Starting phenix.real_space_refine on Mon Sep 30 09:37:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etj_24396/09_2024/8etj_24396.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etj_24396/09_2024/8etj_24396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etj_24396/09_2024/8etj_24396.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etj_24396/09_2024/8etj_24396.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etj_24396/09_2024/8etj_24396.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8etj_24396/09_2024/8etj_24396.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1961 5.49 5 S 99 5.16 5 C 42587 2.51 5 N 14882 2.21 5 O 20327 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 79857 Number of models: 1 Model: "" Number of chains: 36 Chain: "1" Number of atoms: 38913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1817, 38913 Classifications: {'RNA': 1817} Modifications used: {'rna2p_pur': 191, 'rna2p_pyr': 124, 'rna3p_pur': 839, 'rna3p_pyr': 663} Link IDs: {'rna2p': 314, 'rna3p': 1502} Chain breaks: 23 Chain: "2" Number of atoms: 3069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 3069 Classifications: {'RNA': 144} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 8, 'rna3p_pur': 62, 'rna3p_pyr': 59} Link IDs: {'rna2p': 23, 'rna3p': 120} Chain breaks: 3 Chain: "3" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1042 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "B" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2662 Classifications: {'peptide': 335} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 321} Chain breaks: 1 Chain: "C" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2553 Classifications: {'peptide': 325} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 307} Chain breaks: 1 Chain: "E" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1283 Classifications: {'peptide': 165} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 152} Chain: "F" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1750 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 10, 'TRANS': 206} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 1307 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 168, 1291 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 160} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Conformer: "B" Number of residues, atoms: 168, 1291 Classifications: {'peptide': 168} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 160} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 bond proxies already assigned to first conformer: 1290 Chain: "H" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1451 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain: "L" Number of atoms: 1427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1427 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 11, 'TRANS': 168} Chain: "M" Number of atoms: 1007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1007 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "N" Number of atoms: 1406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1406 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain breaks: 2 Chain: "O" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1557 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 186} Chain: "P" Number of atoms: 1220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1220 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain breaks: 2 Chain: "Q" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1032 Classifications: {'peptide': 133} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 5, 'TRANS': 127} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 278 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 2, 'TRANS': 53} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 178 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 147 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 84 Chain: "S" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1408 Classifications: {'peptide': 168} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 156} Chain breaks: 1 Chain: "V" Number of atoms: 1026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1026 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 129} Chain: "W" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1057 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 180} Link IDs: {'PTRANS': 8, 'TRANS': 206} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 670 Unresolved non-hydrogen angles: 855 Unresolved non-hydrogen dihedrals: 564 Unresolved non-hydrogen chiralities: 65 Planarities with less than four sites: {'GLN:plan1': 10, 'HIS:plan': 6, 'TYR:plan': 6, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 13, 'GLU:plan': 11, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 346 Chain: "Y" Number of atoms: 998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 998 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 4, 'TRANS': 120} Chain: "a" Number of atoms: 747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 747 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain breaks: 1 Chain: "b" Number of atoms: 2837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 2837 Classifications: {'peptide': 415} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'PTRANS': 17, 'TRANS': 397} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 512 Unresolved non-hydrogen angles: 660 Unresolved non-hydrogen dihedrals: 417 Unresolved non-hydrogen chiralities: 60 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 3, 'TYR:plan': 7, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 11, 'PHE:plan': 6, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 246 Chain: "d" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 810 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain breaks: 1 Chain: "e" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 944 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "f" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 839 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "h" Number of atoms: 999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 999 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "i" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 748 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "j" Number of atoms: 563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 563 Classifications: {'peptide': 71} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 68} Chain: "r" Number of atoms: 1086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1086 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 82} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 282 Unresolved non-hydrogen angles: 358 Unresolved non-hydrogen dihedrals: 226 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 119 Chain: "s" Number of atoms: 257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 257 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "u" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 944 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "w" Number of atoms: 521 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 104, 516 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 3, 'TRANS': 100} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 347 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 11, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 198 Conformer: "B" Number of residues, atoms: 104, 516 Classifications: {'peptide': 104} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 3, 'TRANS': 100} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 347 Unresolved non-hydrogen angles: 442 Unresolved non-hydrogen dihedrals: 283 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 11, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 198 bond proxies already assigned to first conformer: 509 Chain: "y" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1697 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "z" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 292 Classifications: {'peptide': 35} Link IDs: {'PTRANS': 1, 'TRANS': 33} Chain: "T" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 126 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 2, 'TRANS': 13} Chain: "j" 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 74416 SG CYS j 19 102.156 110.610 169.175 1.00 64.08 S ATOM 74444 SG CYS j 22 104.321 111.786 166.256 1.00 65.72 S ATOM 74540 SG CYS j 34 103.712 108.119 166.669 1.00 70.97 S ATOM 74557 SG CYS j 37 105.785 109.789 169.278 1.00 62.80 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AASN G 182 " occ=0.62 ... (14 atoms not shown) pdb=" ND2BASN G 182 " occ=0.38 residue: pdb=" N AASP G 227 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP G 227 " occ=0.50 residue: pdb=" N AGLU w 243 " occ=0.50 ... (8 atoms not shown) pdb=" CB BGLU w 243 " occ=0.50 Time building chain proxies: 33.62, per 1000 atoms: 0.42 Number of scatterers: 79857 At special positions: 0 Unit cell: (217.3, 178.08, 256.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 99 16.00 P 1961 15.00 O 20327 8.00 N 14882 7.00 C 42587 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: 15.04 Conformation dependent library (CDL) restraints added in 4.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " Number of angles added : 6 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9394 Finding SS restraints... Secondary structure from input PDB file: 199 helices and 57 sheets defined 43.2% alpha, 14.2% beta 586 base pairs and 1132 stacking pairs defined. Time for finding SS restraints: 28.25 Creating SS restraints... Processing helix chain '3' and resid 3 through 12 Processing helix chain '3' and resid 72 through 77 removed outlier: 4.558A pdb=" N TRP 3 77 " --> pdb=" O PRO 3 73 " (cutoff:3.500A) Processing helix chain '3' and resid 85 through 96 Processing helix chain '3' and resid 104 through 124 removed outlier: 3.752A pdb=" N GLN 3 110 " --> pdb=" O HIS 3 106 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR 3 113 " --> pdb=" O LYS 3 109 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ARG 3 114 " --> pdb=" O GLN 3 110 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU 3 119 " --> pdb=" O LEU 3 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 17 removed outlier: 4.035A pdb=" N PHE B 16 " --> pdb=" O SER B 13 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU B 17 " --> pdb=" O LEU B 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 13 through 17' Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 130 through 140 Processing helix chain 'B' and resid 141 through 155 Processing helix chain 'B' and resid 187 through 197 Processing helix chain 'B' and resid 204 through 208 Processing helix chain 'B' and resid 347 through 352 Processing helix chain 'B' and resid 372 through 380 Processing helix chain 'C' and resid 25 through 30 Processing helix chain 'C' and resid 33 through 45 Processing helix chain 'C' and resid 46 through 49 removed outlier: 3.738A pdb=" N ARG C 49 " --> pdb=" O LYS C 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 46 through 49' Processing helix chain 'C' and resid 116 through 131 Processing helix chain 'C' and resid 133 through 141 Processing helix chain 'C' and resid 156 through 161 Processing helix chain 'C' and resid 163 through 174 Processing helix chain 'C' and resid 177 through 186 Processing helix chain 'C' and resid 194 through 198 removed outlier: 4.095A pdb=" N ASN C 198 " --> pdb=" O LYS C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 222 Processing helix chain 'C' and resid 241 through 245 Processing helix chain 'C' and resid 254 through 265 removed outlier: 4.872A pdb=" N ASP C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N SER C 262 " --> pdb=" O GLY C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 294 Processing helix chain 'C' and resid 295 through 300 Processing helix chain 'C' and resid 323 through 331 removed outlier: 3.576A pdb=" N LEU C 327 " --> pdb=" O ASN C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 337 removed outlier: 4.186A pdb=" N TYR C 337 " --> pdb=" O ALA C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 Processing helix chain 'E' and resid 62 through 66 removed outlier: 3.996A pdb=" N PHE E 65 " --> pdb=" O ALA E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 125 Processing helix chain 'E' and resid 137 through 142 Processing helix chain 'E' and resid 150 through 171 removed outlier: 3.902A pdb=" N ILE E 154 " --> pdb=" O PRO E 150 " (cutoff:3.500A) Proline residue: E 166 - end of helix removed outlier: 3.709A pdb=" N ILE E 171 " --> pdb=" O ALA E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 180 Processing helix chain 'F' and resid 36 through 80 Processing helix chain 'F' and resid 103 through 114 Processing helix chain 'F' and resid 127 through 135 removed outlier: 3.708A pdb=" N GLN