Starting phenix.real_space_refine on Wed Feb 21 18:26:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6udo_20741/02_2024/6udo_20741_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6udo_20741/02_2024/6udo_20741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6udo_20741/02_2024/6udo_20741.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6udo_20741/02_2024/6udo_20741.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6udo_20741/02_2024/6udo_20741_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6udo_20741/02_2024/6udo_20741_updated.pdb" } resolution = 3.21 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= 0.058 sd= 3.698 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: 5 Type Number sf(0) Gaussians P 80 5.49 5 S 176 5.16 5 C 19544 2.51 5 N 5376 2.21 5 O 6216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 126": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 231": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 149": "NH1" <-> "NH2" Residue "D ARG 182": "NH1" <-> "NH2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "D ARG 231": "NH1" <-> "NH2" Residue "D ARG 355": "NH1" <-> "NH2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "E ARG 126": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 149": "NH1" <-> "NH2" Residue "E ARG 182": "NH1" <-> "NH2" Residue "E ARG 203": "NH1" <-> "NH2" Residue "E ARG 231": "NH1" <-> "NH2" Residue "E ARG 355": "NH1" <-> "NH2" Residue "E ARG 356": "NH1" <-> "NH2" Residue "E ARG 407": "NH1" <-> "NH2" Residue "E ARG 512": "NH1" <-> "NH2" Residue "F ARG 126": "NH1" <-> "NH2" Residue "F ARG 128": "NH1" <-> "NH2" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 149": "NH1" <-> "NH2" Residue "F ARG 182": "NH1" <-> "NH2" Residue "F ARG 203": "NH1" <-> "NH2" Residue "F ARG 231": "NH1" <-> "NH2" Residue "F ARG 355": "NH1" <-> "NH2" Residue "F ARG 356": "NH1" <-> "NH2" Residue "F ARG 407": "NH1" <-> "NH2" Residue "F ARG 512": "NH1" <-> "NH2" Residue "G ARG 126": "NH1" <-> "NH2" Residue "G ARG 128": "NH1" <-> "NH2" Residue "G PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 149": "NH1" <-> "NH2" Residue "G ARG 182": "NH1" <-> "NH2" Residue "G ARG 203": "NH1" <-> "NH2" Residue "G ARG 231": "NH1" <-> "NH2" Residue "G ARG 355": "NH1" <-> "NH2" Residue "G ARG 356": "NH1" <-> "NH2" Residue "G ARG 407": "NH1" <-> "NH2" Residue "G ARG 512": "NH1" <-> "NH2" Residue "H ARG 126": "NH1" <-> "NH2" Residue "H ARG 128": "NH1" <-> "NH2" Residue "H PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 149": "NH1" <-> "NH2" Residue "H ARG 182": "NH1" <-> "NH2" Residue "H ARG 203": "NH1" <-> "NH2" Residue "H ARG 231": "NH1" <-> "NH2" Residue "H ARG 355": "NH1" <-> "NH2" Residue "H ARG 356": "NH1" <-> "NH2" Residue "H ARG 407": "NH1" <-> "NH2" Residue "H ARG 512": "NH1" <-> "NH2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31392 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3704 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 469} Chain breaks: 1 Chain: "B" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3704 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 469} Chain breaks: 1 Chain: "C" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3704 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 469} Chain breaks: 1 Chain: "D" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3704 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 469} Chain breaks: 1 Chain: "E" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3704 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 469} Chain breaks: 1 Chain: "F" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3704 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 469} Chain breaks: 1 Chain: "G" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3704 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 469} Chain breaks: 1 Chain: "H" Number of atoms: 3704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 487, 3704 Classifications: {'peptide': 487} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 469} Chain breaks: 1 Chain: "I" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "J" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "K" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "L" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "M" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "N" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "O" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "P" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 102 Classifications: {'peptide': 14} Link IDs: {'PTRANS': 1, 'TRANS': 12} Chain: "A" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "G" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 118 Unusual residues: {'ATP': 1, 'GTP': 2} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 16.87, per 1000 atoms: 0.54 Number of scatterers: 31392 At special positions: 0 Unit cell: (149.597, 149.597, 118.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 176 16.00 P 80 15.00 O 6216 8.00 N 5376 7.00 C 19544 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.25 Conformation dependent library (CDL) restraints added in 5.8 seconds 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7264 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 144 helices and 48 sheets defined 30.3% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.79 Creating SS restraints... Processing helix chain 'A' and resid 20 through 23 No H-bonds generated for 'chain 'A' and resid 20 through 23' Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 76 through 84 Processing helix chain 'A' and resid 97 through 108 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 194 through 203 Processing helix chain 'A' and resid 225 through 232 Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.615A pdb=" N LYS A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 292 removed outlier: 4.053A pdb=" N ASP A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 314 removed outlier: 3.783A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 336 No H-bonds generated for 'chain 'A' and resid 333 through 336' Processing helix chain 'A' and resid 343 through 354 Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 476 through 485 Processing helix chain 'A' and resid 497 through 501 Processing helix chain 'B' and resid 20 through 23 No H-bonds generated for 'chain 'B' and resid 20 through 23' Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 76 through 84 Processing helix chain 'B' and resid 97 through 108 Processing helix chain 'B' and resid 127 through 137 Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 194 through 203 Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.615A pdb=" N LYS B 257 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 292 removed outlier: 4.053A pdb=" N ASP B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 314 removed outlier: 3.782A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 336 No H-bonds generated for 'chain 'B' and resid 333 through 336' Processing helix chain 'B' and resid 343 through 354 Processing helix chain 'B' and resid 370 through 379 Processing helix chain 'B' and resid 457 through 471 Processing helix chain 'B' and resid 476 through 485 Processing helix chain 'B' and resid 497 through 501 Processing helix chain 'C' and resid 20 through 23 No H-bonds generated for 'chain 'C' and resid 20 through 23' Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 76 through 84 Processing helix chain 'C' and resid 97 through 108 Processing helix chain 'C' and resid 127 through 137 Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 194 through 203 Processing helix chain 'C' and resid 225 through 232 Processing helix chain 'C' and resid 254 through 266 removed outlier: 3.614A pdb=" N LYS C 257 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU C 260 " --> pdb=" O LYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 292 removed outlier: 4.051A pdb=" N ASP C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 314 removed outlier: 3.783A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 336 No H-bonds generated for 'chain 'C' and resid 333 through 336' Processing helix chain 'C' and resid 343 through 354 Processing helix chain 'C' and resid 370 through 379 Processing helix chain 'C' and resid 457 through 471 Processing helix chain 'C' and resid 476 through 485 Processing helix chain 'C' and resid 497 through 501 Processing helix chain 'D' and resid 20 through 23 No H-bonds generated for 'chain 'D' and resid 20 through 23' Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 97 through 108 Processing helix chain 'D' and resid 127 through 137 Processing helix chain 'D' and resid 182 through 184 No H-bonds generated for 'chain 'D' and resid 182 through 184' Processing helix chain 'D' and resid 194 through 203 Processing helix chain 'D' and resid 225 through 232 Processing helix chain 'D' and resid 254 through 266 removed outlier: 3.615A pdb=" N LYS D 257 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU D 260 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 292 removed outlier: 4.052A pdb=" N ASP D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 314 removed outlier: 3.783A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 336 No H-bonds generated for 'chain 'D' and resid 333 through 336' Processing helix chain 'D' and resid 343 through 354 Processing helix chain 'D' and resid 370 through 379 Processing helix chain 'D' and resid 457 through 471 Processing helix chain 'D' and resid 476 through 485 Processing helix chain 'D' and resid 497 through 501 Processing helix chain 'E' and resid 20 through 23 No H-bonds generated for 'chain 'E' and resid 20 through 23' Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 76 through 84 Processing helix chain 'E' and resid 97 through 108 Processing helix chain 'E' and resid 127 through 137 Processing helix chain 'E' and resid 182 through 184 No H-bonds generated for 'chain 'E' and resid 182 through 184' Processing helix chain 'E' and resid 194 through 203 Processing helix chain 'E' and resid 225 through 232 Processing helix chain 'E' and resid 254 through 266 removed outlier: 3.615A pdb=" N