234 ARG Chi-restraints excluded: chain Z residue 222 LYS Chi-restraints excluded: chain Z residue 378 MET Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain b residue 92 ARG Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 46 HIS Chi-restraints excluded: chain d residue 115 VAL Chi-restraints excluded: chain e residue 107 THR Chi-restraints excluded: chain g residue 107 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 799 optimal weight: 1.9990 chunk 93 optimal weight: 0.0270 chunk 472 optimal weight: 50.0000 chunk 605 optimal weight: 50.0000 chunk 469 optimal weight: 5.9990 chunk 697 optimal weight: 20.0000 chunk 463 optimal weight: 10.0000 chunk 826 optimal weight: 7.9990 chunk 516 optimal weight: 30.0000 chunk 503 optimal weight: 20.0000 chunk 381 optimal weight: 30.0000 overall best weight: 5.2048 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1021 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 114 HIS ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 420 GLN ** Q 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 575 HIS ** Q 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 672 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 762 GLN Q 834 GLN Z 607 HIS ** b 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 82 HIS ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6083 moved from start: 0.5576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.131 68399 Z= 0.537 Angle : 0.761 13.174 93650 Z= 0.402 Chirality : 0.047 0.236 10148 Planarity : 0.005 0.076 11378 Dihedral : 18.670 174.954 12684 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.31 % Favored : 93.65 % Rotamer: Outliers : 2.50 % Allowed : 14.04 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.06 % Twisted Proline : 0.29 % 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: -0.84 (0.09), residues: 8242 helix: 0.98 (0.09), residues: 3411 sheet: -1.74 (0.18), residues: 804 loop : -1.71 (0.09), residues: 4027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 27 HIS 0.010 0.002 HIS b 75 PHE 0.030 0.003 PHE K 58 TYR 0.033 0.002 TYR d 37 ARG 0.020 0.001 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16484 Ramachandran restraints generated. 8242 Oldfield, 0 Emsley, 8242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16484 Ramachandran restraints generated. 8242 Oldfield, 0 Emsley, 8242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 7356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 316 time to evaluate : 5.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8792 (mtp180) cc_final: 0.8378 (mtp-110) REVERT: A 136 GLN cc_start: 0.8069 (mp10) cc_final: 0.7707 (mp10) REVERT: A 266 MET cc_start: 0.2433 (OUTLIER) cc_final: 0.1989 (tmm) REVERT: A 470 MET cc_start: 0.8726 (mtm) cc_final: 0.8509 (mtt) REVERT: A 561 MET cc_start: 0.8535 (mtt) cc_final: 0.8318 (mtt) REVERT: A 868 MET cc_start: 0.8512 (mtp) cc_final: 0.7336 (ptp) REVERT: A 1228 MET cc_start: 0.8783 (mmm) cc_final: 0.8473 (mmt) REVERT: A 1344 MET cc_start: 0.8305 (tpp) cc_final: 0.7972 (tpp) REVERT: A 1428 MET cc_start: 0.8810 (ttt) cc_final: 0.8247 (tmm) REVERT: A 1459 MET cc_start: 0.8701 (mtm) cc_final: 0.8488 (mtm) REVERT: B 298 MET cc_start: 0.9280 (ttm) cc_final: 0.8845 (ttm) REVERT: B 550 MET cc_start: 0.9065 (OUTLIER) cc_final: 0.8129 (ppp) REVERT: B 744 MET cc_start: 0.8752 (mmm) cc_final: 0.8210 (mtm) REVERT: B 1075 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8366 (mpp) REVERT: B 1106 ARG cc_start: 0.8496 (OUTLIER) cc_final: 0.7860 (mpt180) REVERT: B 1163 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8524 (mtp) REVERT: B 1172 MET cc_start: 0.8790 (mpt) cc_final: 0.8569 (mpt) REVERT: D 74 PHE cc_start: 0.6378 (OUTLIER) cc_final: 0.5957 (p90) REVERT: F 80 MET cc_start: 0.7921 (mmm) cc_final: 0.7585 (mmt) REVERT: F 88 ASP cc_start: 0.8377 (t0) cc_final: 0.8113 (t0) REVERT: H 51 ASP cc_start: 0.8672 (OUTLIER) cc_final: 0.8271 (p0) REVERT: H 87 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.8711 (mp10) REVERT: I 92 LYS cc_start: 0.8940 (pptt) cc_final: 0.8713 (pptt) REVERT: L 31 ARG cc_start: 0.8938 (mmm160) cc_final: 0.8669 (tpm170) REVERT: Q 310 TYR cc_start: 0.4949 (OUTLIER) cc_final: 0.4508 (t80) REVERT: Q 865 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.8992 (tm) REVERT: R 493 GLU cc_start: 0.4326 (OUTLIER) cc_final: 0.3782 (mm-30) REVERT: R 498 GLU cc_start: 0.6065 (OUTLIER) cc_final: 0.5357 (pt0) REVERT: R 503 ARG cc_start: 0.0478 (tmm160) cc_final: -0.1506 (ttm170) REVERT: R 567 ASN cc_start: 0.0523 (m-40) cc_final: -0.0504 (t0) REVERT: R 582 GLU cc_start: -0.1698 (pt0) cc_final: -0.2993 (pp20) REVERT: R 597 ARG cc_start: -0.1210 (ptt-90) cc_final: -0.2281 (ptt180) REVERT: W 234 TRP cc_start: 0.7632 (OUTLIER) cc_final: 0.7061 (m-90) REVERT: Y 64 MET cc_start: 0.3455 (ppp) cc_final: 0.3098 (ppp) REVERT: Z 222 LYS cc_start: 0.4278 (OUTLIER) cc_final: 0.3950 (mmtt) REVERT: Z 307 MET cc_start: 0.0151 (pmt) cc_final: -0.0180 (pmm) REVERT: Z 378 MET cc_start: 0.1644 (OUTLIER) cc_final: 0.0532 (ptp) REVERT: c 110 ASN cc_start: 0.9003 (t0) cc_final: 0.8601 (p0) REVERT: c 118 LYS cc_start: 0.8501 (OUTLIER) cc_final: 0.6204 (tmtt) REVERT: d 46 HIS cc_start: 0.6786 (OUTLIER) cc_final: 0.6422 (m-70) REVERT: d 59 MET cc_start: 0.8839 (tpp) cc_final: 0.8499 (mmm) outliers start: 138 outliers final: 43 residues processed: 422 average time/residue: 1.4161 time to fit residues: 806.8778 Evaluate side-chains 363 residues out of total 7356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 303 time to evaluate : 5.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1210 TRP Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 279 VAL Chi-restraints excluded: chain B residue 347 MET Chi-restraints excluded: chain B residue 388 TYR Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 1043 ILE Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1106 ARG Chi-restraints excluded: chain B residue 1163 MET Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 121 MET Chi-restraints excluded: chain E residue 173 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain Q residue 310 TYR Chi-restraints excluded: chain Q residue 466 ASN Chi-restraints excluded: chain Q residue 531 VAL Chi-restraints excluded: chain Q residue 603 SER Chi-restraints excluded: chain Q residue 669 VAL Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 714 HIS Chi-restraints excluded: chain Q residue 717 THR Chi-restraints excluded: chain Q residue 837 GLU Chi-restraints excluded: chain Q residue 865 LEU Chi-restraints excluded: chain R residue 493 GLU Chi-restraints excluded: chain R residue 498 GLU Chi-restraints excluded: chain W residue 234 TRP Chi-restraints excluded: chain W residue 241 CYS Chi-restraints excluded: chain Y residue 36 CYS Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Z residue 222 LYS Chi-restraints excluded: chain Z residue 378 MET Chi-restraints excluded: chain Z residue 429 CYS Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 118 LYS Chi-restraints excluded: chain d residue 45 VAL Chi-restraints excluded: chain d residue 46 HIS Chi-restraints excluded: chain f residue 63 GLU Chi-restraints excluded: chain g residue 107 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 511 optimal weight: 7.9990 chunk 329 optimal weight: 7.9990 chunk 493 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 525 optimal weight: 10.0000 chunk 562 optimal weight: 0.2980 chunk 408 optimal weight: 50.0000 chunk 76 optimal weight: 3.9990 chunk 649 optimal weight: 1.