F 135 " --> pdb=" O LYS F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 139 Proline residue: F 139 - end of helix No H-bonds generated for 'chain 'F' and resid 136 through 139' Processing helix chain 'F' and resid 147 through 159 removed outlier: 3.512A pdb=" N VAL F 151 " --> pdb=" O ASN F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 181 removed outlier: 4.112A pdb=" N ILE F 176 " --> pdb=" O ASP F 172 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA F 179 " --> pdb=" O ILE F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 184 No H-bonds generated for 'chain 'F' and resid 182 through 184' Processing helix chain 'F' and resid 187 through 197 Processing helix chain 'F' and resid 199 through 201 No H-bonds generated for 'chain 'F' and resid 199 through 201' Processing helix chain 'F' and resid 202 through 207 removed outlier: 3.565A pdb=" N ALA F 206 " --> pdb=" O PHE F 202 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASN F 207 " --> pdb=" O LYS F 203 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 202 through 207' Processing helix chain 'F' and resid 228 through 232 removed outlier: 3.523A pdb=" N GLY F 232 " --> pdb=" O PHE F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 241 No H-bonds generated for 'chain 'F' and resid 239 through 241' Processing helix chain 'F' and resid 242 through 250 Processing helix chain 'G' and resid 63 through 69 removed outlier: 3.678A pdb=" N LEU G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 80 removed outlier: 5.113A pdb=" N PHE G 78 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN G 79 " --> pdb=" O ILE G 75 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LYS G 80 " --> pdb=" O ALA G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 83 through 96 removed outlier: 3.713A pdb=" N LYS G 96 " --> pdb=" O LYS G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 118 Processing helix chain 'G' and resid 135 through 145 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 165 through 174 Processing helix chain 'G' and resid 182 through 190 removed outlier: 4.054A pdb=" N LEU G 186 " --> pdb=" O AASN G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 222 removed outlier: 4.116A pdb=" N ASN G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLU G 210 " --> pdb=" O GLU G 206 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 227 Processing helix chain 'H' and resid 21 through 23 No H-bonds generated for 'chain 'H' and resid 21 through 23' Processing helix chain 'H' and resid 61 through 66 Processing helix chain 'H' and resid 66 through 84 removed outlier: 3.815A pdb=" N SER H 70 " --> pdb=" O ALA H 66 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 118 Processing helix chain 'H' and resid 148 through 163 removed outlier: 3.528A pdb=" N CYS H 163 " --> pdb=" O ILE H 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 46 Processing helix chain 'L' and resid 76 through 84 Processing helix chain 'L' and resid 86 through 93 removed outlier: 3.882A pdb=" N SER L 91 " --> pdb=" O ARG L 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 122 removed outlier: 3.575A pdb=" N ASN L 112 " --> pdb=" O SER L 108 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ARG L 115 " --> pdb=" O ARG L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 132 removed outlier: 3.996A pdb=" N GLY L 131 " --> pdb=" O PRO L 127 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLN L 132 " --> pdb=" O ARG L 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 127 through 132' Processing helix chain 'L' and resid 148 through 153 removed outlier: 3.645A pdb=" N VAL L 152 " --> pdb=" O ASP L 148 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 173 Processing helix chain 'L' and resid 175 through 200 removed outlier: 4.456A pdb=" N ASN L 181 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLY L 190 " --> pdb=" O ALA L 186 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ALA L 191 " --> pdb=" O ARG L 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 70 through 82 Processing helix chain 'M' and resid 90 through 104 Processing helix chain 'M' and resid 106 through 122 Processing helix chain 'N' and resid 3 through 13 removed outlier: 3.841A pdb=" N LEU N 7 " --> pdb=" O ALA N 3 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU N 8 " --> pdb=" O TYR N 4 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU N 9 " --> pdb=" O LYS N 5 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 33 removed outlier: 3.509A pdb=" N ARG N 24 " --> pdb=" O LEU N 20 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN N 32 " --> pdb=" O TRP N 28 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 51 Processing helix chain 'N' and resid 97 through 110 Processing helix chain 'N' and resid 139 through 144 removed outlier: 3.717A pdb=" N ARG N 144 " --> pdb=" O LYS N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 148 through 152 Processing helix chain 'N' and resid 153 through 157 removed outlier: 3.579A pdb=" N LYS N 157 " --> pdb=" O PRO N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 172 Processing helix chain 'O' and resid 16 through 30 removed outlier: 3.624A pdb=" N VAL O 23 " --> pdb=" O ARG O 19 " (cutoff:3.500A) Processing helix chain 'O' and resid 38 through 41 removed outlier: 3.649A pdb=" N GLU O 41 " --> pdb=" O ARG O 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 38 through 41' Processing helix chain 'O' and resid 47 through 59 removed outlier: 3.681A pdb=" N TYR O 58 " --> pdb=" O LYS O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 88 Processing helix chain 'O' and resid 93 through 101 Processing helix chain 'O' and resid 125 through 130 Processing helix chain 'O' and resid 139 through 144 Processing helix chain 'O' and resid 150 through 186 Processing helix chain 'O' and resid 187 through 196 removed outlier: 3.921A pdb=" N SER O 193 " --> pdb=" O GLN O 190 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLN O 194 " --> pdb=" O LYS O 191 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 36 Processing helix chain 'P' and resid 40 through 53 Processing helix chain 'P' and resid 70 through 74 Processing helix chain 'P' and resid 84 through 106 removed outlier: 3.541A pdb=" N VAL P 88 " --> pdb=" O PRO P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 112 removed outlier: 3.707A pdb=" N LEU P 112 " --> pdb=" O MET P 109 " (cutoff:3.500A) Processing helix chain 'P' and resid 168 through 183 removed outlier: 3.793A pdb=" N ALA P 183 " --> pdb=" O ALA P 179 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 39 Processing helix chain 'Q' and resid 41 through 52 removed outlier: 3.511A pdb=" N LYS Q 45 " --> pdb=" O SER Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 54 through 58 Processing helix chain 'Q' and resid 63 through 71 Processing helix chain 'Q' and resid 108 through 118 removed outlier: 3.757A pdb=" N ALA Q 118 " --> pdb=" O ARG Q 114 " (cutoff:3.500A) Processing helix chain 'Q' and resid 124 through 132 Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 28 through 35 Processing helix chain 'R' and resid 37 through 48 Processing helix chain 'S' and resid 32 through 49 Processing helix chain 'S' and resid 97 through 113 Processing helix chain 'S' and resid 130 through 134 Processing helix chain 'S' and resid 136 through 143 Processing helix chain 'V' and resid 122 through 128 Processing helix chain 'V' and resid 128 through 134 Processing helix chain 'W' and resid 19 through 35 Processing helix chain 'W' and resid 49 through 59 removed outlier: 3.661A pdb=" N LEU W 53 " --> pdb=" O ARG W 49 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 78 Processing helix chain 'W' and resid 88 through 96 removed outlier: 3.632A pdb=" N LEU W 92 " --> pdb=" O ASN W 88 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS W 94 " --> pdb=" O SER W 90 " (cutoff:3.500A) Processing helix chain 'W' and resid 113 through 119 Processing helix chain 'W' and resid 161 through 169 removed outlier: 3.532A pdb=" N VAL W 165 " --> pdb=" O LEU W 161 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG W 166 " --> pdb=" O GLU W 162 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY W 169 " --> pdb=" O VAL W 165 " (cutoff:3.500A) Processing helix chain 'W' and resid 195 through 204 removed outlier: 3.697A pdb=" N LEU W 204 " --> pdb=" O ARG W 200 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 20 Processing helix chain 'Y' and resid 22 through 30 removed outlier: 4.574A pdb=" N VAL Y 28 " --> pdb=" O SER Y 24 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 43 Processing helix chain 'Y' and resid 74 through 77 Processing helix chain 'Y' and resid 99 through 101 No H-bonds generated for 'chain 'Y' and resid 99 through 101' Processing helix chain 'Y' and resid 111 through 121 Processing helix chain 'a' and resid 7 through 11 Processing helix chain 'a' and resid 77 through 81 Processing helix chain 'a' and resid 83 through 91 Processing helix chain 'a' and resid 104 through 107 Processing helix chain 'a' and resid 132 through 140 removed outlier: 3.716A pdb=" N ILE a 137 " --> pdb=" O ALA a 133 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 9 removed outlier: 4.114A pdb=" N ASN b 8 " --> pdb=" O VAL b 5 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ILE b 9 " --> pdb=" O PHE b 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 5 through 9' Processing helix chain 'b' and resid 15 through 30 Processing helix chain 'b' and resid 39 through 69 Processing helix chain 'b' and resid 76 through 88 removed outlier: 3.585A pdb=" N ILE b 85 " --> pdb=" O ASP b 81 " (cutoff:3.500A) Processing helix chain 'b' and resid 88 through 118 removed outlier: 3.568A pdb=" N LYS b 118 " --> pdb=" O ILE b 114 " (cutoff:3.500A) Processing helix chain 'b' and resid 122 through 143 removed outlier: 3.720A pdb=" N ARG b 143 " --> pdb=" O THR b 139 " (cutoff:3.500A) Processing helix chain 'b' and resid 144 through 159 Processing helix chain 'b' and resid 180 through 189 Processing helix chain 'b' and resid 235 through 246 removed outlier: 3.546A pdb=" N HIS b 246 " --> pdb=" O THR b 242 " (cutoff:3.500A) Processing helix chain 'b' and resid 264 through 276 Processing helix chain 'b' and resid 306 through 312 Processing helix chain 'b' and resid 328 through 344 Processing helix chain 'b' and resid 379 through 384 removed outlier: 3.588A pdb=" N LYS b 383 " --> pdb=" O PRO b 379 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR b 384 " --> pdb=" O ASP b 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 379 through 384' Processing helix chain 'b' and resid 398 through 406 Processing helix chain 'b' and resid 415 through 420 removed outlier: 4.025A pdb=" N LYS b 419 " --> pdb=" O LEU b 416 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR b 420 " --> pdb=" O ARG b 417 " (cutoff:3.500A) Processing helix chain 'b' and resid 426 through 430 removed outlier: 3.574A pdb=" N TYR b 429 " --> pdb=" O SER b 426 " (cutoff:3.500A) Processing helix chain 'b' and resid 442 through 445 Processing helix chain 'b' and resid 448 through 465 removed outlier: 3.747A pdb=" N GLU b 458 " --> pdb=" O LEU b 454 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLU b 459 " --> pdb=" O ALA b 455 " (cutoff:3.500A) Processing helix chain 'd' and resid 21 through 25 Processing helix chain 'd' and resid 29 through 31 No H-bonds generated for 'chain 'd' and resid 29 through 31' Processing helix chain 'd' and resid 32 through 50 Processing helix chain 'd' and resid 57 through 65 Processing helix chain 'e' and resid 51 through 55 Processing helix chain 'e' and resid 75 through 81 removed outlier: 3.892A pdb=" N VAL e 79 " --> pdb=" O ASN e 75 " (cutoff:3.500A) Processing helix chain 'e' and resid 82 through 86 removed outlier: 3.855A pdb=" N ASN e 86 " --> pdb=" O LEU e 83 " (cutoff:3.500A) Processing helix chain 'e' and resid 98 through 113 Processing helix chain 'f' and resid 38 through 43 Processing helix chain 'f' and resid 91 through 95 removed outlier: 3.800A pdb=" N PHE f 95 " --> pdb=" O ALA f 92 " (cutoff:3.500A) Processing helix chain 'h' and resid 4 through 9 removed outlier: 3.529A pdb=" N LEU h 8 " --> pdb=" O LYS h 4 " (cutoff:3.500A) Processing helix chain 'h' and resid 12 through 36 removed outlier: 3.540A pdb=" N GLU h 26 " --> pdb=" O GLU h 22 " (cutoff:3.500A) Processing helix chain 'h' and resid 39 through 72 removed outlier: 4.418A pdb=" N LYS h 47 " --> pdb=" O LEU h 43 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR h 48 " --> pdb=" O SER h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 87 through 93 Processing helix chain 'h' and resid 95 through 100 Processing helix chain 'h' and resid 103 through 113 Processing helix chain 'i' and resid 23 through 28 Processing helix chain 'i' and resid 32 through 47 Processing helix chain 'i' and resid 49 through 61 removed outlier: 