LYS E 257 " --> pdb=" O GLU E 254 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU E 260 " --> pdb=" O LYS E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 292 removed outlier: 4.052A pdb=" N ASP E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 314 removed outlier: 3.783A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 336 No H-bonds generated for 'chain 'E' and resid 333 through 336' Processing helix chain 'E' and resid 343 through 354 Processing helix chain 'E' and resid 370 through 379 Processing helix chain 'E' and resid 457 through 471 Processing helix chain 'E' and resid 476 through 485 Processing helix chain 'E' and resid 497 through 501 Processing helix chain 'F' and resid 20 through 23 No H-bonds generated for 'chain 'F' and resid 20 through 23' Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 76 through 84 Processing helix chain 'F' and resid 97 through 108 Processing helix chain 'F' and resid 127 through 137 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 194 through 203 Processing helix chain 'F' and resid 225 through 232 Processing helix chain 'F' and resid 254 through 266 removed outlier: 3.615A pdb=" N LYS F 257 " --> pdb=" O GLU F 254 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU F 260 " --> pdb=" O LYS F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 292 removed outlier: 4.052A pdb=" N ASP F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 314 removed outlier: 3.783A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 336 No H-bonds generated for 'chain 'F' and resid 333 through 336' Processing helix chain 'F' and resid 343 through 354 Processing helix chain 'F' and resid 370 through 379 Processing helix chain 'F' and resid 457 through 471 Processing helix chain 'F' and resid 476 through 485 Processing helix chain 'F' and resid 497 through 501 Processing helix chain 'G' and resid 20 through 23 No H-bonds generated for 'chain 'G' and resid 20 through 23' Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 76 through 84 Processing helix chain 'G' and resid 97 through 108 Processing helix chain 'G' and resid 127 through 137 Processing helix chain 'G' and resid 182 through 184 No H-bonds generated for 'chain 'G' and resid 182 through 184' Processing helix chain 'G' and resid 194 through 203 Processing helix chain 'G' and resid 225 through 232 Processing helix chain 'G' and resid 254 through 266 removed outlier: 3.615A pdb=" N LYS G 257 " --> pdb=" O GLU G 254 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU G 260 " --> pdb=" O LYS G 257 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 292 removed outlier: 4.053A pdb=" N ASP G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 314 removed outlier: 3.783A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 336 No H-bonds generated for 'chain 'G' and resid 333 through 336' Processing helix chain 'G' and resid 343 through 354 Processing helix chain 'G' and resid 370 through 379 Processing helix chain 'G' and resid 457 through 471 Processing helix chain 'G' and resid 476 through 485 Processing helix chain 'G' and resid 497 through 501 Processing helix chain 'H' and resid 20 through 23 No H-bonds generated for 'chain 'H' and resid 20 through 23' Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 76 through 84 Processing helix chain 'H' and resid 97 through 108 Processing helix chain 'H' and resid 127 through 137 Processing helix chain 'H' and resid 182 through 184 No H-bonds generated for 'chain 'H' and resid 182 through 184' Processing helix chain 'H' and resid 194 through 203 Processing helix chain 'H' and resid 225 through 232 Processing helix chain 'H' and resid 254 through 266 removed outlier: 3.615A pdb=" N LYS H 257 " --> pdb=" O GLU H 254 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU H 260 " --> pdb=" O LYS H 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 292 removed outlier: 4.052A pdb=" N ASP H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 314 removed outlier: 3.783A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 336 No H-bonds generated for 'chain 'H' and resid 333 through 336' Processing helix chain 'H' and resid 343 through 354 Processing helix chain 'H' and resid 370 through 379 Processing helix chain 'H' and resid 457 through 471 Processing helix chain 'H' and resid 476 through 485 Processing helix chain 'H' and resid 497 through 501 Processing helix chain 'I' and resid 2 through 5 No H-bonds generated for 'chain 'I' and resid 2 through 5' Processing helix chain 'J' and resid 2 through 5 No H-bonds generated for 'chain 'J' and resid 2 through 5' Processing helix chain 'K' and resid 2 through 5 No H-bonds generated for 'chain 'K' and resid 2 through 5' Processing helix chain 'L' and resid 2 through 5 No H-bonds generated for 'chain 'L' and resid 2 through 5' Processing helix chain 'M' and resid 2 through 5 No H-bonds generated for 'chain 'M' and resid 2 through 5' Processing helix chain 'N' and resid 2 through 5 No H-bonds generated for 'chain 'N' and resid 2 through 5' Processing helix chain 'O' and resid 2 through 5 No H-bonds generated for 'chain 'O' and resid 2 through 5' Processing helix chain 'P' and resid 2 through 5 No H-bonds generated for 'chain 'P' and resid 2 through 5' Processing sheet with id= A, first strand: chain 'A' and resid 35 through 37 Processing sheet with id= B, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.114A pdb=" N VAL A 384 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 383 " --> pdb=" O VAL A 361 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.515A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ILE A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL A 272 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLN A 298 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 400 through 403 Processing sheet with id= E, first strand: chain 'A' and resid 142 through 145 removed outlier: 3.623A pdb=" N GLY A 156 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 209 through 212 removed outlier: 3.844A pdb=" N ALA A 220 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= H, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.114A pdb=" N VAL B 384 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B 383 " --> pdb=" O VAL B 361 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.514A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ILE B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL B 272 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLN B 298 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'B' and resid 400 through 403 Processing sheet with id= K, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.624A pdb=" N GLY B 156 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 209 through 212 removed outlier: 3.845A pdb=" N ALA B 220 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= N, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.113A pdb=" N VAL C 384 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR C 383 " --> pdb=" O VAL C 361 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 247 through 250 removed outlier: 6.514A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ILE C 250 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL C 272 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLN C 298 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'C' and resid 400 through 403 Processing sheet with id= Q, first strand: chain 'C' and resid 142 through 145 removed outlier: 3.623A pdb=" N GLY C 156 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 209 through 212 removed outlier: 3.844A pdb=" N ALA C 220 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= T, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.112A pdb=" N VAL D 384 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR D 383 " --> pdb=" O VAL D 361 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.514A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE D 250 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL D 272 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN D 298 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'D' and resid 400 through 403 Processing sheet with id= W, first strand: chain 'D' and resid 142 through 145 removed outlier: 3.623A pdb=" N GLY D 156 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'D' and resid 209 through 212 removed outlier: 3.845A pdb=" N ALA D 220 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= Z, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.113A pdb=" N VAL E 384 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR E 383 " --> pdb=" O VAL E 361 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 247 through 250 removed outlier: 6.514A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL E 272 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN E 298 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'E' and resid 400 through 403 Processing sheet with id= AC, first strand: chain 'E' and resid 142 through 145 removed outlier: 3.623A pdb=" N GLY E 156 " --> pdb=" O ILE E 144 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'E' and resid 209 through 212 removed outlier: 3.844A pdb=" N ALA E 220 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= AF, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.113A pdb=" N VAL F 384 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR F 383 " --> pdb=" O VAL F 361 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 247 through 250 removed outlier: 6.514A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ILE F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N VAL F 272 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLN F 298 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'F' and resid 400 through 403 Processing sheet with id= AI, first strand: chain 'F' and resid 142 through 145 removed outlier: 3.623A pdb=" N GLY F 156 " --> pdb=" O ILE F 144 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'F' and resid 209 through 212 removed outlier: 3.845A pdb=" N ALA F 220 " --> pdb=" O ILE F 211 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= AL, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.113A