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 GLN ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 420 GLN Q 487 HIS ** Q 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 834 GLN Z 272 ASN Z 632 ASN ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6007 moved from start: 0.5626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 68399 Z= 0.233 Angle : 0.604 15.584 93650 Z= 0.315 Chirality : 0.042 0.225 10148 Planarity : 0.004 0.063 11378 Dihedral : 18.720 176.202 12682 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.61 % Favored : 95.37 % Rotamer: Outliers : 1.57 % Allowed : 15.40 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.06 % Twisted Proline : 0.29 % 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 (0.09), residues: 8242 helix: 1.31 (0.09), residues: 3397 sheet: -1.61 (0.18), residues: 787 loop : -1.56 (0.09), residues: 4058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 176 HIS 0.008 0.001 HIS f 75 PHE 0.025 0.001 PHE Q 335 TYR 0.024 0.001 TYR B 766 ARG 0.010 0.000 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16484 Ramachandran restraints generated. 8242 Oldfield, 0 Emsley, 8242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16484 Ramachandran restraints generated. 8242 Oldfield, 0 Emsley, 8242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 7356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 318 time to evaluate : 5.430 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 67 ARG cc_start: 0.8755 (mtp180) cc_final: 0.8273 (mtp-110) REVERT: A 266 MET cc_start: 0.2299 (OUTLIER) cc_final: 0.1994 (tmm) REVERT: A 470 MET cc_start: 0.8754 (mtm) cc_final: 0.8421 (mtt) REVERT: A 501 MET cc_start: 0.8100 (mtp) cc_final: 0.6170 (mmt) REVERT: A 561 MET cc_start: 0.8260 (mtt) cc_final: 0.7913 (mtt) REVERT: A 868 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.7525 (ptp) REVERT: A 1221 MET cc_start: 0.8883 (ttt) cc_final: 0.8544 (ttt) REVERT: A 1228 MET cc_start: 0.8766 (mmm) cc_final: 0.8540 (mmm) REVERT: A 1344 MET cc_start: 0.8137 (tpp) cc_final: 0.7850 (tpp) REVERT: A 1428 MET cc_start: 0.8726 (ttt) cc_final: 0.8134 (tmm) REVERT: A 1459 MET cc_start: 0.8512 (mtm) cc_final: 0.8286 (mtm) REVERT: B 200 MET cc_start: 0.8654 (tpp) cc_final: 0.8317 (tpt) REVERT: B 239 MET cc_start: 0.8297 (ptm) cc_final: 0.8077 (ptm) REVERT: B 298 MET cc_start: 0.9222 (ttm) cc_final: 0.8748 (ttm) REVERT: B 508 MET cc_start: 0.9042 (mpt) cc_final: 0.8633 (mtt) REVERT: B 550 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8150 (ppp) REVERT: B 744 MET cc_start: 0.8618 (mmm) cc_final: 0.8007 (mtm) REVERT: B 1075 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8342 (mpp) REVERT: B 1106 ARG cc_start: 0.8397 (OUTLIER) cc_final: 0.7844 (mpt180) REVERT: B 1172 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.8506 (mpt) REVERT: D 74 PHE cc_start: 0.6142 (OUTLIER) cc_final: 0.5784 (p90) REVERT: E 110 MET cc_start: 0.5338 (mtm) cc_final: 0.5118 (mtt) REVERT: F 80 MET cc_start: 0.7887 (mmm) cc_final: 0.7473 (mmt) REVERT: F 88 ASP cc_start: 0.8181 (t0) cc_final: 0.7764 (t0) REVERT: G 84 VAL cc_start: 0.7874 (OUTLIER) cc_final: 0.7566 (p) REVERT: G 131 MET cc_start: 0.3110 (tmm) cc_final: 0.2005 (tpt) REVERT: G 164 MET cc_start: 0.6344 (mpt) cc_final: 0.6122 (mmm) REVERT: H 13 LYS cc_start: 0.8899 (mmmm) cc_final: 0.8665 (mmmm) REVERT: H 75 TYR cc_start: 0.8410 (t80) cc_final: 0.8179 (t80) REVERT: H 87 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8582 (mp10) REVERT: I 92 LYS cc_start: 0.8950 (pptt) cc_final: 0.8734 (pptt) REVERT: L 15 MET cc_start: 0.6941 (tpp) cc_final: 0.6562 (tpp) REVERT: L 31 ARG cc_start: 0.8877 (mmm160) cc_final: 0.8635 (tpm170) REVERT: L 38 GLU cc_start: 0.7714 (pm20) cc_final: 0.7349 (pm20) REVERT: L 44 MET cc_start: 0.8183 (tmm) cc_final: 0.7941 (tmm) REVERT: Q 270 MET cc_start: 0.7808 (tmm) cc_final: 0.6977 (mmm) REVERT: Q 310 TYR cc_start: 0.5002 (OUTLIER) cc_final: 0.4430 (t80) REVERT: Q 865 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8954 (tm) REVERT: R 498 GLU cc_start: 0.5783 (OUTLIER) cc_final: 0.5124 (pt0) REVERT: R 503 ARG cc_start: 0.0319 (tmm160) cc_final: -0.2915 (ttt180) REVERT: R 557 ILE cc_start: -0.4154 (mt) cc_final: -0.4548 (mt) REVERT: R 567 ASN cc_start: 0.0445 (m-40) cc_final: -0.0327 (t0) REVERT: R 582 GLU cc_start: -0.1691 (pt0) cc_final: -0.2838 (pp20) REVERT: W 234 TRP cc_start: 0.7423 (OUTLIER) cc_final: 0.6821 (m-10) REVERT: Y 48 MET cc_start: 0.1243 (ppp) cc_final: -0.0086 (ttt) REVERT: Y 64 MET cc_start: 0.3669 (ppp) cc_final: 0.3351 (ppp) REVERT: Z 222 LYS cc_start: 0.4348 (OUTLIER) cc_final: 0.4088 (mmtt) REVERT: Z 307 MET cc_start: 0.0147 (pmt) cc_final: -0.0160 (pmm) REVERT: Z 460 MET cc_start: 0.1714 (tpp) cc_final: 0.1002 (tpp) REVERT: a 90 MET cc_start: 0.8520 (mmp) cc_final: 0.8253 (mmp) REVERT: c 110 ASN cc_start: 0.9014 (t0) cc_final: 0.8628 (p0) REVERT: c 118 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.6257 (tmtt) REVERT: d 46 HIS cc_start: 0.6560 (OUTLIER) cc_final: 0.6191 (m-70) REVERT: d 59 MET cc_start: 0.8773 (tpp) cc_final: 0.8466 (mmm) REVERT: e 134 ARG cc_start: 0.7667 (ttp80) cc_final: 0.7182 (ppp80) outliers start: 87 outliers final: 31 residues processed: 386 average time/residue: 1.4096 time to fit residues: 720.6061 Evaluate side-chains 353 residues out of total 7356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 306 time to evaluate : 5.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1106 ARG Chi-restraints excluded: chain B residue 1163 MET Chi-restraints excluded: chain B residue 1172 MET Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain Q residue 310 TYR Chi-restraints excluded: chain Q residue 340 PHE Chi-restraints excluded: chain Q residue 466 ASN Chi-restraints excluded: chain Q residue 531 VAL Chi-restraints excluded: chain Q residue 669 VAL Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 714 HIS Chi-restraints excluded: chain Q residue 837 GLU Chi-restraints excluded: chain Q residue 865 LEU Chi-restraints excluded: chain R residue 496 VAL Chi-restraints excluded: chain R residue 498 GLU Chi-restraints excluded: chain W residue 234 TRP Chi-restraints excluded: chain W residue 241 CYS Chi-restraints excluded: chain Z residue 222 LYS Chi-restraints excluded: chain Z residue 429 CYS Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 118 LYS Chi-restraints excluded: chain d residue 46 HIS Chi-restraints excluded: chain d residue 95 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 751 optimal weight: 30.0000 chunk 791 optimal weight: 0.6980 chunk 721 optimal weight: 10.0000 chunk 769 optimal weight: 20.0000 chunk 463 optimal weight: 0.0570 chunk 335 optimal weight: 0.9980 chunk 604 optimal weight: 30.0000 chunk 236 optimal weight: 0.7980 chunk 695 optimal weight: 8.9990 chunk 728 optimal weight: 20.0000 chunk 767 optimal weight: 40.0000 overall best weight: 2.3100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 420 GLN ** Q 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 756 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 781 ASN ** R 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6028 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 68399 Z= 0.277 Angle : 0.614 13.208 93650 Z= 0.321 Chirality : 0.042 0.212 10148 Planarity : 0.004 0.072 11378 Dihedral : 18.659 177.435 12682 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.64 % Favored : 94.33 % Rotamer: Outliers : 1.38 % Allowed : 15.87 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.06 % Twisted Proline : 0.29 % 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: -0.44 (0.09), residues: 8242 helix: 1.37 (0.09), residues: 3405 sheet: -1.62 (0.18), residues: 764 loop : -1.51 (0.10), residues: 4073 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 27 HIS 0.006 0.001 HIS f 75 PHE 0.026 0.002 PHE Q 335 TYR 0.026 0.001 TYR B 766 ARG 0.013 0.000 ARG X 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16484 Ramachandran restraints generated. 