3.870A pdb=" N GLU i 57 " --> pdb=" O ARG i 53 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU i 58 " --> pdb=" O ARG i 54 " (cutoff:3.500A) Processing helix chain 'i' and resid 63 through 76 Processing helix chain 'i' and resid 77 through 95 removed outlier: 3.534A pdb=" N GLU i 87 " --> pdb=" O GLY i 83 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 58 Processing helix chain 'j' and resid 64 through 75 removed outlier: 3.643A pdb=" N LYS j 69 " --> pdb=" O SER j 65 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS j 75 " --> pdb=" O HIS j 71 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 15 Processing helix chain 'r' and resid 19 through 42 removed outlier: 3.636A pdb=" N GLU r 31 " --> pdb=" O LYS r 27 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ALA r 32 " --> pdb=" O ALA r 28 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N HIS r 33 " --> pdb=" O ALA r 29 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR r 42 " --> pdb=" O TYR r 38 " (cutoff:3.500A) Processing helix chain 'r' and resid 44 through 73 removed outlier: 3.651A pdb=" N GLU r 69 " --> pdb=" O ILE r 65 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU r 70 " --> pdb=" O LYS r 66 " (cutoff:3.500A) Processing helix chain 'r' and resid 205 through 212 Processing helix chain 'r' and resid 247 through 252 Processing helix chain 's' and resid 12 through 32 removed outlier: 4.617A pdb=" N GLU s 20 " --> pdb=" O ARG s 16 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS s 21 " --> pdb=" O SER s 17 " (cutoff:3.500A) Processing helix chain 'u' and resid 33 through 42 Processing helix chain 'u' and resid 45 through 49 removed outlier: 3.591A pdb=" N VAL u 49 " --> pdb=" O PRO u 46 " (cutoff:3.500A) Processing helix chain 'u' and resid 52 through 59 Processing helix chain 'u' and resid 67 through 71 Processing helix chain 'u' and resid 83 through 114 removed outlier: 3.629A pdb=" N LYS u 95 " --> pdb=" O LEU u 91 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN u 99 " --> pdb=" O LYS u 95 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU u 107 " --> pdb=" O LYS u 103 " (cutoff:3.500A) Processing helix chain 'w' and resid 227 through 234 removed outlier: 4.026A pdb=" N LYS w 231 " --> pdb=" O ASN w 227 " (cutoff:3.500A) Processing helix chain 'w' and resid 258 through 264 Processing helix chain 'w' and resid 266 through 274 Processing helix chain 'w' and resid 283 through 292 Processing helix chain 'w' and resid 296 through 305 removed outlier: 4.023A pdb=" N ASP w 305 " --> pdb=" O LEU w 301 " (cutoff:3.500A) Processing helix chain 'w' and resid 310 through 329 Processing helix chain 'y' and resid 31 through 43 removed outlier: 3.757A pdb=" N TYR y 35 " --> pdb=" O SER y 31 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLU y 41 " --> pdb=" O VAL y 37 " (cutoff:3.500A) Processing helix chain 'y' and resid 58 through 63 Processing helix chain 'y' and resid 77 through 88 Processing helix chain 'y' and resid 103 through 107 removed outlier: 3.568A pdb=" N ILE y 107 " --> pdb=" O ALA y 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'y' and resid 103 through 107' Processing helix chain 'y' and resid 122 through 134 Processing helix chain 'y' and resid 147 through 152 Processing helix chain 'y' and resid 166 through 178 Processing helix chain 'y' and resid 192 through 196 Processing helix chain 'y' and resid 211 through 223 Processing helix chain 'z' and resid 88 through 99 Processing helix chain 'z' and resid 101 through 116 removed outlier: 4.371A pdb=" N ASN z 107 " --> pdb=" O LYS z 103 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N PHE z 110 " --> pdb=" O LYS z 106 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS z 112 " --> pdb=" O SER z 108 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU z 114 " --> pdb=" O PHE z 110 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '3' and resid 19 through 21 Processing sheet with id=AA2, first strand: chain '3' and resid 52 through 56 removed outlier: 3.635A pdb=" N MET 3 64 " --> pdb=" O GLN 3 78 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLN 3 78 " --> pdb=" O MET 3 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.318A pdb=" N VAL B 158 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL B 93 " --> pdb=" O SER B 101 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N SER B 101 " --> pdb=" O VAL B 93 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 42 through 43 removed outlier: 5.318A pdb=" N VAL B 158 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N HIS B 163 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N VAL B 86 " --> pdb=" O HIS B 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 356 through 359 removed outlier: 6.680A pdb=" N VAL B 57 " --> pdb=" O LYS B 357 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N ILE B 359 " --> pdb=" O HIS B 55 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N HIS B 55 " --> pdb=" O ILE B 359 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL B 335 " --> pdb=" O VAL B 220 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL B 220 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL B 217 " --> pdb=" O LEU B 278 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N LEU B 278 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLY B 219 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N THR B 276 " --> pdb=" O GLY B 219 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LYS B 281 " --> pdb=" O ASN B 325 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N MET B 323 " --> pdb=" O TYR B 283 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N ILE B 285 " --> pdb=" O PHE B 321 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE B 321 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLU B 80 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N LYS B 50 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 223 through 225 Processing sheet with id=AA7, first strand: chain 'C' and resid 17 through 23 removed outlier: 5.110A pdb=" N ILE C 10 " --> pdb=" O SER C 18 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLU C 20 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N VAL C 8 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N VAL C 153 " --> pdb=" O SER C 9 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N LEU C 152 " --> pdb=" O VAL C 250 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU C 208 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 7.778A pdb=" N THR C 253 " --> pdb=" O LEU C 208 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N VAL C 210 " --> pdb=" O THR C 253 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL C 209 " --> pdb=" O VAL C 230 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AA9, first strand: chain 'E' and resid 94 through 97 removed outlier: 7.115A pdb=" N THR E 79 " --> pdb=" O GLN E 75 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N GLN E 75 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL E 81 " --> pdb=" O LEU E 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 82 through 83 Processing sheet with id=AB2, first strand: chain 'F' and resid 122 through 125 removed outlier: 3.566A pdb=" N ILE F 91 " --> pdb=" O VAL F 124 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N VAL F 141 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AB4, first strand: chain 'G' and resid 133 through 134 Processing sheet with id=AB5, first strand: chain 'H' and resid 6 through 12 Processing sheet with id=AB6, first strand: chain 'H' and resid 18 through 20 removed outlier: 4.008A pdb=" N ASP H 20 " --> pdb=" O THR H 27 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 130 through 134 removed outlier: 6.667A pdb=" N ARG H 87 " --> pdb=" O ARG H 182 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ARG H 182 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LYS H 89 " --> pdb=" O SER H 180 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 100 through 104 Processing sheet with id=AB9, first strand: chain 'L' and resid 22 through 24 Processing sheet with id=AC1, first strand: chain 'L' and resid 57 through 58 Processing sheet with id=AC2, first strand: chain 'L' and resid 123 through 125 Processing sheet with id=AC3, first strand: chain 'M' and resid 49 through 52 removed outlier: 7.677A pdb=" N ARG M 36 " --> pdb=" O ILE M 31 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ILE M 31 " --> pdb=" O ARG M 36 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU M 38 " --> pdb=" O VAL M 29 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG M 12 " --> pdb=" O ILE M 28 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL M 13 " --> pdb=" O THR M 59 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 36 through 39 removed outlier: 4.474A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N GLU N 131 " --> pdb=" O TRP N 120 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N TRP N 120 " --> pdb=" O GLU N 131 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE N 133 " --> pdb=" O SER N 118 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N SER N 118 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N VAL N 135 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU N 116 " --> pdb=" O VAL N 135 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'O' and resid 7 through 11 removed outlier: 6.059A pdb=" N VAL O 8 " --> pdb=" O VAL O 35 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL O 37 " --> pdb=" O VAL O 8 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE O 10 " --> pdb=" O VAL O 37 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 43 through 45 Processing sheet with id=AC7, first strand: chain 'P' and resid 15 through 22 removed outlier: 3.890A pdb=" N TYR P 21 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N SER P 144 " --> pdb=" O TYR P 21 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA P 151 " --> pdb=" O ILE P 114 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ILE P 114 " --> pdb=" O ALA P 151 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'P' and resid 58 through 59 Processing sheet with id=AC9, first strand: chain 'Q' and resid 61 through 62 Processing sheet with id=AD1, first strand: chain 'Q' and resid 121 through 123 removed outlier: 6.433A pdb=" N ILE Q 102 " --> pdb=" O LEU Q 123 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR Q 82 " --> pdb=" O ALA Q 103 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL Q 139 " --> pdb=" O THR Q 81 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'R' and resid 22 through 24 Processing sheet with id=AD3, first strand: chain 'S' and resid 55 through 63 removed outlier: 5.095A pdb=" N ILE S 57 " --> pdb=" O ARG S 11 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ARG S 11 " --> pdb=" O ILE S 57 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N GLU S 5 " --> pdb=" O ILE S 63 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'S' and resid 87 through 95 removed outlier: 4.311A pdb=" N VAL S 73 " --> pdb=" O VAL S 128 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ARG S 79 " --> pdb=" O ILE S 122 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ILE S 122 " --> pdb=" O ARG S 79 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'V' and resid 19 through 20 Processing sheet with id=AD6, first strand: chain 'V' and resid 24 through 27 removed outlier: 6.839A pdb=" N LEU V 61 " --> pdb=" O VAL V 39 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N VAL V 41 " --> pdb=" O MET V 59 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N MET V 59 " --> pdb=" O VAL V 41 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP V 58 " --> pdb=" O VAL V 80 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N GLY V 102 " --> pdb=" O ILE V 24 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N ASN V 26 " --> pdb=" O GLY V 102 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N ILE V 104 " --> pdb=" O ASN V 26 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'V' and resid 87 through 88 Processing sheet with id=AD8, first strand: chain 'V' and resid 119 through 121 removed outlier: 5.828A pdb=" N VAL V 120 " --> pdb=" O VAL V 139 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'W' and resid 135 through 137 removed outlier: 6.360A pdb=" N ILE W 137 " --> pdb=" O PRO W 186 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'W' and resid 140 through 141 Processing sheet with id=AE2, first strand: chain 'Y' and resid 31 through 33 Processing sheet with id=AE3, first strand: chain 'Y' and resid 93 through 98 removed outlier: 7.007A pdb=" N VAL Y 84 " --> pdb=" O VAL Y 96 " (cutoff:3.500A) removed outlier: 10.849A pdb=" N ILE Y 98 " --> pdb=" O GLU Y 82 " (cutoff:3.500A) removed outlier: 10.680A pdb=" N GLU Y 82 " --> pdb=" O ILE Y 98 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N SER Y 71 " --> pdb=" O