pdb=" N VAL G 384 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR G 383 " --> pdb=" O VAL G 361 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.514A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N ILE G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N VAL G 272 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLN G 298 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'G' and resid 400 through 403 Processing sheet with id= AO, first strand: chain 'G' and resid 142 through 145 removed outlier: 3.623A pdb=" N GLY G 156 " --> pdb=" O ILE G 144 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'G' and resid 209 through 212 removed outlier: 3.844A pdb=" N ALA G 220 " --> pdb=" O ILE G 211 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AR, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.112A pdb=" N VAL H 384 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N THR H 383 " --> pdb=" O VAL H 361 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'H' and resid 247 through 250 removed outlier: 6.514A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL H 272 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLN H 298 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'H' and resid 400 through 403 Processing sheet with id= AU, first strand: chain 'H' and resid 142 through 145 removed outlier: 3.623A pdb=" N GLY H 156 " --> pdb=" O ILE H 144 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'H' and resid 209 through 212 removed outlier: 3.844A pdb=" N ALA H 220 " --> pdb=" O ILE H 211 " (cutoff:3.500A) 808 hydrogen bonds defined for protein. 2160 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.60 Time building geometry restraints manager: 13.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 5288 1.30 - 1.43: 7628 1.43 - 1.56: 18510 1.56 - 1.68: 206 1.68 - 1.81: 288 Bond restraints: 31920 Sorted by residual: bond pdb=" C2' GTP G 603 " pdb=" C3' GTP G 603 " ideal model delta sigma weight residual 1.524 1.231 0.293 2.00e-02 2.50e+03 2.15e+02 bond pdb=" C2' GTP E 603 " pdb=" C3' GTP E 603 " ideal model delta sigma weight residual 1.524 1.231 0.293 2.00e-02 2.50e+03 2.15e+02 bond pdb=" C2' GTP C 603 " pdb=" C3' GTP C 603 " ideal model delta sigma weight residual 1.524 1.231 0.293 2.00e-02 2.50e+03 2.15e+02 bond pdb=" C2' GTP A 603 " pdb=" C3' GTP A 603 " ideal model delta sigma weight residual 1.524 1.231 0.293 2.00e-02 2.50e+03 2.14e+02 bond pdb=" C2' GTP D 603 " pdb=" C3' GTP D 603 " ideal model delta sigma weight residual 1.524 1.231 0.293 2.00e-02 2.50e+03 2.14e+02 ... (remaining 31915 not shown) Histogram of bond angle deviations from ideal: 98.69 - 106.18: 823 106.18 - 113.68: 18174 113.68 - 121.18: 15782 121.18 - 128.67: 8341 128.67 - 136.17: 168 Bond angle restraints: 43288 Sorted by residual: angle pdb=" PB ATP F 604 " pdb=" O3B ATP F 604 " pdb=" PG ATP F 604 " ideal model delta sigma weight residual 139.87 120.03 19.84 1.00e+00 1.00e+00 3.94e+02 angle pdb=" PB ATP H 604 " pdb=" O3B ATP H 604 " pdb=" PG ATP H 604 " ideal model delta sigma weight residual 139.87 120.05 19.82 1.00e+00 1.00e+00 3.93e+02 angle pdb=" PB ATP A 604 " pdb=" O3B ATP A 604 " pdb=" PG ATP A 604 " ideal model delta sigma weight residual 139.87 120.05 19.82 1.00e+00 1.00e+00 3.93e+02 angle pdb=" PB ATP D 604 " pdb=" O3B ATP D 604 " pdb=" PG ATP D 604 " ideal model delta sigma weight residual 139.87 120.07 19.80 1.00e+00 1.00e+00 3.92e+02 angle pdb=" PB ATP G 604 " pdb=" O3B ATP G 604 " pdb=" PG ATP G 604 " ideal model delta sigma weight residual 139.87 120.07 19.80 1.00e+00 1.00e+00 3.92e+02 ... (remaining 43283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.22: 18927 34.22 - 68.43: 341 68.43 - 102.65: 24 102.65 - 136.86: 8 136.86 - 171.08: 36 Dihedral angle restraints: 19336 sinusoidal: 7952 harmonic: 11384 Sorted by residual: dihedral pdb=" O2G GTP H 602 " pdb=" O3B GTP H 602 " pdb=" PG GTP H 602 " pdb=" PB GTP H 602 " ideal model delta sinusoidal sigma weight residual 177.30 6.22 171.08 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O2G GTP D 602 " pdb=" O3B GTP D 602 " pdb=" PG GTP D 602 " pdb=" PB GTP D 602 " ideal model delta sinusoidal sigma weight residual 177.30 6.23 171.07 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O2G GTP C 602 " pdb=" O3B GTP C 602 " pdb=" PG GTP C 602 " pdb=" PB GTP C 602 " ideal model delta sinusoidal sigma weight residual 177.30 6.24 171.06 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 19333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3071 0.050 - 0.101: 1411 0.101 - 0.151: 390 0.151 - 0.202: 48 0.202 - 0.252: 8 Chirality restraints: 4928 Sorted by residual: chirality pdb=" CB THR A 74 " pdb=" CA THR A 74 " pdb=" OG1 THR A 74 " pdb=" CG2 THR A 74 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB THR B 74 " pdb=" CA THR B 74 " pdb=" OG1 THR B 74 " pdb=" CG2 THR B 74 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CB THR C 74 " pdb=" CA THR C 74 " pdb=" OG1 THR C 74 " pdb=" CG2 THR C 74 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 4925 not shown) Planarity restraints: 5424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN F 334 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" CD GLN F 334 " 0.038 2.00e-02 2.50e+03 pdb=" OE1 GLN F 334 " -0.014 2.00e-02 2.50e+03 pdb=" NE2 GLN F 334 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN G 334 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.83e+00 pdb=" CD GLN G 334 " 0.038 2.00e-02 2.50e+03 pdb=" OE1 GLN G 334 " -0.014 2.00e-02 2.50e+03 pdb=" NE2 GLN G 334 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 334 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.81e+00 pdb=" CD GLN A 334 " -0.038 2.00e-02 2.50e+03 pdb=" OE1 GLN A 334 " 0.014 2.00e-02 2.50e+03 pdb=" NE2 GLN A 334 " 0.013 2.00e-02 2.50e+03 ... (remaining 5421 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 8722 2.81 - 3.33: 28348 3.33 - 3.85: 51843 3.85 - 4.38: 62086 4.38 - 4.90: 104736 Nonbonded interactions: 255735 Sorted by model distance: nonbonded pdb=" OG SER A 327 " pdb=" OE1 GLN A 343 " model vdw 2.284 2.440 nonbonded pdb=" OG SER E 327 " pdb=" OE1 GLN E 343 " model vdw 2.284 2.440 nonbonded pdb=" OG SER D 327 " pdb=" OE1 GLN D 343 " model vdw 2.285 2.440 nonbonded pdb=" OG SER F 327 " pdb=" OE1 GLN F 343 " model vdw 2.285 2.440 nonbonded pdb=" OG SER C 327 " pdb=" OE1 GLN C 343 " model vdw 2.285 2.440 ... (remaining 255730 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.190 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: 0.020 Extract box with map and model: 14.540 Check model and map are aligned: 0.450 Set scattering table: 0.300 Process input model: 83.620 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 108.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 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 : 0.014 0.293 31920 Z= 0.940 Angle : 1.231 19.841 43288 Z= 0.737 Chirality : 0.059 0.252 4928 Planarity : 0.006 0.046 5424 Dihedral : 15.770 171.080 12072 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 2.21 % Allowed : 5.15 % Favored : 92.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.10), residues: 3960 helix: -3.27 (0.09), residues: 1312 sheet: -2.33 (0.18), residues: 544 loop : -2.33 (0.12), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 504 PHE 0.015 0.003 PHE C 401 TYR 0.031 0.003 TYR F 484 ARG 0.011 0.001 ARG D 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 816 time to evaluate : 3.616 Fit side-chains REVERT: A 105 ARG cc_start: 0.7351 (mtp-110) cc_final: 0.6953 (ttt-90) REVERT: A 149 ARG cc_start: 0.6430 (mpp-170) cc_final: 0.6197 (mpt180) REVERT: A 170 GLU cc_start: 0.2783 (OUTLIER) cc_final: 0.2321 (mp0) REVERT: A 203 ARG cc_start: 0.7818 (mpt90) cc_final: 0.7116 (mtm110) REVERT: A 228 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7532 (ptmm) REVERT: A 232 ASP cc_start: 0.8604 (m-30) cc_final: 0.8360 (m-30) REVERT: A 235 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.6933 (pp) REVERT: A 410 LYS cc_start: 0.7570 (pttt) cc_final: 0.6363 (mmtt) REVERT: A 509 TYR cc_start: 0.8038 (p90) cc_final: 0.7683 (p90) REVERT: B 105 ARG cc_start: 0.7322 (mtp-110) cc_final: 0.6913 (ttt-90) REVERT: B 149 ARG cc_start: 0.6484 (mpp-170) cc_final: 0.6136 (mpt180) REVERT: B 170 GLU cc_start: 0.2801 (OUTLIER) cc_final: 0.2182 (mp0) REVERT: B 203 ARG cc_start: 0.7831 (mpt90) cc_final: 0.7033 (mtm110) REVERT: B 228 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7454 (ptmm) REVERT: B 232 ASP cc_start: 0.8551 (m-30) cc_final: 0.8347 (m-30) REVERT: B 235 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.6708 (pp) REVERT: B 408 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6721 (pp) REVERT: B 410 LYS cc_start: 0.7600 (pttt) cc_final: 0.6227 (mmtt) REVERT: B 509 TYR cc_start: 0.8074 (p90) cc_final: 0.7768 (p90) REVERT: C 13 VAL cc_start: 0.8678 (t) cc_final: 0.8437 (p) REVERT: C 105 ARG cc_start: 0.7364 (mtp-110) cc_final: 0.6973 (ttt-90) REVERT: C 149 ARG cc_start: 0.6465 (mpp-170) cc_final: 0.6263 (mpt180) REVERT: C 170 GLU cc_start: 0.2860 (OUTLIER) cc_final: 0.2377 (mp0) REVERT: C 203 ARG cc_start: 0.7823 (mpt90) cc_final: 0.7023 (mtm110) REVERT: C 228 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7434 (ptmm) REVERT: C 232 ASP cc_start: 0.8600 (m-30) cc_final: 0.8333 (m-30) REVERT: C 235 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.6948 (pp) REVERT: C 408 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6595 (pp) REVERT: C 410 LYS cc_start: 0.7639 (pttt) cc_final: 0.6331 (mmtt) REVERT: C 509 TYR cc_start: 0.8068 (p90) cc_final: 0.7687 (p90) REVERT: D 13 VAL cc_start: 0.8552 (t) cc_final: 0.8272 (p) REVERT: D 149 ARG cc_start: 0.6472 (mpp-170) cc_final: 0.6148 (mpt180) REVERT: D 170 GLU cc_start: 0.2645 (OUTLIER) cc_final: 0.2219 (mp0) REVERT: D 203 ARG cc_start: 0.7769 (mpt90) cc_final: 0.6930 (mtm110) REVERT: D 235 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.6668 (pp) REVERT: D 408 LEU cc_start: 0.6966 (OUTLIER) cc_final: 0.6704 (pp) REVERT: D 410 LYS cc_start: 0.7646 (pttt) cc_final: 0.6218 (mmtt) REVERT: D 509 TYR cc_start: 0.8094 (p90) cc_final: 0.7768 (p90) REVERT: E 105 ARG cc_start: 0.7340 (mtp-110) cc_final: 0.6909 (ttt-90) REVERT: E 170 GLU cc_start: 0.2708 (OUTLIER) cc_final: 0.2186 (mp0) REVERT: E 203 ARG cc_start: 0.7886 (mpt90) cc_final: 0.7159 (mtm110) REVERT: E 228 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7425 (ptmm) REVERT: E 232 ASP cc_start: 0.8580 (m-30) cc_final: 0.8334 (m-30) REVERT: E 235 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.6899 (pp) REVERT: E 386 MET cc_start: 0.8472 (mtm) cc_final: 0.8214 (mtp) REVERT: E 408 LEU cc_start: 0.6787 (OUTLIER) cc_final: 0.6547 (pp) REVERT: E 410 LYS cc_start: 0.7557 (pttt) cc_final: 0.6356 (mmtt) REVERT: E 509 TYR cc_start: 0.8085 (p90) cc_final: 0.7689 (p90) REVERT: F 13 VAL cc_start: 0.8574 (t) cc_final: 0.8301 (p) REVERT: F 149 ARG cc_start: 0.6561 (mpp-170) cc_final: 0.6261 (mpt180) REVERT: F 170 GLU cc_start: 0.2675 (OUTLIER) cc_final: 0.2035 (mp0) REVERT: F 203 ARG cc_start: 0.7799 (mpt90) cc_final: 0.6969 (mtm110) REVERT: F 235 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.6676 (pp) REVERT: F 408 LEU cc_start: 0.6919 (OUTLIER) cc_final: 0.6669 (pp) REVERT: F 410 LYS cc_start: 0.7663 (pttt) cc_final: 0.6259 (mmtt) REVERT: F 509 TYR cc_start: 0.8097 (p90) cc_final: 0.7771 (p90) REVERT: G 149 ARG cc_start: 0.6461 (mpp-170) cc_final: 0.6217 (mpt180) REVERT: G 170 GLU cc_start: 0.2585 (OUTLIER) cc_final: 0.2064 (mp0) REVERT: G 203 ARG cc_start: 0.7798 (mpt90) cc_final: 0.7197 (mtp180) REVERT: G 228 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7416 (ptmm) REVERT: G 232 ASP cc_start: 0.8563 (m-30) cc_final: 0.8308 (m-30) REVERT: G 235 LEU cc_start: 0.7703 (OUTLIER) cc_final: 0.6895 (pp) REVERT: G 410 LYS cc_start: 0.7576 (pttt) cc_final: 0.6346 (mmtt) REVERT: G 509 TYR cc_start: 0.8072 (p90) cc_final: 0.7666 (p90) REVERT: H 13 VAL cc_start: 0.8555 (t) cc_final: 0.8291 (p) REVERT: H 105 ARG cc_start: 0.7286 (mtp-110) cc_final: 0.6862 (ttt-90) REVERT: H 149 ARG cc_start: 0.6365 (mpp-170) cc_final: 0.6062 (mpt180) REVERT: H 170 GLU cc_start: 0.2727 (OUTLIER) cc_final: 0.2151 (mp0) REVERT: H 203 ARG cc_start: 0.7873 (mpt90) cc_final: 0.7034 (mtm110) REVERT: H 235 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.6696 (pp) REVERT: H 401 PHE cc_start: 0.7896 (p90) cc_final: 0.7521 (p90) REVERT: H 408 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6727 (pp) REVERT: H 410 LYS cc_start: 0.7624 (pttt) cc_final: 0.6287 (mmtt) REVERT: H 509 TYR cc_start: 0.8078 (p90) cc_final: 0.7751 (p90) outliers start: 72 outliers final: 20 residues processed: 856 average time/residue: 0.4246 time to fit residues: 576.9484 Evaluate side-chains 597 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 550 time to evaluate : 3.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 228 LYS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 228 LYS Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 228 LYS Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 228 LYS Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain H residue 408 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 0.6980 chunk 297 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 158 optimal weight: 0.9980 chunk 307 optimal weight: 0.9980 chunk 118 optimal weight: 5.9990 chunk 186 optimal weight: 0.6980 chunk 228 optimal weight: 1.9990 chunk 355 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 198 ASN A 253 HIS A 298 GLN ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN A 368 GLN A 466 HIS A 504 HIS A 507 HIS B 48 GLN B 198 ASN B 253 HIS ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 GLN ** B 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN B 368 GLN B 498 GLN B 504 HIS B 507 HIS C 48 GLN C 198 ASN C 253 HIS C 298 GLN ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 343 GLN C 368 GLN C 466 HIS C 504 HIS C 507 HIS D 48 GLN D 198 ASN D 253 HIS D 298 GLN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN D 368 GLN D 466 HIS D 498 GLN D 504 HIS D 507 HIS E 48 GLN E 198 ASN E 253 HIS E 298 GLN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN E 368 GLN E 466 HIS E 504 HIS E 507 HIS F 48 GLN F 198 ASN F 253 HIS ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 298 GLN ** F 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 343 GLN F 368 GLN F 498 GLN F 504 HIS F 507 HIS G 48 GLN G 198 ASN G 253 HIS G 298 GLN ** G 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 343 GLN G 368 GLN G 466 HIS G 498 GLN G 504 HIS G 507 HIS H 48 GLN H 198 ASN H 253 HIS ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 GLN ** H 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 GLN H 466 HIS H 498 GLN H 504 HIS H 507 HIS Total number of N/Q/H flips: 74 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 31920 Z= 0.208 Angle : 0.579 7.290 43288 Z= 0.292 Chirality : 0.044 0.167 4928 Planarity : 0.004 0.042 5424 Dihedral : 18.393 175.727 4983 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.85 % Allowed : 11.12 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.12), residues: 3960 helix: -1.59 (0.12), residues: 1320 sheet: -1.91 (0.19), residues: 592 loop : -1.89 (0.12), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 137 PHE 0.008 0.001 PHE F 401 TYR 0.016 0.001 TYR B 353 ARG 0.003 0.000 ARG E 259 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 588 time to evaluate : 3.570 Fit side-chains REVERT: A 105 ARG cc_start: 0.7221 (mtp-110) cc_final: 0.6944 (ttp80) REVERT: A 170 GLU cc_start: 0.3387 (OUTLIER) cc_final: 0.3060 (tp30) REVERT: A 203 ARG cc_start: 0.7777 (mpt90) cc_final: 0.7255 (mtp180) REVERT: A 228 LYS cc_start: 0.7643 (ptmm) cc_final: 0.7345 (ptmm) REVERT: A 232 ASP cc_start: 0.8527 (m-30) cc_final: 0.8217 (m-30) REVERT: A 235 LEU cc_start: 0.7764 (OUTLIER) cc_final: 0.6904 (pp) REVERT: A 351 SER cc_start: 0.8299 (t) cc_final: 0.7958 (m) REVERT: A 410 LYS cc_start: 0.7347 (pttt) cc_final: 0.6049 (mmtt) REVERT: A 494 THR cc_start: 0.8123 (p) cc_final: 0.7897 (p) REVERT: B 105 ARG cc_start: 0.7171 (mtp-110) cc_final: 0.6894 (ttp80) REVERT: B 149 ARG cc_start: 0.6405 (mpp-170) cc_final: 0.6016 (mpt180) REVERT: B 170 GLU cc_start: 0.3012 (OUTLIER) cc_final: 0.2516 (tp30) REVERT: B 203 ARG cc_start: 0.7826 (mpt90) cc_final: 0.7123 (mtm110) REVERT: B 228 LYS cc_start: 0.7546 (ptmm) cc_final: 0.7263 (ptmm) REVERT: B 232 ASP cc_start: 0.8492 (m-30) cc_final: 0.8224 (m-30) REVERT: B 235 LEU cc_start: 0.7609 (OUTLIER) cc_final: 0.6690 (pp) REVERT: B 351 SER cc_start: 0.8314 (t) cc_final: 0.7973 (m) REVERT: B 410 LYS cc_start: 0.7494 (pttt) cc_final: 0.6093 (mmtt) REVERT: B 509 TYR cc_start: 0.8040 (p90) cc_final: 0.7592 (p90) REVERT: C 105 ARG cc_start: 0.7253 (mtp-110) cc_final: 0.6969 (ttp80) REVERT: C 149 ARG cc_start: 0.6562 (mpp-170) cc_final: 0.6203 (mpt180) REVERT: C 170 GLU cc_start: 0.3378 (OUTLIER) cc_final: 0.2659 (tp30) REVERT: C 203 ARG cc_start: 0.7775 (mpt90) cc_final: 0.7208 (mtp180) REVERT: C 228 LYS cc_start: 0.7517 (ptmm) cc_final: 0.7197 (ptmm) REVERT: C 232 ASP cc_start: 0.8504 (m-30) cc_final: 0.8172 (m-30) REVERT: C 235 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.6918 (pp) REVERT: C 351 SER cc_start: 0.8306 (t) cc_final: 0.7952 (m) REVERT: C 410 LYS cc_start: 0.7492 (pttt) cc_final: 0.6194 (mmtt) REVERT: C 459 TYR cc_start: 0.8680 (t80) cc_final: 0.8432 (t80) REVERT: D 170 GLU cc_start: 0.3244 (OUTLIER) cc_final: 0.2752 (tp30) REVERT: D 203 ARG cc_start: 0.7717 (mpt90) cc_final: 0.7087 (mtp180) REVERT: D 235 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.6645 (pp) REVERT: D 351 SER cc_start: 0.8352 (t) cc_final: 0.8024 (m) REVERT: D 408 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6778 (pp) REVERT: D 410 LYS cc_start: 0.7557 (pttt) cc_final: 0.6096 (mmtt) REVERT: E 105 ARG cc_start: 0.7216 (mtp-110) cc_final: 0.6923 (ttp80) REVERT: E 149 ARG cc_start: 0.6810 (mpt180) cc_final: 0.6357 (mpt180) REVERT: E 170 GLU cc_start: 0.3108 (OUTLIER) cc_final: 0.2438 (tp30) REVERT: E 203 ARG cc_start: 0.7829 (mpt90) cc_final: 0.7322 (mtp180) REVERT: E 228 LYS cc_start: 0.7557 (ptmm) cc_final: 0.7238 (ptmm) REVERT: E 232 ASP cc_start: 0.8516 (m-30) cc_final: 0.8205 (m-30) REVERT: E 235 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.6931 (pp) REVERT: E 351 SER cc_start: 0.8345 (t) cc_final: 0.8022 (m) REVERT: E 410 LYS cc_start: 0.7459 (pttt) cc_final: 0.6276 (mmtt) REVERT: E 459 TYR cc_start: 0.8631 (t80) cc_final: 0.8392 (t80) REVERT: F 149 ARG cc_start: 0.6447 (mpp-170) cc_final: 0.6082 (mpt180) REVERT: F 170 GLU cc_start: 0.3057 (OUTLIER) cc_final: 0.2716 (tp30) REVERT: F 203 ARG cc_start: 0.7780 (mpt90) cc_final: 0.7162 (mtp180) REVERT: F 235 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.6639 (pp) REVERT: F 351 SER cc_start: 0.8336 (t) cc_final: 0.8012 (m) REVERT: F 408 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6765 (pp) REVERT: F 410 LYS cc_start: 0.7553 (pttt) cc_final: 0.6138 (mmtt) REVERT: F 459 TYR cc_start: 0.8724 (t80) cc_final: 0.8486 (t80) REVERT: G 170 GLU cc_start: 0.3206 (OUTLIER) cc_final: 0.2889 (tp30) REVERT: G 203 ARG cc_start: 0.7765 (mpt90) cc_final: 0.7213 (mtp180) REVERT: G 228 LYS cc_start: 0.7577 (ptmm) cc_final: 0.7265 (ptmm) REVERT: G 232 ASP cc_start: 0.8502 (m-30) cc_final: 0.8183 (m-30) REVERT: G 235 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.6880 (pp) REVERT: G 351 SER cc_start: 0.8283 (t) cc_final: 0.7970 (m) REVERT: G 410 LYS cc_start: 0.7339 (pttt) cc_final: 0.6053 (mmtt) REVERT: G 459 TYR cc_start: 0.8658 (t80) cc_final: 0.8402 (t80) REVERT: H 105 ARG cc_start: 0.7087 (mtp-110) cc_final: 0.6787 (ttp80) REVERT: H 149 ARG cc_start: 0.6346 (mpp-170) cc_final: 0.6012 (mpt180) REVERT: H 170 GLU cc_start: 0.3096 (OUTLIER) cc_final: 0.2461 (tp30) REVERT: H 235 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.6683 (pp) REVERT: H 351 SER cc_start: 0.8326 (t) cc_final: 0.8006 (m) REVERT: H 410 LYS cc_start: 0.7544 (pttt) cc_final: 0.6187 (mmtt) REVERT: O 1 MET cc_start: 0.4838 (mtt) cc_final: 0.4572 (mmm) REVERT: O 5 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8332 (mp) REVERT: P 5 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8486 (mp) outliers start: 93 outliers final: 50 residues processed: 654 average time/residue: 0.3973 time to fit residues: 427.3313 Evaluate side-chains 591 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 521 time to evaluate : 3.