8242 Oldfield, 0 Emsley, 8242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16484 Ramachandran restraints generated. 8242 Oldfield, 0 Emsley, 8242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 7356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 317 time to evaluate : 5.393 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 67 ARG cc_start: 0.8700 (mtp180) cc_final: 0.8247 (mtp-110) REVERT: A 470 MET cc_start: 0.8526 (mtm) cc_final: 0.8174 (mtt) REVERT: A 501 MET cc_start: 0.8149 (mtp) cc_final: 0.7848 (mmm) REVERT: A 561 MET cc_start: 0.8064 (mtt) cc_final: 0.7639 (mtt) REVERT: A 1221 MET cc_start: 0.8892 (ttt) cc_final: 0.8556 (ttt) REVERT: A 1344 MET cc_start: 0.8188 (tpp) cc_final: 0.7882 (tpp) REVERT: A 1428 MET cc_start: 0.8716 (ttt) cc_final: 0.8145 (tmm) REVERT: A 1459 MET cc_start: 0.8558 (mtm) cc_final: 0.8316 (mtm) REVERT: B 200 MET cc_start: 0.8551 (tpp) cc_final: 0.8171 (tpt) REVERT: B 239 MET cc_start: 0.8335 (ptm) cc_final: 0.8125 (ptm) REVERT: B 298 MET cc_start: 0.9235 (ttm) cc_final: 0.8777 (ttm) REVERT: B 550 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8523 (ttt) REVERT: B 744 MET cc_start: 0.8722 (mmm) cc_final: 0.8107 (mtm) REVERT: B 1075 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8383 (mpp) REVERT: B 1106 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7871 (mpt180) REVERT: B 1163 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8444 (mtp) REVERT: B 1172 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8437 (mpt) REVERT: D 74 PHE cc_start: 0.6219 (OUTLIER) cc_final: 0.5860 (p90) REVERT: E 110 MET cc_start: 0.5263 (mtm) cc_final: 0.4997 (mtt) REVERT: E 168 ASN cc_start: 0.9013 (t0) cc_final: 0.8664 (p0) REVERT: F 80 MET cc_start: 0.7900 (mmm) cc_final: 0.7485 (mmt) REVERT: F 88 ASP cc_start: 0.8199 (t0) cc_final: 0.7849 (t0) REVERT: G 164 MET cc_start: 0.6514 (mpt) cc_final: 0.6255 (mmm) REVERT: H 75 TYR cc_start: 0.8489 (t80) cc_final: 0.8229 (t80) REVERT: H 87 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8605 (mp10) REVERT: I 92 LYS cc_start: 0.8926 (pptt) cc_final: 0.8726 (pptt) REVERT: K 111 ASP cc_start: 0.9206 (t70) cc_final: 0.8816 (t0) REVERT: L 15 MET cc_start: 0.6993 (tpp) cc_final: 0.6605 (tpp) REVERT: L 31 ARG cc_start: 0.8898 (mmm160) cc_final: 0.8639 (tpm170) REVERT: L 38 GLU cc_start: 0.7611 (pm20) cc_final: 0.7074 (pm20) REVERT: Q 310 TYR cc_start: 0.4959 (OUTLIER) cc_final: 0.4391 (t80) REVERT: R 493 GLU cc_start: 0.3833 (mm-30) cc_final: 0.3564 (mm-30) REVERT: R 498 GLU cc_start: 0.5241 (OUTLIER) cc_final: 0.4554 (pt0) REVERT: R 503 ARG cc_start: 0.0202 (tmm160) cc_final: -0.1341 (ttm110) REVERT: R 557 ILE cc_start: -0.3957 (mt) cc_final: -0.4374 (mt) REVERT: R 567 ASN cc_start: 0.0189 (m-40) cc_final: -0.0842 (t160) REVERT: R 582 GLU cc_start: -0.1390 (pt0) cc_final: -0.2599 (pp20) REVERT: R 586 MET cc_start: -0.1898 (mtt) cc_final: -0.2971 (mmt) REVERT: W 234 TRP cc_start: 0.7546 (OUTLIER) cc_final: 0.7102 (m-10) REVERT: Y 48 MET cc_start: 0.1207 (ppp) cc_final: -0.0295 (ttt) REVERT: Y 64 MET cc_start: 0.3710 (ppp) cc_final: 0.3394 (ppp) REVERT: Z 307 MET cc_start: 0.0185 (pmt) cc_final: -0.0099 (pmm) REVERT: Z 460 MET cc_start: 0.1574 (tpp) cc_final: 0.1009 (tpp) REVERT: a 90 MET cc_start: 0.8573 (mmp) cc_final: 0.8277 (mmp) REVERT: b 23 ARG cc_start: 0.6256 (ppt90) cc_final: 0.6043 (ppt90) REVERT: c 110 ASN cc_start: 0.9018 (t0) cc_final: 0.8630 (p0) REVERT: c 118 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.6425 (tmtt) REVERT: d 59 MET cc_start: 0.8785 (tpp) cc_final: 0.8492 (mmm) outliers start: 76 outliers final: 35 residues processed: 376 average time/residue: 1.3768 time to fit residues: 691.4016 Evaluate side-chains 356 residues out of total 7356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 310 time to evaluate : 5.