LEU Y 80 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N GLU Y 82 " --> pdb=" O ILE Y 69 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ILE Y 69 " --> pdb=" O GLU Y 82 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N VAL Y 84 " --> pdb=" O GLY Y 67 " (cutoff:3.500A) removed outlier: 10.019A pdb=" N GLY Y 67 " --> pdb=" O VAL Y 84 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLN Y 54 " --> pdb=" O THR Y 106 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'a' and resid 72 through 74 removed outlier: 5.905A pdb=" N VAL a 73 " --> pdb=" O LEU a 112 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'a' and resid 100 through 102 removed outlier: 6.315A pdb=" N ILE a 101 " --> pdb=" O GLN a 125 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL a 124 " --> pdb=" O GLU a 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'b' and resid 206 through 212 Processing sheet with id=AE7, first strand: chain 'b' and resid 254 through 256 Processing sheet with id=AE8, first strand: chain 'b' and resid 435 through 436 Processing sheet with id=AE9, first strand: chain 'd' and resid 55 through 56 Processing sheet with id=AF1, first strand: chain 'e' and resid 69 through 73 Processing sheet with id=AF2, first strand: chain 'f' and resid 9 through 19 removed outlier: 6.892A pdb=" N ILE f 30 " --> pdb=" O LEU f 15 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N PHE f 17 " --> pdb=" O THR f 28 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N THR f 28 " --> pdb=" O PHE f 17 " (cutoff:3.500A) removed outlier: 9.402A pdb=" N ARG f 19 " --> pdb=" O PRO f 26 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N GLY f 27 " --> pdb=" O PHE f 86 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N PHE f 86 " --> pdb=" O GLY f 27 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ALA f 81 " --> pdb=" O PRO f 75 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ARG f 83 " --> pdb=" O ALA f 73 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL f 60 " --> pdb=" O SER f 63 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE f 65 " --> pdb=" O LYS f 58 " (cutoff:3.500A) removed outlier: 10.251A pdb=" N LYS f 58 " --> pdb=" O ILE f 65 " (cutoff:3.500A) removed outlier: 11.144A pdb=" N VAL f 67 " --> pdb=" O SER f 56 " (cutoff:3.500A) removed outlier: 11.051A pdb=" N SER f 56 " --> pdb=" O VAL f 67 " (cutoff:3.500A) removed outlier: 10.952A pdb=" N TRP f 69 " --> pdb=" O TYR f 54 " (cutoff:3.500A) removed outlier: 11.470A pdb=" N TYR f 54 " --> pdb=" O TRP f 69 " (cutoff:3.500A) removed outlier: 10.942A pdb=" N THR f 71 " --> pdb=" O TYR f 52 " (cutoff:3.500A) removed outlier: 10.477A pdb=" N TYR f 52 " --> pdb=" O THR f 71 " (cutoff:3.500A) removed outlier: 9.854A pdb=" N ALA f 73 " --> pdb=" O VAL f 50 " (cutoff:3.500A) removed outlier: 11.407A pdb=" N VAL f 50 " --> pdb=" O ALA f 73 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG f 49 " --> pdb=" O MET f 102 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N VAL f 53 " --> pdb=" O SER f 98 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N SER f 98 " --> pdb=" O VAL f 53 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'j' and resid 16 through 18 Processing sheet with id=AF4, first strand: chain 'r' and resid 180 through 184 removed outlier: 6.545A pdb=" N VAL r 219 " --> pdb=" O LYS r 200 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'u' and resid 4 through 5 removed outlier: 3.523A pdb=" N HIS u 4 " --> pdb=" O VAL u 13 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'u' and resid 19 through 22 Processing sheet with id=AF7, first strand: chain 'w' and resid 255 through 257 removed outlier: 6.084A pdb=" N VAL w 256 " --> pdb=" O VAL w 278 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'y' and resid 3 through 4 removed outlier: 5.883A pdb=" N LEU y 3 " --> pdb=" O ALA y 206 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'y' and resid 17 through 19 removed outlier: 6.408A pdb=" N ALA y 24 " --> pdb=" O VAL y 49 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'y' and resid 64 through 65 Processing sheet with id=AG2, first strand: chain 'y' and resid 108 through 110 Processing sheet with id=AG3, first strand: chain 'y' and resid 153 through 154 removed outlier: 6.230A pdb=" N ALA y 159 " --> pdb=" O VAL y 182 " (cutoff:3.500A) 1648 hydrogen bonds defined for protein. 4638 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1435 hydrogen bonds 2330 hydrogen bond angles 0 basepair planarities 586 basepair parallelities 1132 stacking parallelities Total time for adding SS restraints: 73.82 Time building geometry restraints manager: 18.31 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: 13229 1.33 - 1.45: 32556 1.45 - 1.58: 35611 1.58 - 1.70: 3894 1.70 - 1.83: 156 Bond restraints: 85446 Sorted by residual: bond pdb=" CA PRO F 103 " pdb=" C PRO F 103 " ideal model delta sigma weight residual 1.514 1.528 -0.014 5.50e-03 3.31e+04 6.32e+00 bond pdb=" CA TRP N 120 " pdb=" C TRP N 120 " ideal model delta sigma weight residual 1.524 1.499 0.025 1.25e-02 6.40e+03 3.90e+00 bond pdb=" N LYS C 347 " pdb=" CA LYS C 347 " ideal model delta sigma weight residual 1.455 1.431 0.024 1.25e-02 6.40e+03 3.76e+00 bond pdb=" O3' A 13267 " pdb=" P U 13268 " ideal model delta sigma weight residual 1.607 1.634 -0.027 1.50e-02 4.44e+03 3.26e+00 bond pdb=" CA TYR H 6 " pdb=" C TYR H 6 " ideal model delta sigma weight residual 1.526 1.504 0.022 1.20e-02 6.94e+03 3.25e+00 ... (remaining 85441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 123855 2.53 - 5.05: 1014 5.05 - 7.58: 102 7.58 - 10.11: 19 10.11 - 12.64: 2 Bond angle restraints: 124992 Sorted by residual: angle pdb=" N ILE b 12 " pdb=" CA ILE b 12 " pdb=" C ILE b 12 " ideal model delta sigma weight residual 108.63 115.30 -6.67 8.60e-01 1.35e+00 6.01e+01 angle pdb=" N TYR H 6 " pdb=" CA TYR H 6 " pdb=" C TYR H 6 " ideal model delta sigma weight residual 107.70 120.34 -12.64 2.09e+00 2.29e-01 3.65e+01 angle pdb=" C4' U 1 270 " pdb=" C3' U 1 270 " pdb=" O3' U 1 270 " ideal model delta sigma weight residual 109.40 116.92 -7.52 1.50e+00 4.44e-01 2.51e+01 angle pdb=" O3' U 13268 " pdb=" C3' U 13268 " pdb=" C2' U 13268 " ideal model delta sigma weight residual 109.50 116.93 -7.43 1.50e+00 4.44e-01 2.45e+01 angle pdb=" CA GLU E 33 " pdb=" CB GLU E 33 " pdb=" CG GLU E 33 " ideal model delta sigma weight residual 114.10 123.88 -9.78 2.00e+00 2.50e-01 2.39e+01 ... (remaining 124987 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 48261 35.96 - 71.93: 4999 71.93 - 107.89: 579 107.89 - 143.86: 31 143.86 - 179.82: 43 Dihedral angle restraints: 53913 sinusoidal: 39448 harmonic: 14465 Sorted by residual: dihedral pdb=" O4' U 11330 " pdb=" C1' U 11330 " pdb=" N1 U 11330 " pdb=" C2 U 11330 " ideal model delta sinusoidal sigma weight residual -160.00 19.82 -179.82 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 2 164 " pdb=" C1' U 2 164 " pdb=" N1 U 2 164 " pdb=" C2 U 2 164 " ideal model delta sinusoidal sigma weight residual 200.00 21.56 178.44 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U 1 140 " pdb=" C1' U 1 140 " pdb=" N1 U 1 140 " pdb=" C2 U 1 140 " ideal model delta sinusoidal sigma weight residual -160.00 16.32 -176.32 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 53910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 15573 0.130 - 0.260: 79 0.260 - 0.390: 5 0.390 - 0.521: 0 0.521 - 0.651: 1 Chirality restraints: 15658 Sorted by residual: chirality pdb=" CG LEU b 456 " pdb=" CB LEU b 456 " pdb=" CD1 LEU b 456 " pdb=" CD2 LEU b 456 " both_signs ideal model delta sigma weight residual False -2.59 -1.94 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CG LEU u 69 " pdb=" CB LEU u 69 " pdb=" CD1 LEU u 69 " pdb=" CD2 LEU u 69 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.45e+00 chirality pdb=" C3' C 1 626 " pdb=" C4' C 1 626 " pdb=" O3' C 1 626 " pdb=" C2' C 1 626 " both_signs ideal model delta sigma weight residual False -2.74 -2.43 -0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 15655 not shown) Planarity restraints: 8644 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR b 10 " 0.053 5.00e-02 4.00e+02 7.88e-02 9.93e+00 pdb=" N PRO b 11 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO b 11 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO b 11 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY i 4 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.01e+00 pdb=" C GLY i 4 " 0.046 2.00e-02 2.50e+03 pdb=" O GLY i 4 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU i 5 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN G 118 " 0.013 2.00e-02 2.50e+03 2.63e-02 6.91e+00 pdb=" C ASN G 118 " -0.045 2.00e-02 2.50e+03 pdb=" O ASN G 118 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY G 119 " 0.015 2.00e-02 2.50e+03 ... (remaining 8641 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 1793 2.63 - 3.20: 70218 3.20 - 3.76: 154614 3.76 - 4.33: 206583 4.33 - 4.90: 285803 Nonbonded interactions: 719011 Sorted by model distance: nonbonded pdb=" O ASP M 82 " pdb=" OD1 ASP M 82 " model vdw 2.061 3.040 nonbonded pdb=" O2' C 11308 " pdb=" O5' A 11309 " model vdw 2.106 3.040 nonbonded pdb=" O2' G 13387 " pdb=" O5' C 13388 " model vdw 2.155 3.040 nonbonded pdb=" N GLU T 144 " pdb=" OE1 GLU T 144 " model vdw 2.172 3.120 nonbonded pdb=" N GLN O 190 " pdb=" OE1 GLN O 190 " model vdw 2.177 3.120 ... (remaining 719006 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.090 Extract box with map and model: 2.610 Check model and map are aligned: 0.470 Set scattering table: 0.590 Process input model: 210.710 Find NCS groups from input model: 1.290 Set up NCS constraints: 0.270 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: 0.030 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 225.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 : 0.004 0.072 85446 Z= 0.230 Angle : 0.606 12.635 124992 Z= 0.322 Chirality : 0.036 0.651 15658 Planarity : 0.005 0.079 8644 Dihedral : 23.137 179.822 44519 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.90 % Favored : 94.91 % Rotamer: Outliers : 0.81 % Allowed : 11.11 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.12), residues: 4886 helix: 0.17 (0.12), residues: 1856 sheet: -0.73 (0.21), residues: 597 loop : -1.03 (0.13), residues: 2433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP b 427 HIS 0.017 0.001 HIS T 139 PHE 0.027 0.002 PHE b 444 TYR 0.040 0.002 TYR 3 32 ARG 0.018 0.001 ARG N 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 682 time to evaluate : 4.565 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: 3 15 PHE cc_start: 0.5822 (t80) cc_final: 0.5553 (p90) REVERT: B 214 MET cc_start: 0.8362 (tpp) cc_final: 0.8075 (ttm) REVERT: C 155 ASP cc_start: 0.6904 (p0) cc_final: 0.6506 (p0) REVERT: E 176 GLU cc_start: 0.7685 (tp30) cc_final: 0.7400 (tp30) REVERT: P 99 GLU cc_start: 0.8259 (tm-30) cc_final: 0.7928 (tm-30) REVERT: b 412 TYR cc_start: 0.8922 (t80) cc_final: 0.8644 (t80) REVERT: b 432 MET cc_start: 0.7197 (ttt) cc_final: 0.6989 (ttt) REVERT: d 107 GLU cc_start: 0.7760 (mp0) cc_final: 0.7551 (mp0) REVERT: e 36 ASP cc_start: 0.7502 (m-30) cc_final: 0.7240 (t0) REVERT: h 22 GLU cc_start: 0.8222 (pp20) cc_final: 0.7866 (tm-30) REVERT: i 85 ILE cc_start: 0.8754 (pt) cc_final: 0.8516 (mt) REVERT: r 67 GLN cc_start: 0.8381 (tm-30) cc_final: 0.8061 (tm-30) REVERT: r 70 GLU cc_start: 0.7655 (mm-30) cc_final: 0.7383 (tm-30) REVERT: u 105 GLU cc_start: 0.8002 (pp20) cc_final: 0.7473 (pp20) REVERT: y 95 GLN cc_start: 0.8487 (tm-30) cc_final: 0.8169 (tm-30) outliers start: 29 outliers final: 13 residues processed: 693 average time/residue: 0.7845 time to fit residues: 927.2681 Evaluate side-chains 612 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 599 time to evaluate : 4.