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 496 SER Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 496 SER Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain F residue 496 SER Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 485 SER Chi-restraints excluded: chain G residue 496 SER Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 485 SER Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain P residue 5 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 296 optimal weight: 3.9990 chunk 242 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 356 optimal weight: 0.0000 chunk 385 optimal weight: 4.9990 chunk 317 optimal weight: 0.0070 chunk 353 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 286 optimal weight: 0.8980 overall best weight: 0.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN A 334 GLN B 243 GLN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN B 343 GLN C 243 GLN C 334 GLN C 343 GLN C 498 GLN D 243 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN E 48 GLN E 243 GLN E 334 GLN E 498 GLN F 243 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN F 343 GLN G 243 GLN G 334 GLN H 243 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN H 343 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 31920 Z= 0.157 Angle : 0.531 6.770 43288 Z= 0.264 Chirality : 0.043 0.143 4928 Planarity : 0.004 0.038 5424 Dihedral : 17.594 176.499 4925 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 3.03 % Allowed : 12.07 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.12), residues: 3960 helix: -0.71 (0.14), residues: 1320 sheet: -1.57 (0.20), residues: 592 loop : -1.66 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 466 PHE 0.014 0.001 PHE H 401 TYR 0.015 0.001 TYR E 509 ARG 0.003 0.000 ARG A 493 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 542 time to evaluate : 3.672 Fit side-chains REVERT: A 105 ARG cc_start: 0.7190 (mtp-110) cc_final: 0.6924 (ttp80) REVERT: A 170 GLU cc_start: 0.3510 (OUTLIER) cc_final: 0.2690 (tp30) REVERT: A 196 GLU cc_start: 0.7341 (mp0) cc_final: 0.6924 (mt-10) REVERT: A 203 ARG cc_start: 0.7799 (mpt90) cc_final: 0.7223 (mtp180) REVERT: A 228 LYS cc_start: 0.7659 (ptmm) cc_final: 0.7386 (ptmm) REVERT: A 232 ASP cc_start: 0.8494 (m-30) cc_final: 0.8220 (m-30) REVERT: A 235 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.6897 (pp) REVERT: A 286 MET cc_start: 0.8677 (tpp) cc_final: 0.7923 (tpt) REVERT: A 410 LYS cc_start: 0.7396 (pttt) cc_final: 0.6167 (mmtt) REVERT: A 411 TYR cc_start: 0.8155 (t80) cc_final: 0.7932 (t80) REVERT: B 15 ASP cc_start: 0.8290 (t0) cc_final: 0.8040 (t70) REVERT: B 170 GLU cc_start: 0.3275 (OUTLIER) cc_final: 0.2419 (tp30) REVERT: B 196 GLU cc_start: 0.7381 (mp0) cc_final: 0.6992 (mt-10) REVERT: B 203 ARG cc_start: 0.7837 (mpt90) cc_final: 0.7128 (mtm110) REVERT: B 228 LYS cc_start: 0.7545 (ptmm) cc_final: 0.7301 (ptmm) REVERT: B 232 ASP cc_start: 0.8465 (m-30) cc_final: 0.8231 (m-30) REVERT: B 235 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.6717 (pp) REVERT: B 410 LYS cc_start: 0.7546 (pttt) cc_final: 0.6222 (mmtt) REVERT: C 13 VAL cc_start: 0.8601 (t) cc_final: 0.8317 (p) REVERT: C 105 ARG cc_start: 0.7214 (mtp-110) cc_final: 0.6922 (ttp80) REVERT: C 170 GLU cc_start: 0.3495 (OUTLIER) cc_final: 0.2581 (tp30) REVERT: C 196 GLU cc_start: 0.7198 (mp0) cc_final: 0.6765 (mt-10) REVERT: C 203 ARG cc_start: 0.7802 (mpt90) cc_final: 0.7156 (mtp180) REVERT: C 221 ILE cc_start: 0.7913 (mp) cc_final: 0.7629 (tt) REVERT: C 228 LYS cc_start: 0.7523 (ptmm) cc_final: 0.7234 (ptmm) REVERT: C 232 ASP cc_start: 0.8460 (m-30) cc_final: 0.8162 (m-30) REVERT: C 235 LEU cc_start: 0.7687 (OUTLIER) cc_final: 0.6892 (pp) REVERT: C 410 LYS cc_start: 0.7515 (pttt) cc_final: 0.6275 (mmtt) REVERT: C 459 TYR cc_start: 0.8638 (t80) cc_final: 0.8389 (t80) REVERT: D 15 ASP cc_start: 0.8323 (t0) cc_final: 0.8089 (t70) REVERT: D 149 ARG cc_start: 0.6573 (mpt180) cc_final: 0.6036 (mpt180) REVERT: D 165 PHE cc_start: 0.8247 (m-80) cc_final: 0.8042 (m-80) REVERT: D 170 GLU cc_start: 0.3476 (OUTLIER) cc_final: 0.2732 (tp30) REVERT: D 196 GLU cc_start: 0.7268 (mp0) cc_final: 0.6865 (mt-10) REVERT: D 203 ARG cc_start: 0.7783 (mpt90) cc_final: 0.7117 (mtp180) REVERT: D 235 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.6664 (pp) REVERT: D 410 LYS cc_start: 0.7619 (pttt) cc_final: 0.6262 (mmtt) REVERT: E 105 ARG cc_start: 0.7182 (mtp-110) cc_final: 0.6895 (ttp80) REVERT: E 149 ARG cc_start: 0.6826 (mpt180) cc_final: 0.6277 (mpt180) REVERT: E 170 GLU cc_start: 0.3303 (OUTLIER) cc_final: 0.2470 (tp30) REVERT: E 196 GLU cc_start: 0.7374 (mp0) cc_final: 0.6940 (mt-10) REVERT: E 203 ARG cc_start: 0.7830 (mpt90) cc_final: 0.7251 (mtp180) REVERT: E 221 ILE cc_start: 0.7847 (mp) cc_final: 0.7564 (tt) REVERT: E 228 LYS cc_start: 0.7531 (ptmm) cc_final: 0.7255 (ptmm) REVERT: E 232 ASP cc_start: 0.8471 (m-30) cc_final: 0.8196 (m-30) REVERT: E 235 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.6911 (pp) REVERT: E 286 MET cc_start: 0.8767 (tpp) cc_final: 0.8032 (tpt) REVERT: E 351 SER cc_start: 0.8228 (t) cc_final: 0.7927 (m) REVERT: E 410 LYS cc_start: 0.7494 (pttt) cc_final: 0.6362 (mmtt) REVERT: E 459 TYR cc_start: 0.8604 (t80) cc_final: 0.8360 (t80) REVERT: F 15 ASP cc_start: 0.8300 (t0) cc_final: 0.8049 (t70) REVERT: F 149 ARG cc_start: 0.6491 (mpp-170) cc_final: 0.6118 (mpt180) REVERT: F 170 GLU cc_start: 0.3106 (OUTLIER) cc_final: 0.2270 (tp30) REVERT: F 196 GLU cc_start: 0.7386 (mp0) cc_final: 0.6974 (mt-10) REVERT: F 203 ARG cc_start: 0.7782 (mpt90) cc_final: 0.7105 (mtp180) REVERT: F 217 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.5930 (mm-30) REVERT: F 235 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.6706 (pp) REVERT: F 410 LYS cc_start: 0.7548 (pttt) cc_final: 0.6227 (mmtt) REVERT: G 149 ARG cc_start: 0.6696 (mpt180) cc_final: 0.6118 (mpt180) REVERT: G 170 GLU cc_start: 0.3313 (OUTLIER) cc_final: 0.2499 (tp30) REVERT: G 196 GLU cc_start: 0.7307 (mp0) cc_final: 0.6855 (mt-10) REVERT: G 203 ARG cc_start: 0.7775 (mpt90) cc_final: 0.7163 (mtp180) REVERT: G 228 LYS cc_start: 0.7590 (ptmm) cc_final: 0.7315 (ptmm) REVERT: G 232 ASP cc_start: 0.8455 (m-30) cc_final: 0.8178 (m-30) REVERT: G 235 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.6898 (pp) REVERT: G 286 MET cc_start: 0.8722 (tpp) cc_final: 0.7960 (tpt) REVERT: G 410 LYS cc_start: 0.7376 (pttt) cc_final: 0.6121 (mmtt) REVERT: G 459 TYR cc_start: 0.8643 (t80) cc_final: 0.8376 (t80) REVERT: H 149 ARG cc_start: 0.6370 (mpp-170) cc_final: 0.6020 (mpt180) REVERT: H 170 GLU cc_start: 0.3348 (OUTLIER) cc_final: 0.2542 (tp30) REVERT: H 196 GLU cc_start: 0.7404 (mp0) cc_final: 0.6976 (mt-10) REVERT: H 203 ARG cc_start: 0.7727 (mpt90) cc_final: 0.7253 (mtp180) REVERT: H 235 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.6711 (pp) REVERT: H 286 MET cc_start: 0.8728 (tpp) cc_final: 0.7994 (tpt) REVERT: H 410 LYS cc_start: 0.7509 (pttt) cc_final: 0.6198 (mmtt) REVERT: J 5 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8405 (mp) REVERT: N 5 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8439 (mp) REVERT: P 5 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8521 (mp) outliers start: 99 outliers final: 53 residues processed: 614 average time/residue: 0.4086 time to fit residues: 412.4121 Evaluate side-chains 581 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 508 time to evaluate : 3.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 257 LYS Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain N residue 5 LEU Chi-restraints excluded: chain P residue 5 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 6.9990 chunk 268 optimal weight: 3.9990 chunk 185 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 170 optimal weight: 0.9980 chunk 239 optimal weight: 0.6980 chunk 357 optimal weight: 0.9990 chunk 378 optimal weight: 5.9990 chunk 186 optimal weight: 0.6980 chunk 339 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN E 48 GLN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN E 498 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31920 Z= 0.186 Angle : 0.528 6.472 43288 Z= 0.263 Chirality : 0.043 0.143 4928 Planarity : 0.004 0.039 5424 Dihedral : 17.172 177.872 4920 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.01 % Allowed : 12.01 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.13), residues: 3960 helix: -0.13 (0.14), residues: 1328 sheet: -1.26 (0.21), residues: 592 loop : -1.44 (0.13), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 466 PHE 0.014 0.001 PHE F 401 TYR 0.015 0.001 TYR B 509 ARG 0.002 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 717 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 586 time to evaluate : 3.456 Fit side-chains REVERT: A 105 ARG cc_start: 0.7233 (mtp-110) cc_final: 0.6927 (ttp80) REVERT: A 170 GLU cc_start: 0.3654 (OUTLIER) cc_final: 0.2553 (tp30) REVERT: A 196 GLU cc_start: 0.7425 (mp0) cc_final: 0.6939 (mt-10) REVERT: A 203 ARG cc_start: 0.7743 (mpt90) cc_final: 0.7087 (mtm110) REVERT: A 228 LYS cc_start: 0.7648 (ptmm) cc_final: 0.7428 (ptmm) REVERT: A 232 ASP cc_start: 0.8514 (m-30) cc_final: 0.8273 (m-30) REVERT: A 235 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7040 (pp) REVERT: A 286 MET cc_start: 0.8750 (tpp) cc_final: 0.8041 (tpt) REVERT: A 351 SER cc_start: 0.8328 (t) cc_final: 0.7945 (m) REVERT: A 408 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6588 (pp) REVERT: A 410 LYS cc_start: 0.7430 (pttt) cc_final: 0.6271 (mmtt) REVERT: B 170 GLU cc_start: 0.3571 (OUTLIER) cc_final: 0.2586 (tp30) REVERT: B 196 GLU cc_start: 0.7449 (mp0) cc_final: 0.7011 (mt-10) REVERT: B 203 ARG cc_start: 0.7805 (mpt90) cc_final: 0.7073 (mtm110) REVERT: B 217 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6050 (mm-30) REVERT: B 232 ASP cc_start: 0.8475 (m-30) cc_final: 0.8264 (m-30) REVERT: B 235 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.6856 (pp) REVERT: B 286 MET cc_start: 0.8794 (tpp) cc_final: 0.8142 (tpt) REVERT: B 351 SER cc_start: 0.8348 (t) cc_final: 0.7969 (m) REVERT: B 408 LEU cc_start: 0.7120 (OUTLIER) cc_final: 0.6671 (pp) REVERT: B 410 LYS cc_start: 0.7506 (pttt) cc_final: 0.6178 (mmtt) REVERT: C 13 VAL cc_start: 0.8665 (t) cc_final: 0.8414 (p) REVERT: C 105 ARG cc_start: 0.7282 (mtp-110) cc_final: 0.6963 (ttp80) REVERT: C 170 GLU cc_start: 0.3454 (OUTLIER) cc_final: 0.2306 (tp30) REVERT: C 196 GLU cc_start: 0.7346 (mp0) cc_final: 0.6874 (mt-10) REVERT: C 203 ARG cc_start: 0.7796 (mpt90) cc_final: 0.7059 (mtm110) REVERT: C 228 LYS cc_start: 0.7540 (ptmm) cc_final: 0.7307 (ptmm) REVERT: C 232 ASP cc_start: 0.8468 (m-30) cc_final: 0.8181 (m-30) REVERT: C 235 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.6982 (pp) REVERT: C 286 MET cc_start: 0.8784 (tpp) cc_final: 0.7989 (tpt) REVERT: C 351 SER cc_start: 0.8361 (t) cc_final: 0.7974 (m) REVERT: C 408 LEU cc_start: 0.6975 (OUTLIER) cc_final: 0.6597 (pp) REVERT: C 410 LYS cc_start: 0.7434 (pttt) cc_final: 0.6213 (mmtt) REVERT: C 459 TYR cc_start: 0.8670 (t80) cc_final: 0.8275 (t80) REVERT: D 13 VAL cc_start: 0.8532 (t) cc_final: 0.8301 (p) REVERT: D 15 ASP cc_start: 0.8351 (t0) cc_final: 0.8120 (t70) REVERT: D 170 GLU cc_start: 0.3406 (OUTLIER) cc_final: 0.2566 (tp30) REVERT: D 196 GLU cc_start: 0.7356 (mp0) cc_final: 0.6899 (mt-10) REVERT: D 203 ARG cc_start: 0.7750 (mpt90) cc_final: 0.6996 (mtm110) REVERT: D 217 GLU cc_start: 0.6436 (OUTLIER) cc_final: 0.5915 (mm-30) REVERT: D 235 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.6807 (pp) REVERT: D 410 LYS cc_start: 0.7479 (pttt) cc_final: 0.6045 (mmtt) REVERT: E 105 ARG cc_start: 0.7223 (mtp-110) cc_final: 0.6892 (ttp80) REVERT: E 170 GLU cc_start: 0.3420 (OUTLIER) cc_final: 0.2290 (tp30) REVERT: E 196 GLU cc_start: 0.7495 (mp0) cc_final: 0.7032 (mt-10) REVERT: E 203 ARG cc_start: 0.7814 (mpt90) cc_final: 0.7120 (mtm110) REVERT: E 228 LYS cc_start: 0.7552 (ptmm) cc_final: 0.7313 (ptmm) REVERT: E 232 ASP cc_start: 0.8493 (m-30) cc_final: 0.8224 (m-30) REVERT: E 235 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7043 (pp) REVERT: E 286 MET cc_start: 0.8830 (tpp) cc_final: 0.8186 (tpt) REVERT: E 351 SER cc_start: 0.8347 (t) cc_final: 0.7982 (m) REVERT: E 408 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6531 (pp) REVERT: E 410 LYS cc_start: 0.7478 (pttt) cc_final: 0.6313 (mmtt) REVERT: F 13 VAL cc_start: 0.8542 (t) cc_final: 0.8299 (p) REVERT: F 170 GLU cc_start: 0.3401 (OUTLIER) cc_final: 0.2411 (tp30) REVERT: F 196 GLU cc_start: 0.7444 (mp0) cc_final: 0.6996 (mt-10) REVERT: F 203 ARG cc_start: 0.7764 (mpt90) cc_final: 0.6996 (mtm110) REVERT: F 217 GLU cc_start: 0.6564 (OUTLIER) cc_final: 0.5952 (mm-30) REVERT: F 235 LEU cc_start: 0.7636 (OUTLIER) cc_final: 0.6855 (pp) REVERT: F 351 SER cc_start: 0.8338 (t) cc_final: 0.7960 (m) REVERT: F 410 LYS cc_start: 0.7500 (pttt) cc_final: 0.6115 (mmtt) REVERT: G 170 GLU cc_start: 0.3387 (OUTLIER) cc_final: 0.2294 (tp30) REVERT: G 196 GLU cc_start: 0.7441 (mp0) cc_final: 0.6951 (mt-10) REVERT: G 203 ARG cc_start: 0.7740 (mpt90) cc_final: 0.7046 (mtm110) REVERT: G 228 LYS cc_start: 0.7591 (ptmm) cc_final: 0.7365 (ptmm) REVERT: G 232 ASP cc_start: 0.8485 (m-30) cc_final: 0.8213 (m-30) REVERT: G 235 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7019 (pp) REVERT: G 286 MET cc_start: 0.8817 (tpp) cc_final: 0.8158 (tpt) REVERT: G 351 SER cc_start: 0.8302 (t) cc_final: 0.7954 (m) REVERT: G 408 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6613 (pp) REVERT: G 410 LYS cc_start: 0.7415 (pttt) cc_final: 0.6175 (mmtt) REVERT: H 13 VAL cc_start: 0.8522 (t) cc_final: 0.8274 (p) REVERT: H 150 MET cc_start: 0.8156 (mmm) cc_final: 0.7853 (mmm) REVERT: H 170 GLU cc_start: 0.3435 (OUTLIER) cc_final: 0.2385 (tp30) REVERT: H 196 GLU cc_start: 0.7548 (mp0) cc_final: 0.7077 (mt-10) REVERT: H 203 ARG cc_start: 0.7720 (mpt90) cc_final: 0.7108 (mtm110) REVERT: H 217 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.6041 (mm-30) REVERT: H 235 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.6824 (pp) REVERT: H 286 MET cc_start: 0.8777 (tpp) cc_final: 0.8138 (tpt) REVERT: H 351 SER cc_start: 0.8315 (t) cc_final: 0.7937 (m) REVERT: H 408 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6667 (pp) REVERT: H 410 LYS cc_start: 0.7592 (pttt) cc_final: 0.6270 (mmtt) outliers start: 131 outliers final: 73 residues processed: 675 average time/residue: 0.4013 time to fit residues: 445.5237 Evaluate side-chains 630 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 531 time to evaluate : 3.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 485 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 485 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 0.9980 chunk 215 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 282 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 323 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 193 optimal weight: 2.9990 chunk 340 optimal weight: 0.0170 chunk 95 optimal weight: 3.9990 overall best weight: 1.1620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 309 GLN A 334 GLN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 GLN B 309 GLN B 334 GLN B 466 HIS ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 309 GLN D 334 GLN E 48 GLN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN F 309 GLN F 334 GLN F 466 HIS ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 GLN G 309 GLN G 334 GLN G 343 GLN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 GLN H 334 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 31920 Z= 0.244 Angle : 0.553 6.352 43288 Z= 0.275 Chirality : 0.044 0.145 4928 Planarity : 0.004 0.039 5424 Dihedral : 17.111 177.005 4920 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.23 % Allowed : 13.14 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.13), residues: 3960 helix: 0.15 (0.15), residues: 1336 sheet: -1.16 (0.21), residues: 592 loop : -1.28 (0.13), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 466 PHE 0.007 0.001 PHE E 401 TYR 0.016 0.002 TYR F 509 ARG 0.005 0.000 ARG G 493 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 581 time to evaluate : 3.430 Fit side-chains REVERT: A 105 ARG cc_start: 0.7295 (mtp-110) cc_final: 0.6930 (ttp80) REVERT: A 170 GLU cc_start: 0.3637 (OUTLIER) cc_final: 0.2433 (tp30) REVERT: A 196 GLU cc_start: 0.7467 (mp0) cc_final: 0.6959 (mt-10) REVERT: A 199 GLU cc_start: 0.7606 (mm-30) cc_final: 0.7176 (mt-10) REVERT: A 203 ARG cc_start: 0.7849 (mpt90) cc_final: 0.7302 (mtp180) REVERT: A 232 ASP cc_start: 0.8493 (m-30) cc_final: 0.8239 (m-30) REVERT: A 235 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.6986 (pp) REVERT: A 274 ASP cc_start: 0.8582 (t0) cc_final: 0.8272 (t0) REVERT: A 408 LEU cc_start: 0.7036 (OUTLIER) cc_final: 0.6612 (pp) REVERT: A 410 LYS cc_start: 0.7607 (pttt) cc_final: 0.6402 (mmtt) REVERT: A 441 GLN cc_start: 0.8454 (mm-40) cc_final: 0.8242 (mm-40) REVERT: B 126 ARG cc_start: 0.5446 (mpt90) cc_final: 0.2709 (mmm-85) REVERT: B 196 GLU cc_start: 0.7541 (mp0) cc_final: 0.7124 (mt-10) REVERT: B 203 ARG cc_start: 0.7892 (mpt90) cc_final: 0.7153 (mtm110) REVERT: B 217 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.6061 (mm-30) REVERT: B 232 ASP cc_start: 0.8476 (m-30) cc_final: 0.8240 (m-30) REVERT: B 235 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.6857 (pp) REVERT: B 408 LEU cc_start: 0.7091 (OUTLIER) cc_final: 0.6665 (pp) REVERT: B 410 LYS cc_start: 0.7562 (pttt) cc_final: 0.6191 (mmtt) REVERT: B 441 GLN cc_start: 0.8434 (mm-40) cc_final: 0.8189 (mm-40) REVERT: C 105 ARG cc_start: 0.7341 (mtp-110) cc_final: 0.6972 (ttp80) REVERT: C 170 GLU cc_start: 0.3489 (OUTLIER) cc_final: 0.2235 (tp30) REVERT: C 196 GLU cc_start: 0.7370 (mp0) cc_final: 0.6905 (mt-10) REVERT: C 203 ARG cc_start: 0.7819 (mpt90) cc_final: 0.7074 (mtm110) REVERT: C 232 ASP cc_start: 0.8457 (m-30) cc_final: 0.8190 (m-30) REVERT: C 235 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.6953 (pp) REVERT: C 286 MET cc_start: 0.8845 (tpp) cc_final: 0.8060 (tpt) REVERT: C 330 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9102 (pp) REVERT: C 408 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6610 (pp) REVERT: C 410 LYS cc_start: 0.7604 (pttt) cc_final: 0.6372 (mmtt) REVERT: C 459 TYR cc_start: 0.8720 (t80) cc_final: 0.8270 (t80) REVERT: D 13 VAL cc_start: 0.8674 (t) cc_final: 0.8429 (p) REVERT: D 170 GLU cc_start: 0.3598 (OUTLIER) cc_final: 0.2477 (tp30) REVERT: D 196 GLU cc_start: 0.7435 (mp0) cc_final: 0.7002 (mt-10) REVERT: D 203 ARG cc_start: 0.7767 (mpt90) cc_final: 0.7143 (mtp180) REVERT: D 217 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.5999 (mm-30) REVERT: D 235 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.6782 (pp) REVERT: D 399 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6573 (mp0) REVERT: D 408 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6700 (pp) REVERT: D 410 LYS cc_start: 0.7512 (pttt) cc_final: 0.6050 (mmtt) REVERT: D 441 GLN cc_start: 0.8386 (mm-40) cc_final: 0.8144 (mm-40) REVERT: E 105 ARG cc_start: 0.7283 (mtp-110) cc_final: 0.6879 (ttp80) REVERT: E 170 GLU cc_start: 0.3444 (OUTLIER) cc_final: 0.2169 (tp30) REVERT: E 196 GLU cc_start: 0.7555 (mp0) cc_final: 0.7012 (mt-10) REVERT: E 203 ARG cc_start: 0.7913 (mpt90) cc_final: 0.7242 (mtm110) REVERT: E 232 ASP cc_start: 0.8482 (m-30) cc_final: 0.8219 (m-30) REVERT: E 235 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.6989 (pp) REVERT: E 286 MET cc_start: 0.8854 (tpp) cc_final: 0.8224 (tpt) REVERT: E 408 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6540 (pp) REVERT: E 410 LYS cc_start: 0.7525 (pttt) cc_final: 0.6389 (mmtt) REVERT: F 13 VAL cc_start: 0.8674 (t) cc_final: 0.8420 (p) REVERT: F 126 ARG cc_start: 0.5426 (mpt90) cc_final: 0.2708 (mmm-85) REVERT: F 196 GLU cc_start: 0.7551 (mp0) cc_final: 0.7072 (mt-10) REVERT: F 203 ARG cc_start: 0.7853 (mpt90) cc_final: 0.7238 (mtp180) REVERT: F 217 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.6043 (mm-30) REVERT: F 235 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.6818 (pp) REVERT: F 408 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6686 (pp) REVERT: F 410 LYS cc_start: 0.7545 (pttt) cc_final: 0.6170 (mmtt) REVERT: G 170 GLU cc_start: 0.3454 (OUTLIER) cc_final: 0.2260 (tp30) REVERT: G 196 GLU cc_start: 0.7490 (mp0) cc_final: 0.6937 (mt-10) REVERT: G 203 ARG cc_start: 0.7822 (mpt90) cc_final: 0.7264 (mtp180) REVERT: G 232 ASP cc_start: 0.8461 (m-30) cc_final: 0.8195 (m-30) REVERT: G 235 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.6929 (pp) REVERT: G 274 ASP cc_start: 0.8634 (t0) cc_final: 0.8310 (t0) REVERT: G 330 ILE cc_start: 0.9338 (OUTLIER) cc_final: 0.9136 (pp) REVERT: G 408 LEU cc_start: 0.7043 (OUTLIER) cc_final: 0.6627 (pp) REVERT: G 410 LYS cc_start: 0.7466 (pttt) cc_final: 0.6208 (mmtt) REVERT: H 13 VAL cc_start: 0.8658 (t) cc_final: 0.8407 (p) REVERT: H 170 GLU cc_start: 0.3412 (OUTLIER) cc_final: 0.2270 (tp30) REVERT: H 196 GLU cc_start: 0.7563 (mp0) cc_final: 0.7068 (mt-10) REVERT: H 199 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7504 (mt-10) REVERT: H 217 GLU cc_start: 0.6570 (OUTLIER) cc_final: 0.5981 (mm-30) REVERT: H 235 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.6812 (pp) REVERT: H 408 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6651 (pp) REVERT: H 410 LYS cc_start: 0.7636 (pttt) cc_final: 0.6304 (mmtt) outliers start: 138 outliers final: 77 residues processed: 671 average time/residue: 0.3983 time to fit residues: 441.8293 Evaluate side-chains 664 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 558 time to evaluate : 3.