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1106 ARG Chi-restraints excluded: chain B residue 1163 MET Chi-restraints excluded: chain B residue 1172 MET Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain Q residue 310 TYR Chi-restraints excluded: chain Q residue 340 PHE Chi-restraints excluded: chain Q residue 466 ASN Chi-restraints excluded: chain Q residue 531 VAL Chi-restraints excluded: chain Q residue 669 VAL Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 714 HIS Chi-restraints excluded: chain Q residue 837 GLU Chi-restraints excluded: chain R residue 495 ILE Chi-restraints excluded: chain R residue 498 GLU Chi-restraints excluded: chain W residue 234 TRP Chi-restraints excluded: chain W residue 241 CYS Chi-restraints excluded: chain Y residue 36 CYS Chi-restraints excluded: chain Z residue 429 CYS Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 118 LYS Chi-restraints excluded: chain d residue 95 VAL Chi-restraints excluded: chain e residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 505 optimal weight: 7.9990 chunk 813 optimal weight: 0.3980 chunk 496 optimal weight: 50.0000 chunk 386 optimal weight: 40.0000 chunk 565 optimal weight: 0.9990 chunk 853 optimal weight: 1.9990 chunk 785 optimal weight: 50.0000 chunk 679 optimal weight: 40.0000 chunk 70 optimal weight: 0.9980 chunk 525 optimal weight: 40.0000 chunk 416 optimal weight: 50.0000 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 HIS G 111 HIS ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 420 GLN Q 490 HIS ** Q 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 221 HIS ** X 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 27 GLN a 76 GLN ** c 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6037 moved from start: 0.6168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 68399 Z= 0.282 Angle : 0.625 13.539 93650 Z= 0.325 Chirality : 0.042 0.208 10148 Planarity : 0.004 0.064 11378 Dihedral : 18.717 179.348 12682 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.91 % Favored : 95.07 % Rotamer: Outliers : 1.12 % Allowed : 16.23 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.06 % Twisted Proline : 0.29 % 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: -0.40 (0.09), residues: 8242 helix: 1.39 (0.09), residues: 3402 sheet: -1.52 (0.18), residues: 758 loop : -1.50 (0.09), residues: 4082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 653 HIS 0.007 0.001 HIS f 75 PHE 0.028 0.002 PHE R 487 TYR 0.033 0.001 TYR B 766 ARG 0.011 0.001 ARG X 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16484 Ramachandran restraints generated. 8242 Oldfield, 0 Emsley, 8242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16484 Ramachandran restraints generated. 8242 Oldfield, 0 Emsley, 8242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 7356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 314 time to evaluate : 5.