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 181 ILE Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain N residue 120 TRP Chi-restraints excluded: chain V residue 76 MET Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain e residue 20 ASP Chi-restraints excluded: chain h residue 13 GLN Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain y residue 118 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 571 optimal weight: 1.9990 chunk 513 optimal weight: 0.0970 chunk 284 optimal weight: 9.9990 chunk 175 optimal weight: 5.9990 chunk 346 optimal weight: 2.9990 chunk 274 optimal weight: 1.9990 chunk 530 optimal weight: 2.9990 chunk 205 optimal weight: 5.9990 chunk 322 optimal weight: 8.9990 chunk 394 optimal weight: 1.9990 chunk 614 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 25 GLN E 75 GLN E 127 GLN ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 19 ASN ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 122 ASN N 149 ASN P 145 HIS Q 78 GLN ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 22 GLN ** b 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 20 HIS h 11 GLN ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 93 GLN j 76 ASN ** r 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 40 GLN y 140 GLN z 98 HIS ** T 152 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 85446 Z= 0.234 Angle : 0.656 11.327 124992 Z= 0.333 Chirality : 0.039 0.274 15658 Planarity : 0.005 0.062 8644 Dihedral : 23.951 179.893 35681 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.00 % Favored : 94.85 % Rotamer: Outliers : 2.19 % Allowed : 11.46 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.12), residues: 4886 helix: 0.54 (0.12), residues: 1888 sheet: -0.66 (0.20), residues: 624 loop : -0.93 (0.13), residues: 2374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP z 94 HIS 0.011 0.001 HIS d 48 PHE 0.015 0.001 PHE z 110 TYR 0.023 0.002 TYR u 55 ARG 0.013 0.001 ARG H 113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 741 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 661 time to evaluate : 4.688 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: 3 15 PHE cc_start: 0.6235 (t80) cc_final: 0.5811 (p90) REVERT: C 155 ASP cc_start: 0.6842 (p0) cc_final: 0.6458 (p0) REVERT: H 175 ASP cc_start: 0.7310 (m-30) cc_final: 0.6964 (m-30) REVERT: L 174 ASN cc_start: 0.8076 (p0) cc_final: 0.7858 (p0) REVERT: M 122 GLU cc_start: 0.7927 (pp20) cc_final: 0.7709 (pp20) REVERT: P 29 SER cc_start: 0.9343 (p) cc_final: 0.9109 (m) REVERT: P 141 SER cc_start: 0.7427 (p) cc_final: 0.7022 (m) REVERT: b 153 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8407 (mm-40) REVERT: b 396 ARG cc_start: 0.5994 (OUTLIER) cc_final: 0.3935 (ppt90) REVERT: d 107 GLU cc_start: 0.7894 (mp0) cc_final: 0.7641 (mp0) REVERT: e 36 ASP cc_start: 0.7612 (m-30) cc_final: 0.7206 (t0) REVERT: i 93 GLN cc_start: 0.7697 (mp10) cc_final: 0.7477 (pp30) REVERT: r 70 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7094 (tm-30) REVERT: u 42 MET cc_start: 0.8385 (mpp) cc_final: 0.7809 (mpp) REVERT: u 105 GLU cc_start: 0.8071 (pp20) cc_final: 0.7475 (pp20) REVERT: y 95 GLN cc_start: 0.8408 (tm-30) cc_final: 0.8098 (tm-30) REVERT: z 96 LYS cc_start: 0.7856 (mtpt) cc_final: 0.7646 (tttm) outliers start: 80 outliers final: 49 residues processed: 699 average time/residue: 0.7714 time to fit residues: 925.9711 Evaluate side-chains 640 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 590 time to evaluate : 4.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain V residue 63 THR Chi-restraints excluded: chain V residue 76 MET Chi-restraints excluded: chain Y residue 99 ASP Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 60 GLU Chi-restraints excluded: chain b residue 391 ASN Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain b residue 456 LEU Chi-restraints excluded: chain d residue 42 VAL Chi-restraints excluded: chain e residue 78 ASP Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 53 ILE Chi-restraints excluded: chain h residue 95 THR Chi-restraints excluded: chain i residue 7 VAL Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain j residue 29 ILE Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain r residue 10 SER Chi-restraints excluded: chain u residue 19 ILE Chi-restraints excluded: chain u residue 85 ASN Chi-restraints excluded: chain y residue 110 CYS Chi-restraints excluded: chain y residue 118 HIS Chi-restraints excluded: chain y residue 162 HIS Chi-restraints excluded: chain z residue 98 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 341 optimal weight: 0.8980 chunk 190 optimal weight: 8.9990 chunk 511 optimal weight: 2.9990 chunk 418 optimal weight: 5.9990 chunk 169 optimal weight: 6.9990 chunk 615 optimal weight: 4.9990 chunk 665 optimal weight: 3.9990 chunk 548 optimal weight: 8.9990 chunk 610 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 chunk 494 optimal weight: 3.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 GLN B 279 ASN C 319 ASN E 75 GLN F 69 GLN H 77 ASN ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 85 ASN ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 55 GLN ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 ASN ** r 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 140 GLN z 98 HIS T 152 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 85446 Z= 0.314 Angle : 0.667 12.342 124992 Z= 0.340 Chirality : 0.040 0.292 15658 Planarity : 0.005 0.069 8644 Dihedral : 23.828 179.971 35669 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.25 % Favored : 94.65 % Rotamer: Outliers : 3.22 % Allowed : 13.71 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.12), residues: 4886 helix: 0.60 (0.12), residues: 1892 sheet: -0.66 (0.20), residues: 611 loop : -0.93 (0.13), residues: 2383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP z 94 HIS 0.036 0.001 HIS z 98 PHE 0.023 0.002 PHE N 129 TYR 0.028 0.002 TYR b 124 ARG 0.014 0.001 ARG G 204 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 746 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 628 time to evaluate : 4.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 15 PHE cc_start: 0.6443 (t80) cc_final: 0.5884 (p90) REVERT: C 337 TYR cc_start: 0.8031 (t80) cc_final: 0.7821 (t80) REVERT: F 69 GLN cc_start: 0.8757 (tp-100) cc_final: 0.8538 (tp40) REVERT: F 110 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8741 (mmt) REVERT: H 24 ARG cc_start: 0.6092 (OUTLIER) cc_final: 0.5412 (mmt90) REVERT: L 110 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8053 (mm110) REVERT: O 59 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8309 (mm) REVERT: P 29 SER cc_start: 0.9372 (p) cc_final: 0.9167 (m) REVERT: P 141 SER cc_start: 0.7581 (p) cc_final: 0.7171 (m) REVERT: S 89 MET cc_start: 0.7779 (mtt) cc_final: 0.7174 (mtt) REVERT: S 109 MET cc_start: 0.8386 (mmp) cc_final: 0.8163 (mmp) REVERT: b 69 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.8027 (t80) REVERT: b 128 GLN cc_start: 0.8704 (mp10) cc_final: 0.8237 (mp10) REVERT: b 144 GLN cc_start: 0.8464 (mp10) cc_final: 0.8193 (mp10) REVERT: b 153 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8490 (mm-40) REVERT: b 396 ARG cc_start: 0.6162 (OUTLIER) cc_final: 0.4349 (ppt90) REVERT: d 21 MET cc_start: 0.8564 (mmm) cc_final: 0.7711 (mmm) REVERT: d 31 LYS cc_start: 0.8891 (mmmt) cc_final: 0.8535 (mmmt) REVERT: e 36 ASP cc_start: 0.7571 (m-30) cc_final: 0.7201 (t0) REVERT: h 21 GLN cc_start: 0.7929 (tm-30) cc_final: 0.7373 (tp-100) REVERT: j 29 ILE cc_start: 0.8515 (OUTLIER) cc_final: 0.8206 (mm) REVERT: j 64 MET cc_start: 0.8484 (mtt) cc_final: 0.8268 (mtt) REVERT: r 70 GLU cc_start: 0.7630 (mm-30) cc_final: 0.7284 (tm-30) REVERT: y 95 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8148 (tm-30) outliers start: 118 outliers final: 71 residues processed: 696 average time/residue: 0.7683 time to fit residues: 920.9199 Evaluate side-chains 648 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 571 time to evaluate : 4.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 110 MET Chi-restraints excluded: chain H residue 24 ARG Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 85 ASN Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 123 GLN Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain O residue 107 GLU Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain O residue 168 PHE Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 168 SER Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain S residue 108 ASP Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain V residue 63 THR Chi-restraints excluded: chain V residue 76 MET Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain Y residue 7 VAL Chi-restraints excluded: chain Y residue 99 ASP Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 126 THR Chi-restraints excluded: chain a residue 139 GLN Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain a residue 146 LEU Chi-restraints excluded: chain b residue 60 GLU Chi-restraints excluded: chain b residue 69 PHE Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain b residue 148 LEU Chi-restraints excluded: chain b residue 391 ASN Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain b residue 435 LEU Chi-restraints excluded: chain b residue 456 LEU Chi-restraints excluded: chain e residue 20 ASP Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 53 ILE Chi-restraints excluded: chain i residue 7 VAL Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain j residue 29 ILE Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain r residue 10 SER Chi-restraints excluded: chain u residue 85 ASN Chi-restraints excluded: chain y residue 13 ILE Chi-restraints excluded: chain y residue 64 CYS Chi-restraints excluded: chain y residue 74 SER Chi-restraints excluded: chain y residue 162 HIS Chi-restraints excluded: chain T residue 142 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 608 optimal weight: 4.9990 chunk 463 optimal weight: 8.9990 chunk 319 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 293 optimal weight: 0.0470 chunk 413 optimal weight: 1.9990 chunk 618 optimal weight: 0.9990 chunk 654 optimal weight: 0.8980 chunk 322 optimal weight: 8.9990 chunk 585 optimal weight: 1.9990 chunk 176 optimal weight: 10.0000 overall best weight: 1.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 25 GLN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN L 181 ASN ** M 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN S 88 ASN ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 22 GLN b 27 GLN ** b 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 394 ASN b 406 ASN h 25 GLN ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 ASN ** r 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 140 GLN z 98 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 85446 Z= 0.196 Angle : 0.608 10.841 124992 Z= 0.310 Chirality : 0.037 0.288 15658 Planarity : 0.004 0.066 8644 Dihedral : 23.753 179.822 35663 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.74 % Favored : 95.18 % Rotamer: Outliers : 2.87 % Allowed : 16.12 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.12), residues: 4886 helix: 0.74 (0.12), residues: 1897 sheet: -0.65 (0.20), residues: 631 loop : -0.84 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP z 94 HIS 0.010 0.001 HIS d 48 PHE 0.014 0.001 PHE i 37 TYR 0.033 0.002 TYR i 51 ARG 0.009 0.000 ARG y 188 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 631 time to evaluate : 5.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 15 PHE cc_start: 0.6568 (t80) cc_final: 0.5984 (p90) REVERT: 3 91 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6698 (mp0) REVERT: 3 123 ARG cc_start: 0.3052 (ttp-170) cc_final: 0.2065 (ttt180) REVERT: B 184 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8275 (m-40) REVERT: C 363 ASN cc_start: 0.7485 (t0) cc_final: 0.7209 (t0) REVERT: H 24 ARG cc_start: 0.6106 (OUTLIER) cc_final: 0.5372 (mmt90) REVERT: O 59 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8278 (mm) REVERT: P 29 SER cc_start: 0.9371 (p) cc_final: 0.9140 (m) REVERT: P 141 SER cc_start: 0.7547 (p) cc_final: 0.7139 (m) REVERT: S 89 MET cc_start: 0.7611 (mtt) cc_final: 0.7316 (mtt) REVERT: b 69 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.8093 (t80) REVERT: b 144 GLN cc_start: 0.8358 (mp10) cc_final: 0.8135 (mp10) REVERT: b 151 LEU cc_start: 0.9229 (mm) cc_final: 0.9007 (mm) REVERT: b 153 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8473 (mm-40) REVERT: b 396 ARG cc_start: 0.6226 (OUTLIER) cc_final: 0.4471 (ppt90) REVERT: d 23 LYS cc_start: 0.8814 (ptmm) cc_final: 0.8604 (pttt) REVERT: d 31 LYS cc_start: 0.8876 (mmmt) cc_final: 0.8502 (mmmt) REVERT: e 36 ASP cc_start: 0.7517 (m-30) cc_final: 0.7205 (t0) REVERT: j 29 ILE cc_start: 0.8481 (OUTLIER) cc_final: 0.8168 (mm) REVERT: r 70 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7261 (tm-30) REVERT: u 42 MET cc_start: 0.8112 (mpp) cc_final: 0.7423 (mpp) REVERT: y 95 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8227 (tm-30) outliers start: 105 outliers final: 63 residues processed: 689 average time/residue: 0.8050 time to fit residues: 974.9333 Evaluate side-chains 654 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 584 time to evaluate : 4.