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain G residue 485 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 408 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 3.9990 chunk 341 optimal weight: 0.0470 chunk 74 optimal weight: 3.9990 chunk 222 optimal weight: 0.5980 chunk 93 optimal weight: 0.9990 chunk 379 optimal weight: 0.7980 chunk 314 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 199 optimal weight: 3.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 343 GLN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 GLN B 334 GLN ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN E 48 GLN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN F 334 GLN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 GLN G 334 GLN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 31920 Z= 0.164 Angle : 0.517 5.983 43288 Z= 0.256 Chirality : 0.043 0.149 4928 Planarity : 0.004 0.040 5424 Dihedral : 16.797 175.803 4913 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.74 % Allowed : 14.28 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -0.95 (0.13), residues: 3960 helix: 0.40 (0.15), residues: 1336 sheet: -1.04 (0.21), residues: 592 loop : -1.18 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 466 PHE 0.008 0.001 PHE E 401 TYR 0.025 0.001 TYR F 110 ARG 0.003 0.000 ARG C 493 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 531 time to evaluate : 3.675 Fit side-chains REVERT: A 105 ARG cc_start: 0.7238 (mtp-110) cc_final: 0.6871 (ttp80) REVERT: A 170 GLU cc_start: 0.3737 (OUTLIER) cc_final: 0.2685 (tp30) REVERT: A 196 GLU cc_start: 0.7434 (mp0) cc_final: 0.6940 (mt-10) REVERT: A 199 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7208 (mt-10) REVERT: A 203 ARG cc_start: 0.7812 (mpt90) cc_final: 0.7279 (mtp180) REVERT: A 235 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.6928 (pp) REVERT: A 274 ASP cc_start: 0.8543 (t0) cc_final: 0.8233 (t0) REVERT: A 408 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6585 (pp) REVERT: A 410 LYS cc_start: 0.7522 (pttt) cc_final: 0.6302 (mmtt) REVERT: B 126 ARG cc_start: 0.5504 (mpt90) cc_final: 0.2827 (mmm-85) REVERT: B 196 GLU cc_start: 0.7530 (mp0) cc_final: 0.7139 (mt-10) REVERT: B 199 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7456 (mt-10) REVERT: B 217 GLU cc_start: 0.6531 (OUTLIER) cc_final: 0.6029 (mm-30) REVERT: B 232 ASP cc_start: 0.8449 (m-30) cc_final: 0.8244 (m-30) REVERT: B 235 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.6751 (pp) REVERT: B 319 ASP cc_start: 0.7694 (m-30) cc_final: 0.7426 (m-30) REVERT: B 408 LEU cc_start: 0.7022 (OUTLIER) cc_final: 0.6650 (pp) REVERT: B 410 LYS cc_start: 0.7472 (pttt) cc_final: 0.6113 (mmtt) REVERT: C 105 ARG cc_start: 0.7288 (mtp-110) cc_final: 0.6908 (ttp80) REVERT: C 170 GLU cc_start: 0.3538 (OUTLIER) cc_final: 0.2512 (tp30) REVERT: C 196 GLU cc_start: 0.7351 (mp0) cc_final: 0.6884 (mt-10) REVERT: C 199 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7205 (mt-10) REVERT: C 221 ILE cc_start: 0.7832 (mp) cc_final: 0.7511 (tt) REVERT: C 228 LYS cc_start: 0.7895 (ptmm) cc_final: 0.7682 (ptmm) REVERT: C 235 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.6958 (pp) REVERT: C 286 MET cc_start: 0.8829 (tpp) cc_final: 0.8139 (tpt) REVERT: C 330 ILE cc_start: 0.9355 (OUTLIER) cc_final: 0.9135 (pp) REVERT: C 408 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6545 (pp) REVERT: C 410 LYS cc_start: 0.7412 (pttt) cc_final: 0.6148 (mmtt) REVERT: C 459 TYR cc_start: 0.8672 (t80) cc_final: 0.8301 (t80) REVERT: D 13 VAL cc_start: 0.8645 (t) cc_final: 0.8401 (p) REVERT: D 149 ARG cc_start: 0.6841 (mpt180) cc_final: 0.6273 (mpt180) REVERT: D 170 GLU cc_start: 0.3666 (OUTLIER) cc_final: 0.2778 (tp30) REVERT: D 196 GLU cc_start: 0.7394 (mp0) cc_final: 0.6996 (mt-10) REVERT: D 203 ARG cc_start: 0.7730 (mpt90) cc_final: 0.7117 (mtp180) REVERT: D 217 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.5961 (mm-30) REVERT: D 235 LEU cc_start: 0.7391 (OUTLIER) cc_final: 0.6703 (pp) REVERT: D 408 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6743 (pp) REVERT: D 410 LYS cc_start: 0.7470 (pttt) cc_final: 0.6040 (mmtt) REVERT: D 441 GLN cc_start: 0.8329 (mm-40) cc_final: 0.8086 (mm-40) REVERT: E 105 ARG cc_start: 0.7234 (mtp-110) cc_final: 0.6844 (ttp80) REVERT: E 170 GLU cc_start: 0.3485 (OUTLIER) cc_final: 0.2391 (tp30) REVERT: E 196 GLU cc_start: 0.7478 (mp0) cc_final: 0.6990 (mt-10) REVERT: E 199 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7173 (mt-10) REVERT: E 203 ARG cc_start: 0.7883 (mpt90) cc_final: 0.7192 (mtm110) REVERT: E 221 ILE cc_start: 0.7830 (mp) cc_final: 0.7508 (tt) REVERT: E 228 LYS cc_start: 0.7912 (ptmm) cc_final: 0.7548 (ptmm) REVERT: E 232 ASP cc_start: 0.8459 (m-30) cc_final: 0.8234 (m-30) REVERT: E 235 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.6960 (pp) REVERT: E 286 MET cc_start: 0.8882 (tpp) cc_final: 0.8278 (tpt) REVERT: E 408 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6510 (pp) REVERT: E 410 LYS cc_start: 0.7492 (pttt) cc_final: 0.6334 (mmtt) REVERT: F 13 VAL cc_start: 0.8649 (t) cc_final: 0.8401 (p) REVERT: F 126 ARG cc_start: 0.5500 (mpt90) cc_final: 0.2855 (mmm-85) REVERT: F 196 GLU cc_start: 0.7512 (mp0) cc_final: 0.7061 (mt-10) REVERT: F 203 ARG cc_start: 0.7799 (mpt90) cc_final: 0.7187 (mtp180) REVERT: F 217 GLU cc_start: 0.6646 (OUTLIER) cc_final: 0.6047 (mm-30) REVERT: F 235 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.6773 (pp) REVERT: F 408 LEU cc_start: 0.7040 (OUTLIER) cc_final: 0.6683 (pp) REVERT: F 410 LYS cc_start: 0.7453 (pttt) cc_final: 0.6111 (mmtt) REVERT: G 170 GLU cc_start: 0.3489 (OUTLIER) cc_final: 0.2450 (tp30) REVERT: G 196 GLU cc_start: 0.7434 (mp0) cc_final: 0.6951 (mt-10) REVERT: G 199 GLU cc_start: 0.7686 (mm-30) cc_final: 0.7236 (mt-10) REVERT: G 203 ARG cc_start: 0.7786 (mpt90) cc_final: 0.7228 (mtp180) REVERT: G 235 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.6932 (pp) REVERT: G 274 ASP cc_start: 0.8575 (t0) cc_final: 0.8263 (t0) REVERT: G 330 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9135 (pp) REVERT: G 351 SER cc_start: 0.8315 (t) cc_final: 0.7868 (m) REVERT: G 408 LEU cc_start: 0.7001 (OUTLIER) cc_final: 0.6616 (pp) REVERT: G 410 LYS cc_start: 0.7459 (pttt) cc_final: 0.6181 (mmtt) REVERT: H 13 VAL cc_start: 0.8619 (t) cc_final: 0.8380 (p) REVERT: H 149 ARG cc_start: 0.6698 (mpt180) cc_final: 0.6143 (mpt180) REVERT: H 170 GLU cc_start: 0.3636 (OUTLIER) cc_final: 0.2705 (tp30) REVERT: H 196 GLU cc_start: 0.7609 (mp0) cc_final: 0.7136 (mt-10) REVERT: H 217 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.6015 (tp30) REVERT: H 235 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.6785 (pp) REVERT: H 408 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6643 (pp) REVERT: H 410 LYS cc_start: 0.7580 (pttt) cc_final: 0.6265 (mmtt) outliers start: 122 outliers final: 65 residues processed: 619 average time/residue: 0.3985 time to fit residues: 404.4943 Evaluate side-chains 615 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 522 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 205 LYS Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 408 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 216 optimal weight: 0.2980 chunk 276 optimal weight: 0.6980 chunk 214 optimal weight: 5.9990 chunk 319 optimal weight: 3.9990 chunk 211 optimal weight: 0.9980 chunk 377 optimal weight: 7.9990 chunk 236 optimal weight: 2.9990 chunk 230 optimal weight: 5.9990 chunk 174 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 GLN ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 343 GLN ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 GLN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 31920 Z= 0.313 Angle : 0.590 6.844 43288 Z= 0.294 Chirality : 0.045 0.146 4928 Planarity : 0.004 0.040 5424 Dihedral : 17.005 174.580 4913 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.95 % Allowed : 14.28 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -0.95 (0.13), residues: 3960 helix: 0.38 (0.15), residues: 1320 sheet: -1.07 (0.21), residues: 592 loop : -1.14 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS A 466 PHE 0.008 0.001 PHE A 24 TYR 0.021 0.002 TYR F 110 ARG 0.004 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 567 time to evaluate : 3.