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ARG cc_start: 0.8693 (mtp180) cc_final: 0.8242 (mtp-110) REVERT: A 470 MET cc_start: 0.8485 (mtm) cc_final: 0.8059 (mtt) REVERT: A 501 MET cc_start: 0.8155 (mtp) cc_final: 0.6155 (mmt) REVERT: A 561 MET cc_start: 0.8063 (mtt) cc_final: 0.7566 (mtt) REVERT: A 1228 MET cc_start: 0.8955 (mmt) cc_final: 0.8753 (mmt) REVERT: A 1344 MET cc_start: 0.8180 (tpp) cc_final: 0.7616 (tpt) REVERT: A 1428 MET cc_start: 0.8735 (ttt) cc_final: 0.8168 (tmm) REVERT: A 1459 MET cc_start: 0.8596 (mtm) cc_final: 0.8337 (mtm) REVERT: B 200 MET cc_start: 0.8507 (tpp) cc_final: 0.8128 (tpt) REVERT: B 298 MET cc_start: 0.9202 (ttm) cc_final: 0.8788 (ttm) REVERT: B 550 MET cc_start: 0.8929 (OUTLIER) cc_final: 0.8571 (ttt) REVERT: B 744 MET cc_start: 0.8725 (mmm) cc_final: 0.8125 (mtm) REVERT: B 954 MET cc_start: 0.8912 (mmm) cc_final: 0.8678 (mmp) REVERT: B 1075 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8358 (mpp) REVERT: B 1106 ARG cc_start: 0.8427 (OUTLIER) cc_final: 0.7839 (mpt180) REVERT: B 1163 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8452 (mtp) REVERT: B 1172 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8376 (mpt) REVERT: D 74 PHE cc_start: 0.6231 (OUTLIER) cc_final: 0.5836 (p90) REVERT: F 80 MET cc_start: 0.7949 (mmm) cc_final: 0.7506 (mmt) REVERT: F 88 ASP cc_start: 0.8192 (t0) cc_final: 0.7839 (t0) REVERT: F 94 MET cc_start: 0.9122 (tpt) cc_final: 0.8864 (tpp) REVERT: G 84 VAL cc_start: 0.7980 (OUTLIER) cc_final: 0.7734 (p) REVERT: G 131 MET cc_start: 0.2687 (tmm) cc_final: 0.1583 (tpt) REVERT: H 13 LYS cc_start: 0.8922 (mmmm) cc_final: 0.8562 (mmmm) REVERT: H 51 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.8310 (p0) REVERT: H 75 TYR cc_start: 0.8500 (t80) cc_final: 0.8241 (t80) REVERT: H 87 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8571 (mp10) REVERT: I 92 LYS cc_start: 0.8939 (pptt) cc_final: 0.8726 (pptt) REVERT: K 111 ASP cc_start: 0.9214 (t70) cc_final: 0.8819 (t0) REVERT: L 15 MET cc_start: 0.6959 (tpp) cc_final: 0.6628 (tpp) REVERT: L 28 ILE cc_start: 0.9397 (mm) cc_final: 0.9156 (mp) REVERT: L 31 ARG cc_start: 0.8906 (mmm160) cc_final: 0.8631 (tpm170) REVERT: Q 310 TYR cc_start: 0.5054 (OUTLIER) cc_final: 0.4408 (t80) REVERT: Q 754 MET cc_start: 0.7157 (pmm) cc_final: 0.6846 (pmm) REVERT: R 493 GLU cc_start: 0.3887 (mm-30) cc_final: 0.3475 (mm-30) REVERT: R 498 GLU cc_start: 0.5278 (OUTLIER) cc_final: 0.4847 (pt0) REVERT: R 499 LYS cc_start: 0.2552 (pttt) cc_final: 0.1199 (pptt) REVERT: R 503 ARG cc_start: 0.0118 (tmm160) cc_final: -0.2211 (ttm170) REVERT: R 557 ILE cc_start: -0.4039 (mt) cc_final: -0.4400 (mt) REVERT: R 567 ASN cc_start: 0.0199 (m-40) cc_final: -0.0761 (t160) REVERT: R 582 GLU cc_start: -0.1518 (pt0) cc_final: -0.2736 (pp20) REVERT: R 597 ARG cc_start: -0.1347 (ptt-90) cc_final: -0.2497 (ptt180) REVERT: W 221 HIS cc_start: 0.5551 (OUTLIER) cc_final: 0.5257 (p90) REVERT: W 234 TRP cc_start: 0.7503 (OUTLIER) cc_final: 0.7039 (m-10) REVERT: Y 48 MET cc_start: 0.1247 (ppp) cc_final: -0.0294 (ttt) REVERT: Y 64 MET cc_start: 0.3622 (ppp) cc_final: 0.3318 (ppp) REVERT: Z 307 MET cc_start: 0.0188 (pmt) cc_final: -0.0066 (pmm) REVERT: Z 460 MET cc_start: 0.1565 (tpp) cc_final: 0.1255 (tpp) REVERT: a 90 MET cc_start: 0.8602 (mmp) cc_final: 0.8318 (mmp) REVERT: b 84 MET cc_start: 0.8094 (mmm) cc_final: 0.7374 (mmm) REVERT: c 110 ASN cc_start: 0.9023 (t0) cc_final: 0.8622 (p0) REVERT: c 118 LYS cc_start: 0.8659 (OUTLIER) cc_final: 0.6595 (tmtt) REVERT: d 59 MET cc_start: 0.8816 (tpp) cc_final: 0.8513 (mmm) outliers start: 62 outliers final: 38 residues processed: 363 average time/residue: 1.3996 time to fit residues: 679.3937 Evaluate side-chains 357 residues out of total 7356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 305 time to evaluate : 5.