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 91 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain H residue 24 ARG Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 181 ASN Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain N residue 34 ASN Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 174 ILE Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain P residue 168 SER Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain S residue 64 SER Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain V residue 63 THR Chi-restraints excluded: chain V residue 76 MET Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 99 ASP Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 139 GLN Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 60 GLU Chi-restraints excluded: chain b residue 69 PHE Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain b residue 435 LEU Chi-restraints excluded: chain b residue 456 LEU Chi-restraints excluded: chain e residue 20 ASP Chi-restraints excluded: chain e residue 106 VAL Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 53 ILE Chi-restraints excluded: chain i residue 7 VAL Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain j residue 29 ILE Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain u residue 26 SER Chi-restraints excluded: chain u residue 85 ASN Chi-restraints excluded: chain u residue 91 LEU Chi-restraints excluded: chain z residue 98 HIS Chi-restraints excluded: chain z residue 113 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 545 optimal weight: 20.0000 chunk 371 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 487 optimal weight: 50.0000 chunk 270 optimal weight: 0.9990 chunk 558 optimal weight: 8.9990 chunk 452 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 334 optimal weight: 7.9990 chunk 587 optimal weight: 5.9990 chunk 165 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 247 GLN L 110 GLN M 85 ASN N 32 GLN ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 123 GLN Q 78 GLN S 88 ASN ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 83 GLN ** b 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 406 ASN ** b 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 46 GLN h 13 GLN h 15 ASN ** h 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 ASN ** r 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 140 GLN y 162 HIS ** z 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.109 85446 Z= 0.534 Angle : 0.810 11.094 124992 Z= 0.405 Chirality : 0.047 0.315 15658 Planarity : 0.006 0.070 8644 Dihedral : 23.834 179.871 35663 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.44 % Favored : 93.46 % Rotamer: Outliers : 4.33 % Allowed : 16.74 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.12), residues: 4886 helix: 0.48 (0.12), residues: 1892 sheet: -0.74 (0.20), residues: 609 loop : -1.08 (0.13), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP z 94 HIS 0.027 0.002 HIS z 98 PHE 0.019 0.002 PHE N 129 TYR 0.030 0.002 TYR i 51 ARG 0.013 0.001 ARG a 132 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 159 poor density : 588 time to evaluate : 4.579 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 91 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6635 (mp0) REVERT: 3 123 ARG cc_start: 0.3509 (ttp-170) cc_final: 0.2196 (ttt180) REVERT: B 184 ASN cc_start: 0.8576 (OUTLIER) cc_final: 0.8207 (m-40) REVERT: C 363 ASN cc_start: 0.7635 (t0) cc_final: 0.7313 (t0) REVERT: H 24 ARG cc_start: 0.6517 (OUTLIER) cc_final: 0.5570 (mmt90) REVERT: M 114 MET cc_start: 0.8414 (tpp) cc_final: 0.8152 (tpt) REVERT: O 59 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8355 (mm) REVERT: P 141 SER cc_start: 0.7692 (p) cc_final: 0.7297 (m) REVERT: b 69 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.8179 (t80) REVERT: b 144 GLN cc_start: 0.8466 (mp10) cc_final: 0.8182 (mp10) REVERT: b 153 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8320 (mm-40) REVERT: b 396 ARG cc_start: 0.6502 (OUTLIER) cc_final: 0.4704 (ppt90) REVERT: d 31 LYS cc_start: 0.8980 (mmmt) cc_final: 0.8597 (mmmt) REVERT: e 36 ASP cc_start: 0.7428 (m-30) cc_final: 0.7156 (t0) REVERT: f 99 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9075 (mt) REVERT: h 22 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8290 (tm-30) REVERT: h 25 GLN cc_start: 0.7820 (mp10) cc_final: 0.7561 (mp10) REVERT: j 43 LYS cc_start: 0.8707 (mmpt) cc_final: 0.8484 (mppt) REVERT: r 70 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7307 (tm-30) REVERT: y 95 GLN cc_start: 0.8537 (tm-30) cc_final: 0.7872 (tm-30) outliers start: 159 outliers final: 114 residues processed: 689 average time/residue: 0.7577 time to fit residues: 897.6130 Evaluate side-chains 684 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 563 time to evaluate : 4.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 38 CYS Chi-restraints excluded: chain 3 residue 43 CYS Chi-restraints excluded: chain 3 residue 91 GLU Chi-restraints excluded: chain B residue 80 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain G residue 197 VAL Chi-restraints excluded: chain H residue 24 ARG Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 37 GLN Chi-restraints excluded: chain H residue 61 SER Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 114 GLU Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 15 LEU Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 85 ASN Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 123 GLN Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain O residue 168 PHE Chi-restraints excluded: chain P residue 39 MET Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 168 SER Chi-restraints excluded: chain Q residue 23 VAL Chi-restraints excluded: chain Q residue 29 VAL Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain Q residue 137 ASN Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain S residue 64 SER Chi-restraints excluded: chain S residue 108 ASP Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain V residue 63 THR Chi-restraints excluded: chain V residue 71 LEU Chi-restraints excluded: chain V residue 76 MET Chi-restraints excluded: chain V residue 116 ILE Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain Y residue 7 VAL Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 119 VAL Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 76 ASP Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 126 THR Chi-restraints excluded: chain a residue 132 ARG Chi-restraints excluded: chain a residue 139 GLN Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 60 GLU Chi-restraints excluded: chain b residue 69 PHE Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain b residue 148 LEU Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain b residue 456 LEU Chi-restraints excluded: chain e residue 20 ASP Chi-restraints excluded: chain e residue 87 LYS Chi-restraints excluded: chain e residue 103 VAL Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain f residue 99 LEU Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 53 ILE Chi-restraints excluded: chain h residue 103 THR Chi-restraints excluded: chain i residue 7 VAL Chi-restraints excluded: chain i residue 77 THR Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain j residue 29 ILE Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain j residue 76 ASN Chi-restraints excluded: chain j residue 80 SER Chi-restraints excluded: chain r residue 37 LEU Chi-restraints excluded: chain u residue 26 SER Chi-restraints excluded: chain u residue 85 ASN Chi-restraints excluded: chain u residue 91 LEU Chi-restraints excluded: chain y residue 13 ILE Chi-restraints excluded: chain y residue 50 HIS Chi-restraints excluded: chain y residue 64 CYS Chi-restraints excluded: chain y residue 74 SER Chi-restraints excluded: chain y residue 110 CYS Chi-restraints excluded: chain z residue 113 PHE Chi-restraints excluded: chain T residue 142 SER Chi-restraints excluded: chain T residue 151 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 220 optimal weight: 2.9990 chunk 589 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 384 optimal weight: 0.6980 chunk 161 optimal weight: 20.0000 chunk 655 optimal weight: 0.0970 chunk 543 optimal weight: 6.9990 chunk 303 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 216 optimal weight: 2.9990 chunk 343 optimal weight: 2.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 25 GLN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 146 GLN ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 88 ASN ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 22 GLN ** b 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 13 GLN ** h 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 21 ASN y 140 GLN y 162 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 85446 Z= 0.207 Angle : 0.622 10.637 124992 Z= 0.317 Chirality : 0.038 0.289 15658 Planarity : 0.004 0.065 8644 Dihedral : 23.744 179.480 35663 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.37 % Favored : 95.53 % Rotamer: Outliers : 3.47 % Allowed : 18.18 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.12), residues: 4886 helix: 0.74 (0.12), residues: 1896 sheet: -0.67 (0.20), residues: 614 loop : -0.93 (0.13), residues: 2376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP z 94 HIS 0.009 0.001 HIS d 48 PHE 0.024 0.001 PHE i 37 TYR 0.033 0.002 TYR i 51 ARG 0.009 0.000 ARG a 132 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 620 time to evaluate : 4.602 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: 3 15 PHE cc_start: 0.6669 (t80) cc_final: 0.6019 (p90) REVERT: 3 74 SER cc_start: 0.7692 (OUTLIER) cc_final: 0.7163 (t) REVERT: 3 91 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6690 (mp0) REVERT: 3 123 ARG cc_start: 0.3564 (ttp-170) cc_final: 0.2269 (ttt180) REVERT: B 184 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.8216 (m-40) REVERT: B 345 HIS cc_start: 0.5737 (OUTLIER) cc_final: 0.4838 (p-80) REVERT: C 363 ASN cc_start: 0.7616 (t0) cc_final: 0.7246 (t0) REVERT: F 101 ASN cc_start: 0.8124 (t0) cc_final: 0.7849 (t0) REVERT: G 131 ASN cc_start: 0.8203 (p0) cc_final: 0.7974 (m-40) REVERT: H 24 ARG cc_start: 0.6279 (OUTLIER) cc_final: 0.5312 (mmt90) REVERT: L 110 GLN cc_start: 0.8361 (mm-40) cc_final: 0.7977 (mm-40) REVERT: M 114 MET cc_start: 0.8178 (tpp) cc_final: 0.7823 (tpt) REVERT: O 59 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8317 (mm) REVERT: P 141 SER cc_start: 0.7633 (p) cc_final: 0.7223 (m) REVERT: S 89 MET cc_start: 0.7664 (mtt) cc_final: 0.7326 (mtt) REVERT: S 109 MET cc_start: 0.8407 (mmp) cc_final: 0.8203 (mmp) REVERT: V 76 MET cc_start: 0.6723 (OUTLIER) cc_final: 0.6298 (ppp) REVERT: b 69 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.8098 (t80) REVERT: b 84 ASN cc_start: 0.6414 (m-40) cc_final: 0.6093 (m110) REVERT: b 124 TYR cc_start: 0.7657 (t80) cc_final: 0.7327 (t80) REVERT: b 128 GLN cc_start: 0.8842 (mp10) cc_final: 0.8288 (mp10) REVERT: b 144 GLN cc_start: 0.8288 (mp10) cc_final: 0.8024 (mp10) REVERT: b 153 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8317 (mm-40) REVERT: b 396 ARG cc_start: 0.6457 (OUTLIER) cc_final: 0.4689 (ppt90) REVERT: d 23 LYS cc_start: 0.8879 (ptmm) cc_final: 0.8598 (pttt) REVERT: d 31 LYS cc_start: 0.8915 (mmmt) cc_final: 0.8543 (mmmt) REVERT: h 22 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8162 (tm-30) REVERT: j 43 LYS cc_start: 0.8624 (mmpt) cc_final: 0.8415 (mppt) outliers start: 127 outliers final: 88 residues processed: 700 average time/residue: 0.7647 time to fit residues: 915.0297 Evaluate side-chains 669 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 572 time to evaluate : 4.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 38 CYS Chi-restraints excluded: chain 3 residue 74 SER Chi-restraints excluded: chain 3 residue 91 GLU Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain H residue 24 ARG Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain L residue 124 ILE Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 85 ASN Chi-restraints excluded: chain M residue 105 LEU Chi-restraints excluded: chain N residue 34 ASN Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain O residue 168 PHE Chi-restraints excluded: chain P residue 39 MET Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 79 THR Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 168 SER Chi-restraints excluded: chain Q residue 66 ILE Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 ILE Chi-restraints excluded: chain S residue 64 SER Chi-restraints excluded: chain S residue 108 ASP Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain V residue 5 ARG Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 63 THR Chi-restraints excluded: chain V residue 76 MET Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 99 ASP Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 119 VAL Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 132 ARG Chi-restraints excluded: chain a residue 139 GLN Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 60 GLU Chi-restraints excluded: chain b residue 69 PHE Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain b residue 148 LEU Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain b residue 435 LEU Chi-restraints excluded: chain b residue 456 LEU Chi-restraints excluded: chain e residue 20 ASP Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 53 ILE Chi-restraints excluded: chain i residue 7 VAL Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain j residue 29 ILE Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain r residue 37 LEU Chi-restraints excluded: chain u residue 26 SER Chi-restraints excluded: chain u residue 85 ASN Chi-restraints excluded: chain y residue 74 SER Chi-restraints excluded: chain z residue 113 PHE Chi-restraints excluded: chain T residue 149 VAL Chi-restraints excluded: chain T residue 151 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 631 optimal weight: 0.4980 chunk 73 optimal weight: 7.9990 chunk 373 optimal weight: 0.9990 chunk 478 optimal weight: 20.0000 chunk 370 optimal weight: 0.9990 chunk 551 optimal weight: 0.9980 chunk 365 optimal weight: 4.9990 chunk 652 optimal weight: 5.9990 chunk 408 optimal weight: 0.4980 chunk 397 optimal weight: 0.8980 chunk 301 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 25 GLN ** 3 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 110 GLN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 212 ASN E 75 GLN N 112 ASN S 88 ASN ** b 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 ASN y 140 GLN y 162 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 85446 Z= 0.163 Angle : 0.594 12.743 124992 Z= 0.303 Chirality : 0.036 0.279 15658 Planarity : 0.004 0.062 8644 Dihedral : 23.576 179.908 35663 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.61 % Favored : 95.28 % Rotamer: Outliers : 3.14 % Allowed : 19.26 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.12), residues: 4886 helix: 0.86 (0.12), residues: 1895 sheet: -0.55 (0.21), residues: 607 loop : -0.77 (0.13), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP z 94 HIS 0.005 0.001 HIS d 48 PHE 0.016 0.001 PHE i 37 TYR 0.032 0.001 TYR i 51 ARG 0.011 0.000 ARG P 181 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 632 time to evaluate : 4.550 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: 3 15 PHE cc_start: 0.6510 (t80) cc_final: 0.5965 (p90) REVERT: 3 74 SER cc_start: 0.7644 (OUTLIER) cc_final: 0.7110 (t) REVERT: 3 91 GLU cc_start: 0.6947 (OUTLIER) cc_final: 0.6603 (pp20) REVERT: 3 123 ARG cc_start: 0.3277 (ttp-170) cc_final: 0.2064 (ttt180) REVERT: B 67 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.6827 (ttm) REVERT: B 184 ASN cc_start: 0.8476 (OUTLIER) cc_final: 0.8189 (m-40) REVERT: B 345 HIS cc_start: 0.5980 (OUTLIER) cc_final: 0.4891 (p-80) REVERT: C 363 ASN cc_start: 0.7630 (t0) cc_final: 0.7280 (t0) REVERT: F 101 ASN cc_start: 0.8015 (t0) cc_final: 0.7736 (t0) REVERT: G 143 ILE cc_start: 0.9323 (tp) cc_final: 0.8906 (tp) REVERT: L 109 LEU cc_start: 0.8318 (mm) cc_final: 0.8081 (tp) REVERT: L 174 ASN cc_start: 0.7761 (p0) cc_final: 0.7319 (p0) REVERT: M 114 MET cc_start: 0.8226 (tpp) cc_final: 0.7920 (tpt) REVERT: O 59 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8442 (mm) REVERT: O 88 MET cc_start: 0.9121 (mtm) cc_final: 0.8919 (mtm) REVERT: P 107 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8127 (mp) REVERT: P 141 SER cc_start: 0.7580 (p) cc_final: 0.7180 (m) REVERT: S 109 MET cc_start: 0.8331 (mmp) cc_final: 0.8128 (mmp) REVERT: V 5 ARG cc_start: 0.5906 (OUTLIER) cc_final: 0.4892 (ppt170) REVERT: V 76 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6247 (ppp) REVERT: b 84 ASN cc_start: 0.6474 (m-40) cc_final: 0.6080 (m110) REVERT: b 128 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8263 (mp10) REVERT: b 144 GLN cc_start: 0.8286 (mp10) cc_final: 0.8063 (mp10) REVERT: b 153 GLN cc_start: 0.8711 (mm-40) cc_final: 0.8474 (mm-40) REVERT: b 396 ARG cc_start: 0.6321 (OUTLIER) cc_final: 0.4701 (ppt90) REVERT: d 23 LYS cc_start: 0.8914 (ptmm) cc_final: 0.8648 (pttt) REVERT: d 31 LYS cc_start: 0.8879 (mmmt) cc_final: 0.8500 (mmmt) REVERT: h 106 GLN cc_start: 0.7963 (tm-30) cc_final: 0.7704 (tm-30) REVERT: j 25 ARG cc_start: 0.8072 (ttm-80) cc_final: 0.7869 (ttt90) REVERT: j 29 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8212 (mm) REVERT: y 95 GLN cc_start: 0.8549 (tm-30) cc_final: 0.8296 (tm-30) outliers start: 115 outliers final: 76 residues processed: 703 average time/residue: 0.7565 time to fit residues: 914.5585 Evaluate side-chains 667 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 579 time to evaluate : 4.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 74 SER Chi-restraints excluded: chain 3 residue 91 GLU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain O residue 168 PHE Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 107 LEU Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 168 SER Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 64 SER Chi-restraints excluded: chain S residue 144 ASN Chi-restraints excluded: chain V residue 5 ARG Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 63 THR Chi-restraints excluded: chain V residue 76 MET Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 119 VAL Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 132 ARG Chi-restraints excluded: chain a residue 139 GLN Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 60 GLU Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain b residue 128 GLN Chi-restraints excluded: chain b residue 148 LEU Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain b residue 435 LEU Chi-restraints excluded: chain b residue 456 LEU Chi-restraints excluded: chain e residue 20 ASP Chi-restraints excluded: chain e residue 87 LYS Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 53 ILE Chi-restraints excluded: chain h residue 103 THR Chi-restraints excluded: chain i residue 7 VAL Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain j residue 29 ILE Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 76 ASN Chi-restraints excluded: chain r residue 37 LEU Chi-restraints excluded: chain u residue 26 SER Chi-restraints excluded: chain u residue 85 ASN Chi-restraints excluded: chain y residue 50 HIS Chi-restraints excluded: chain z residue 113 PHE Chi-restraints excluded: chain T residue 151 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 403 optimal weight: 1.9990 chunk 260 optimal weight: 0.9980 chunk 389 optimal weight: 3.9990 chunk 196 optimal weight: 0.8980 chunk 128 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 414 optimal weight: 3.9990 chunk 444 optimal weight: 0.9990 chunk 322 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 512 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 GLN N 15 GLN O 51 ASN ** S 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 88 ASN ** b 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 13 GLN ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 ASN ** y 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 140 GLN z 98 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 85446 Z= 0.193 Angle : 0.598 11.885 124992 Z= 0.305 Chirality : 0.036 0.293 15658 Planarity : 0.004 0.070 8644 Dihedral : 23.505 179.822 35663 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.47 % Favored : 95.43 % Rotamer: Outliers : 3.06 % Allowed : 20.08 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.12), residues: 4886 helix: 0.94 (0.12), residues: 1874 sheet: -0.46 (0.21), residues: 597 loop : -0.76 (0.13), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP z 94 HIS 0.006 0.001 HIS C 314 PHE 0.027 0.001 PHE i 37 TYR 0.030 0.002 TYR i 51 ARG 0.010 0.000 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 603 time to evaluate : 4.557 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: 3 15 PHE cc_start: 0.6419 (t80) cc_final: 0.5810 (p90) REVERT: 3 74 SER cc_start: 0.7652 (OUTLIER) cc_final: 0.7134 (t) REVERT: 3 91 GLU cc_start: 0.7022 (OUTLIER) cc_final: 0.6635 (pp20) REVERT: 3 123 ARG cc_start: 0.3582 (ttp-170) cc_final: 0.2356 (ttt180) REVERT: B 67 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6865 (ttm) REVERT: B 184 ASN cc_start: 0.8489 (OUTLIER) cc_final: 0.8186 (m-40) REVERT: B 345 HIS cc_start: 0.5803 (OUTLIER) cc_final: 0.4829 (p-80) REVERT: C 101 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.5043 (ppp) REVERT: C 363 ASN cc_start: 0.7645 (t0) cc_final: 0.7287 (t0) REVERT: E 33 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7292 (tm-30) REVERT: E 152 GLU cc_start: 0.7818 (pp20) cc_final: 0.7594 (pp20) REVERT: L 92 THR cc_start: 0.8574 (p) cc_final: 0.8310 (p) REVERT: M 114 MET cc_start: 0.8242 (tpp) cc_final: 0.7962 (tpt) REVERT: O 59 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8336 (mm) REVERT: P 141 SER cc_start: 0.7573 (p) cc_final: 0.7182 (m) REVERT: V 5 ARG cc_start: 0.5917 (OUTLIER) cc_final: 0.4885 (ppt170) REVERT: V 76 MET cc_start: 0.6848 (OUTLIER) cc_final: 0.6282 (ppp) REVERT: b 84 ASN cc_start: 0.6490 (m-40) cc_final: 0.6110 (m110) REVERT: b 144 GLN cc_start: 0.8204 (mp10) cc_final: 0.7873 (mp10) REVERT: b 396 ARG cc_start: 0.6333 (OUTLIER) cc_final: 0.4771 (ppt90) REVERT: d 21 MET cc_start: 0.8540 (mmm) cc_final: 0.7860 (mmm) REVERT: d 23 LYS cc_start: 0.8736 (ptmm) cc_final: 0.8519 (pttt) REVERT: d 31 LYS cc_start: 0.8921 (mmmt) cc_final: 0.8523 (mmmt) REVERT: h 106 GLN cc_start: 0.8099 (tm-30) cc_final: 0.7821 (tm-30) REVERT: j 25 ARG cc_start: 0.8091 (ttm-80) cc_final: 0.7882 (ttt90) REVERT: j 29 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.8142 (mm) outliers start: 112 outliers final: 85 residues processed: 674 average time/residue: 0.7765 time to fit residues: 900.5019 Evaluate side-chains 667 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 571 time to evaluate : 4.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 74 SER Chi-restraints excluded: chain 3 residue 91 GLU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain G residue 77 GLN Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain O residue 168 PHE Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 168 SER Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 64 SER Chi-restraints excluded: chain V residue 5 ARG Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 63 THR Chi-restraints excluded: chain V residue 76 MET Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain Y residue 7 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 99 ASP Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 119 VAL Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 126 THR Chi-restraints excluded: chain a residue 139 GLN Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 60 GLU Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain b residue 416 LEU Chi-restraints excluded: chain b residue 432 MET Chi-restraints excluded: chain b residue 435 LEU Chi-restraints excluded: chain b residue 456 LEU Chi-restraints excluded: chain e residue 20 ASP Chi-restraints excluded: chain e residue 87 LYS Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain f residue 8 LEU Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 53 ILE Chi-restraints excluded: chain h residue 103 THR Chi-restraints excluded: chain i residue 7 VAL Chi-restraints excluded: chain i residue 77 THR Chi-restraints excluded: chain i residue 91 VAL Chi-restraints excluded: chain j residue 29 ILE Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 76 ASN Chi-restraints excluded: chain r residue 37 LEU Chi-restraints excluded: chain u residue 26 SER Chi-restraints excluded: chain u residue 85 ASN Chi-restraints excluded: chain y residue 13 ILE Chi-restraints excluded: chain y residue 64 CYS Chi-restraints excluded: chain z residue 98 HIS Chi-restraints excluded: chain z residue 113 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 593 optimal weight: 6.9990 chunk 625 optimal weight: 50.0000 chunk 570 optimal weight: 0.8980 chunk 608 optimal weight: 0.9980 chunk 624 optimal weight: 50.0000 chunk 365 optimal weight: 4.9990 chunk 264 optimal weight: 0.7980 chunk 477 optimal weight: 8.9990 chunk 186 optimal weight: 10.0000 chunk 549 optimal weight: 2.9990 chunk 575 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN G 77 GLN S 88 ASN V 22 GLN ** b 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 140 GLN z 98 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 85446 Z= 0.204 Angle : 0.604 12.005 124992 Z= 0.308 Chirality : 0.036 0.300 15658 Planarity : 0.004 0.062 8644 Dihedral : 23.471 179.867 35663 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.65 % Favored : 95.24 % Rotamer: Outliers : 3.01 % Allowed : 20.21 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.12), residues: 4886 helix: 0.92 (0.12), residues: 1878 sheet: -0.47 (0.21), residues: 602 loop : -0.75 (0.13), residues: 2406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP z 94 HIS 0.010 0.001 HIS C 314 PHE 0.038 0.001 PHE G 78 TYR 0.046 0.002 TYR i 51 ARG 0.011 0.000 ARG L 31 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 596 time to evaluate : 4.551 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: 3 15 PHE cc_start: 0.6421 (t80) cc_final: 0.5804 (p90) REVERT: 3 74 SER cc_start: 0.7615 (OUTLIER) cc_final: 0.7102 (t) REVERT: 3 91 GLU cc_start: 0.7024 (OUTLIER) cc_final: 0.6628 (pp20) REVERT: 3 123 ARG cc_start: 0.3323 (ttp-170) cc_final: 0.2189 (ttt180) REVERT: B 67 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.6881 (ttm) REVERT: B 184 ASN cc_start: 0.8487 (OUTLIER) cc_final: 0.8175 (m-40) REVERT: B 345 HIS cc_start: 0.5935 (OUTLIER) cc_final: 0.4936 (p-80) REVERT: C 101 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.5023 (ppp) REVERT: C 363 ASN cc_start: 0.7654 (t0) cc_final: 0.7288 (t0) REVERT: L 92 THR cc_start: 0.8555 (p) cc_final: 0.8294 (p) REVERT: M 114 MET cc_start: 0.8260 (tpp) cc_final: 0.8000 (tpt) REVERT: O 59 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8337 (mm) REVERT: P 141 SER cc_start: 0.7578 (p) cc_final: 0.7187 (m) REVERT: S 109 MET cc_start: 0.7833 (tpp) cc_final: 0.7529 (mmp) REVERT: V 5 ARG cc_start: 0.5937 (OUTLIER) cc_final: 0.4825 (ppt170) REVERT: V 76 MET cc_start: 0.6906 (OUTLIER) cc_final: 0.6407 (ppp) REVERT: b 84 ASN cc_start: 0.6494 (m-40) cc_final: 0.6128 (m110) REVERT: b 128 GLN cc_start: 0.8791 (mp10) cc_final: 0.8454 (mp10) REVERT: b 396 ARG cc_start: 0.6273 (OUTLIER) cc_final: 0.4696 (ppt90) REVERT: d 23 LYS cc_start: 0.8687 (ptmm) cc_final: 0.8442 (pttt) REVERT: d 31 LYS cc_start: 0.8937 (mmmt) cc_final: 0.8540 (mmmt) REVERT: h 106 GLN cc_start: 0.8137 (tm-30) cc_final: 0.7872 (tm-30) REVERT: j 25 ARG cc_start: 0.8104 (ttm-80) cc_final: 0.7880 (ttt90) REVERT: j 29 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8094 (mm) REVERT: y 202 TRP cc_start: 0.7916 (p90) cc_final: 0.7628 (p90) outliers start: 110 outliers final: 88 residues processed: 668 average time/residue: 0.7532 time to fit residues: 865.4252 Evaluate side-chains 667 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 568 time to evaluate : 4.