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 978 VAL Chi-restraints excluded: chain A residue 1175 ILE Chi-restraints excluded: chain A residue 1262 MET Chi-restraints excluded: chain B residue 108 MET Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 422 PHE Chi-restraints excluded: chain B residue 520 VAL Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 565 THR Chi-restraints excluded: chain B residue 596 ILE Chi-restraints excluded: chain B residue 746 THR Chi-restraints excluded: chain B residue 1055 VAL Chi-restraints excluded: chain B residue 1075 MET Chi-restraints excluded: chain B residue 1106 ARG Chi-restraints excluded: chain B residue 1163 MET Chi-restraints excluded: chain B residue 1172 MET Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 74 PHE Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain E residue 29 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 84 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 87 GLN Chi-restraints excluded: chain L residue 34 ILE Chi-restraints excluded: chain Q residue 310 TYR Chi-restraints excluded: chain Q residue 340 PHE Chi-restraints excluded: chain Q residue 380 ILE Chi-restraints excluded: chain Q residue 466 ASN Chi-restraints excluded: chain Q residue 531 VAL Chi-restraints excluded: chain Q residue 669 VAL Chi-restraints excluded: chain Q residue 707 CYS Chi-restraints excluded: chain Q residue 714 HIS Chi-restraints excluded: chain Q residue 837 GLU Chi-restraints excluded: chain R residue 495 ILE Chi-restraints excluded: chain R residue 498 GLU Chi-restraints excluded: chain W residue 221 HIS Chi-restraints excluded: chain W residue 234 TRP Chi-restraints excluded: chain W residue 241 CYS Chi-restraints excluded: chain Z residue 429 CYS Chi-restraints excluded: chain a residue 124 ILE Chi-restraints excluded: chain b residue 50 ILE Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain c residue 118 LYS Chi-restraints excluded: chain d residue 95 VAL Chi-restraints excluded: chain d residue 115 VAL Chi-restraints excluded: chain e residue 107 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 857 random chunks: chunk 540 optimal weight: 6.9990 chunk 724 optimal weight: 9.9990 chunk 208 optimal weight: 0.9980 chunk 626 optimal weight: 7.9990 chunk 100 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 680 optimal weight: 40.0000 chunk 284 optimal weight: 2.9990 chunk 699 optimal weight: 8.9990 chunk 86 optimal weight: 0.9990 chunk 125 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 449 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 400 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 573 ASN ** Q 585 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 73 ASN ** d 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.091766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.068554 restraints weight = 381673.663| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 5.51 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 393 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 393 | |-----------------------------------------------------------------------------| r_final: 0.3696 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.6268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 68399 Z= 0.246 Angle : 0.612 12.743 93650 Z= 0.319 Chirality : 0.042 0.232 10148 Planarity : 0.004 0.068 11378 Dihedral : 18.708 178.987 12682 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.21 % Favored : 94.78 % Rotamer: Outliers : 1.23 % Allowed : 16.23 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.59 % Cis-general : 0.06 % Twisted Proline : 0.29 % 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: -0.31 (0.09), residues: 8242 helix: 1.45 (0.09), residues: 3416 sheet: -1.43 (0.19), residues: 763 loop : -1.46 (0.10), residues: 4063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 99 HIS 0.018 0.001 HIS W 221 PHE 0.027 0.001 PHE Q 335 TYR 0.030 0.001 TYR B 766 ARG 0.011 0.000 ARG X 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16015.03 seconds wall clock time: 280 minutes 0.34 seconds (16800.34 seconds total)