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 74 SER Chi-restraints excluded: chain 3 residue 91 GLU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain H residue 12 THR Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain H residue 169 ASP Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain N residue 34 ASN Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain O residue 168 PHE Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 168 SER Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain S residue 28 LEU Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 64 SER Chi-restraints excluded: chain V residue 5 ARG Chi-restraints excluded: chain V residue 19 LEU Chi-restraints excluded: chain V residue 22 GLN Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 63 THR Chi-restraints excluded: chain V residue 76 MET Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain Y residue 7 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 99 ASP Chi-restraints excluded: chain Y residue 119 VAL Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 126 THR Chi-restraints excluded: chain a residue 132 ARG Chi-restraints excluded: chain a residue 139 GLN Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 60 GLU Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain b residue 432 MET Chi-restraints excluded: chain b residue 435 LEU Chi-restraints excluded: chain b residue 456 LEU Chi-restraints excluded: chain e residue 20 ASP Chi-restraints excluded: chain e residue 48 SER Chi-restraints excluded: chain e residue 87 LYS Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain f residue 8 LEU Chi-restraints excluded: chain h residue 15 ASN Chi-restraints excluded: chain h residue 16 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 53 ILE Chi-restraints excluded: chain h residue 103 THR Chi-restraints excluded: chain i residue 7 VAL Chi-restraints excluded: chain i residue 77 THR Chi-restraints excluded: chain j residue 29 ILE Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain r residue 37 LEU Chi-restraints excluded: chain u residue 26 SER Chi-restraints excluded: chain u residue 83 ASP Chi-restraints excluded: chain u residue 85 ASN Chi-restraints excluded: chain y residue 13 ILE Chi-restraints excluded: chain y residue 64 CYS Chi-restraints excluded: chain z residue 113 PHE Chi-restraints excluded: chain T residue 151 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 605 optimal weight: 2.9990 chunk 399 optimal weight: 0.5980 chunk 642 optimal weight: 0.8980 chunk 392 optimal weight: 0.5980 chunk 305 optimal weight: 0.6980 chunk 446 optimal weight: 0.6980 chunk 674 optimal weight: 3.9990 chunk 620 optimal weight: 50.0000 chunk 537 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 414 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN G 77 GLN L 110 GLN V 22 GLN ** b 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 ASN y 140 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 85446 Z= 0.157 Angle : 0.596 12.268 124992 Z= 0.304 Chirality : 0.035 0.278 15658 Planarity : 0.004 0.062 8644 Dihedral : 23.423 179.363 35663 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.41 % Favored : 95.51 % Rotamer: Outliers : 2.68 % Allowed : 20.81 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.12), residues: 4886 helix: 0.92 (0.12), residues: 1875 sheet: -0.48 (0.21), residues: 613 loop : -0.68 (0.13), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP N 28 HIS 0.013 0.001 HIS C 314 PHE 0.032 0.001 PHE i 37 TYR 0.052 0.001 TYR i 51 ARG 0.011 0.000 ARG L 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9772 Ramachandran restraints generated. 4886 Oldfield, 0 Emsley, 4886 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 614 time to evaluate : 4.547 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: 3 15 PHE cc_start: 0.6460 (t80) cc_final: 0.5838 (p90) REVERT: 3 74 SER cc_start: 0.7564 (OUTLIER) cc_final: 0.7050 (t) REVERT: 3 91 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.6611 (pp20) REVERT: 3 123 ARG cc_start: 0.3338 (ttp-170) cc_final: 0.2213 (ttt180) REVERT: B 67 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.6869 (ttm) REVERT: B 184 ASN cc_start: 0.8414 (OUTLIER) cc_final: 0.8141 (m-40) REVERT: B 345 HIS cc_start: 0.5851 (OUTLIER) cc_final: 0.4857 (p-80) REVERT: C 101 MET cc_start: 0.8062 (OUTLIER) cc_final: 0.4857 (ppp) REVERT: C 363 ASN cc_start: 0.7639 (t0) cc_final: 0.7289 (t0) REVERT: G 173 MET cc_start: 0.6680 (mmm) cc_final: 0.6323 (mmm) REVERT: L 92 THR cc_start: 0.8525 (p) cc_final: 0.8273 (p) REVERT: O 59 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8424 (mm) REVERT: S 109 MET cc_start: 0.7960 (tpp) cc_final: 0.7634 (mmp) REVERT: V 5 ARG cc_start: 0.5813 (OUTLIER) cc_final: 0.4800 (ppt170) REVERT: V 76 MET cc_start: 0.6846 (OUTLIER) cc_final: 0.6340 (ppp) REVERT: b 84 ASN cc_start: 0.6353 (m-40) cc_final: 0.6022 (m110) REVERT: b 396 ARG cc_start: 0.6183 (OUTLIER) cc_final: 0.4696 (ppt90) REVERT: d 21 MET cc_start: 0.8457 (mmm) cc_final: 0.7726 (mmm) REVERT: d 23 LYS cc_start: 0.8721 (ptmm) cc_final: 0.8489 (pttt) REVERT: d 31 LYS cc_start: 0.8920 (mmmt) cc_final: 0.8515 (mmmt) REVERT: h 106 GLN cc_start: 0.8114 (tm-30) cc_final: 0.7841 (tm-30) REVERT: i 52 GLU cc_start: 0.7474 (pm20) cc_final: 0.7019 (pm20) REVERT: j 25 ARG cc_start: 0.8074 (ttm-80) cc_final: 0.7850 (ttt90) REVERT: j 29 ILE cc_start: 0.8369 (OUTLIER) cc_final: 0.8078 (mm) REVERT: r 23 ARG cc_start: 0.7788 (mtm-85) cc_final: 0.7553 (mtm180) REVERT: u 83 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.7256 (m-30) REVERT: y 202 TRP cc_start: 0.7876 (p90) cc_final: 0.7562 (p90) outliers start: 98 outliers final: 79 residues processed: 676 average time/residue: 0.8025 time to fit residues: 938.3698 Evaluate side-chains 668 residues out of total 4253 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 577 time to evaluate : 4.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 74 SER Chi-restraints excluded: chain 3 residue 91 GLU Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 184 ASN Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 345 HIS Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 145 ILE Chi-restraints excluded: chain F residue 247 GLN Chi-restraints excluded: chain G residue 77 GLN Chi-restraints excluded: chain G residue 107 GLN Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain H residue 123 VAL Chi-restraints excluded: chain H residue 162 ILE Chi-restraints excluded: chain L residue 51 VAL Chi-restraints excluded: chain L residue 110 GLN Chi-restraints excluded: chain M residue 58 LEU Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain N residue 34 ASN Chi-restraints excluded: chain N residue 36 ILE Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain O residue 7 VAL Chi-restraints excluded: chain O residue 8 VAL Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 152 ASP Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 167 VAL Chi-restraints excluded: chain P residue 168 SER Chi-restraints excluded: chain Q residue 85 VAL Chi-restraints excluded: chain Q residue 97 VAL Chi-restraints excluded: chain S residue 46 MET Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 64 SER Chi-restraints excluded: chain V residue 5 ARG Chi-restraints excluded: chain V residue 19 LEU Chi-restraints excluded: chain V residue 22 GLN Chi-restraints excluded: chain V residue 41 VAL Chi-restraints excluded: chain V residue 63 THR Chi-restraints excluded: chain V residue 76 MET Chi-restraints excluded: chain V residue 127 LEU Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain Y residue 7 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 47 LEU Chi-restraints excluded: chain Y residue 99 ASP Chi-restraints excluded: chain Y residue 108 LEU Chi-restraints excluded: chain Y residue 119 VAL Chi-restraints excluded: chain a residue 15 VAL Chi-restraints excluded: chain a residue 117 LEU Chi-restraints excluded: chain a residue 139 GLN Chi-restraints excluded: chain a residue 144 VAL Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 60 GLU Chi-restraints excluded: chain b residue 122 SER Chi-restraints excluded: chain b residue 394 ASN Chi-restraints excluded: chain b residue 395 ARG Chi-restraints excluded: chain b residue 396 ARG Chi-restraints excluded: chain b residue 416 LEU Chi-restraints excluded: chain b residue 432 MET Chi-restraints excluded: chain b residue 435 LEU Chi-restraints excluded: chain b residue 456 LEU Chi-restraints excluded: chain e residue 20 ASP Chi-restraints excluded: chain e residue 48 SER Chi-restraints excluded: chain e residue 87 LYS Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain f residue 8 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 53 ILE Chi-restraints excluded: chain h residue 103 THR Chi-restraints excluded: chain i residue 7 VAL Chi-restraints excluded: chain i residue 77 THR Chi-restraints excluded: chain j residue 29 ILE Chi-restraints excluded: chain j residue 46 SER Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 76 ASN Chi-restraints excluded: chain r residue 37 LEU Chi-restraints excluded: chain u residue 26 SER Chi-restraints excluded: chain u residue 83 ASP Chi-restraints excluded: chain u residue 85 ASN Chi-restraints excluded: chain z residue 113 PHE Chi-restraints excluded: chain T residue 151 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 677 random chunks: chunk 329 optimal weight: 8.9990 chunk 426 optimal weight: 0.9990 chunk 572 optimal weight: 0.9990 chunk 164 optimal weight: 10.0000 chunk 495 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 537 optimal weight: 7.9990 chunk 225 optimal weight: 1.9990 chunk 552 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 25 GLN ** B 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 GLN ** F 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 77 GLN L 110 GLN Q 78 GLN ** S 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 22 GLN ** V 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 440 ASN d 46 GLN ** h 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 140 GLN ** z 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.115302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.090322 restraints weight = 260754.548| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 2.46 r_work: 0.3096 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 85446 Z= 0.213 Angle : 0.611 12.217 124992 Z= 0.312 Chirality : 0.036 0.258 15658 Planarity : 0.004 0.063 8644 Dihedral : 23.377 179.784 35663 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.74 % Favored : 95.18 % Rotamer: Outliers : 2.71 % Allowed : 20.92 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.99 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.12), residues: 4886 helix: 0.95 (0.12), residues: 1873 sheet: -0.47 (0.20), residues: 616 loop : -0.69 (0.13), residues: 2397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP z 94 HIS 0.007 0.001 HIS S 87 PHE 0.031 0.001 PHE i 37 TYR 0.043 0.002 TYR i 51 ARG 0.012 0.000 ARG L 31 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17623.68 seconds wall clock time: 307 minutes 19.00 seconds (18439.00 seconds total)