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ARG cc_start: 0.7462 (mtp-110) cc_final: 0.7052 (ttp80) REVERT: A 170 GLU cc_start: 0.3609 (OUTLIER) cc_final: 0.2474 (tp30) REVERT: A 196 GLU cc_start: 0.7504 (mp0) cc_final: 0.7006 (mt-10) REVERT: A 199 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7164 (mt-10) REVERT: A 203 ARG cc_start: 0.7849 (mpt90) cc_final: 0.7331 (mtp180) REVERT: A 217 GLU cc_start: 0.6122 (tp30) cc_final: 0.5771 (tp30) REVERT: A 235 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7209 (pp) REVERT: A 274 ASP cc_start: 0.8665 (t0) cc_final: 0.8362 (t0) REVERT: A 408 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6671 (pp) REVERT: A 410 LYS cc_start: 0.7531 (pttt) cc_final: 0.6206 (mmtt) REVERT: A 441 GLN cc_start: 0.8518 (mm-40) cc_final: 0.8287 (mm-40) REVERT: B 196 GLU cc_start: 0.7522 (mp0) cc_final: 0.7155 (mt-10) REVERT: B 217 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.6083 (tp30) REVERT: B 235 LEU cc_start: 0.7552 (OUTLIER) cc_final: 0.7013 (pp) REVERT: B 330 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.9119 (pp) REVERT: B 408 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6681 (pp) REVERT: B 410 LYS cc_start: 0.7636 (pttt) cc_final: 0.6238 (mmtt) REVERT: B 441 GLN cc_start: 0.8446 (mm-40) cc_final: 0.8190 (mm-40) REVERT: C 105 ARG cc_start: 0.7448 (mtp-110) cc_final: 0.7017 (ttp80) REVERT: C 126 ARG cc_start: 0.5617 (mpt90) cc_final: 0.2629 (mtp85) REVERT: C 196 GLU cc_start: 0.7373 (mp0) cc_final: 0.6900 (mt-10) REVERT: C 217 GLU cc_start: 0.6133 (tp30) cc_final: 0.5803 (tp30) REVERT: C 235 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7159 (pp) REVERT: C 286 MET cc_start: 0.8867 (tpp) cc_final: 0.8190 (tpt) REVERT: C 330 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9131 (pp) REVERT: C 408 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6652 (pp) REVERT: C 410 LYS cc_start: 0.7600 (pttt) cc_final: 0.6283 (mmtt) REVERT: C 441 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8298 (mm-40) REVERT: D 170 GLU cc_start: 0.3607 (OUTLIER) cc_final: 0.2556 (tp30) REVERT: D 196 GLU cc_start: 0.7452 (mp0) cc_final: 0.7050 (mt-10) REVERT: D 199 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7262 (mt-10) REVERT: D 203 ARG cc_start: 0.7766 (mpt90) cc_final: 0.7162 (mtp180) REVERT: D 217 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.6039 (mm-30) REVERT: D 235 LEU cc_start: 0.7504 (OUTLIER) cc_final: 0.6967 (pp) REVERT: D 408 LEU cc_start: 0.7184 (OUTLIER) cc_final: 0.6791 (pp) REVERT: D 410 LYS cc_start: 0.7580 (pttt) cc_final: 0.6055 (mmtt) REVERT: D 441 GLN cc_start: 0.8526 (mm-40) cc_final: 0.8257 (mm-40) REVERT: E 170 GLU cc_start: 0.3448 (OUTLIER) cc_final: 0.2230 (tp30) REVERT: E 196 GLU cc_start: 0.7577 (mp0) cc_final: 0.7259 (mp0) REVERT: E 203 ARG cc_start: 0.7950 (mpt90) cc_final: 0.7226 (mtm110) REVERT: E 235 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7228 (pp) REVERT: E 286 MET cc_start: 0.8901 (tpp) cc_final: 0.8330 (tpt) REVERT: E 330 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.9093 (pp) REVERT: E 408 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6633 (pp) REVERT: E 410 LYS cc_start: 0.7535 (pttt) cc_final: 0.6343 (mmtt) REVERT: F 196 GLU cc_start: 0.7617 (mp0) cc_final: 0.7160 (mt-10) REVERT: F 203 ARG cc_start: 0.7843 (mpt90) cc_final: 0.7236 (mtp180) REVERT: F 217 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.6136 (mm-30) REVERT: F 235 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.7025 (pp) REVERT: F 408 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6849 (pp) REVERT: F 410 LYS cc_start: 0.7550 (pttt) cc_final: 0.6095 (mmtt) REVERT: G 170 GLU cc_start: 0.3421 (OUTLIER) cc_final: 0.2287 (tp30) REVERT: G 196 GLU cc_start: 0.7517 (mp0) cc_final: 0.6992 (mt-10) REVERT: G 203 ARG cc_start: 0.7829 (mpt90) cc_final: 0.7292 (mtp180) REVERT: G 235 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.7129 (pp) REVERT: G 274 ASP cc_start: 0.8638 (t0) cc_final: 0.8345 (t0) REVERT: G 330 ILE cc_start: 0.9396 (OUTLIER) cc_final: 0.9170 (pp) REVERT: G 408 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6720 (pp) REVERT: G 410 LYS cc_start: 0.7542 (pttt) cc_final: 0.6221 (mmtt) REVERT: H 170 GLU cc_start: 0.3565 (OUTLIER) cc_final: 0.2466 (tp30) REVERT: H 196 GLU cc_start: 0.7700 (mp0) cc_final: 0.7242 (mt-10) REVERT: H 199 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7459 (mt-10) REVERT: H 217 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6109 (tp30) REVERT: H 235 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7013 (pp) REVERT: H 286 MET cc_start: 0.8851 (tpp) cc_final: 0.8315 (tpt) REVERT: H 408 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6759 (pp) REVERT: H 410 LYS cc_start: 0.7605 (pttt) cc_final: 0.6256 (mmtt) outliers start: 129 outliers final: 84 residues processed: 650 average time/residue: 0.3991 time to fit residues: 423.4973 Evaluate side-chains 662 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 549 time to evaluate : 3.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 339 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 339 CYS Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 48 GLN Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 339 CYS Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 280 SER Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 339 CYS Chi-restraints excluded: chain H residue 408 LEU Chi-restraints excluded: chain H residue 485 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 7.9990 chunk 150 optimal weight: 0.5980 chunk 225 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 240 optimal weight: 5.9990 chunk 257 optimal weight: 4.9990 chunk 186 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 296 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 GLN B 277 GLN ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN C 334 GLN ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN D 343 GLN E 48 GLN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN F 334 GLN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 GLN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31920 Z= 0.176 Angle : 0.535 6.847 43288 Z= 0.266 Chirality : 0.043 0.145 4928 Planarity : 0.004 0.041 5424 Dihedral : 16.752 173.162 4910 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.55 % Allowed : 15.32 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -0.84 (0.14), residues: 3960 helix: 0.48 (0.15), residues: 1320 sheet: -1.01 (0.21), residues: 592 loop : -1.08 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 466 PHE 0.014 0.001 PHE F 401 TYR 0.018 0.001 TYR D 110 ARG 0.013 0.000 ARG A 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 518 time to evaluate : 3.169 Fit side-chains revert: symmetry clash REVERT: A 105 ARG cc_start: 0.7396 (mtp-110) cc_final: 0.7005 (ttp80) REVERT: A 170 GLU cc_start: 0.3625 (OUTLIER) cc_final: 0.2832 (tp30) REVERT: A 196 GLU cc_start: 0.7434 (mp0) cc_final: 0.6974 (mt-10) REVERT: A 199 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7113 (mt-10) REVERT: A 203 ARG cc_start: 0.7818 (mpt90) cc_final: 0.7319 (mtp180) REVERT: A 217 GLU cc_start: 0.6048 (tp30) cc_final: 0.5679 (tp30) REVERT: A 235 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7304 (pp) REVERT: A 274 ASP cc_start: 0.8557 (t0) cc_final: 0.8237 (t0) REVERT: A 330 ILE cc_start: 0.9398 (OUTLIER) cc_final: 0.9156 (pp) REVERT: A 408 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6627 (pp) REVERT: A 410 LYS cc_start: 0.7509 (pttt) cc_final: 0.6174 (mmtt) REVERT: B 126 ARG cc_start: 0.5524 (mpt90) cc_final: 0.2827 (mmm-85) REVERT: B 196 GLU cc_start: 0.7431 (mp0) cc_final: 0.7034 (mt-10) REVERT: B 199 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7304 (mt-10) REVERT: B 217 GLU cc_start: 0.6544 (OUTLIER) cc_final: 0.6016 (tp30) REVERT: B 235 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7093 (pp) REVERT: B 330 ILE cc_start: 0.9342 (OUTLIER) cc_final: 0.9098 (pp) REVERT: B 408 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6646 (pp) REVERT: B 410 LYS cc_start: 0.7492 (pttt) cc_final: 0.6083 (mmtt) REVERT: B 441 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8148 (mm-40) REVERT: C 105 ARG cc_start: 0.7419 (mtp-110) cc_final: 0.7005 (ttp80) REVERT: C 126 ARG cc_start: 0.5605 (mpt90) cc_final: 0.2693 (mtp85) REVERT: C 196 GLU cc_start: 0.7304 (mp0) cc_final: 0.6619 (mp0) REVERT: C 203 ARG cc_start: 0.7597 (mpt180) cc_final: 0.6763 (mtm110) REVERT: C 217 GLU cc_start: 0.6084 (tp30) cc_final: 0.5722 (tp30) REVERT: C 221 ILE cc_start: 0.7589 (mp) cc_final: 0.7370 (tt) REVERT: C 235 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7364 (pp) REVERT: C 330 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9105 (pp) REVERT: C 408 LEU cc_start: 0.6952 (OUTLIER) cc_final: 0.6558 (pp) REVERT: C 410 LYS cc_start: 0.7564 (pttt) cc_final: 0.6272 (mmtt) REVERT: C 459 TYR cc_start: 0.8640 (t80) cc_final: 0.8278 (t80) REVERT: D 170 GLU cc_start: 0.3566 (OUTLIER) cc_final: 0.2948 (tp30) REVERT: D 196 GLU cc_start: 0.7411 (mp0) cc_final: 0.7007 (mt-10) REVERT: D 199 GLU cc_start: 0.7654 (mm-30) cc_final: 0.7342 (mt-10) REVERT: D 217 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.5984 (tp30) REVERT: D 235 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.7049 (pp) REVERT: D 408 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6676 (pp) REVERT: D 410 LYS cc_start: 0.7465 (pttt) cc_final: 0.6007 (mmtt) REVERT: D 441 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8176 (mm-40) REVERT: E 170 GLU cc_start: 0.3431 (OUTLIER) cc_final: 0.2612 (tp30) REVERT: E 196 GLU cc_start: 0.7503 (mp0) cc_final: 0.7243 (mp0) REVERT: E 199 GLU cc_start: 0.7493 (mm-30) cc_final: 0.7091 (mt-10) REVERT: E 203 ARG cc_start: 0.7919 (mpt90) cc_final: 0.7084 (mtm110) REVERT: E 221 ILE cc_start: 0.7592 (mp) cc_final: 0.7348 (tt) REVERT: E 235 LEU cc_start: 0.7622 (OUTLIER) cc_final: 0.7377 (pp) REVERT: E 330 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9088 (pp) REVERT: E 408 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6514 (pp) REVERT: E 410 LYS cc_start: 0.7429 (pttt) cc_final: 0.6226 (mmtt) REVERT: F 126 ARG cc_start: 0.5559 (mpt90) cc_final: 0.2559 (mtp85) REVERT: F 196 GLU cc_start: 0.7464 (mp0) cc_final: 0.7025 (mt-10) REVERT: F 199 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7368 (mt-10) REVERT: F 217 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6126 (tp30) REVERT: F 235 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7159 (pp) REVERT: F 408 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6702 (pp) REVERT: F 410 LYS cc_start: 0.7548 (pttt) cc_final: 0.6095 (mmtt) REVERT: G 170 GLU cc_start: 0.3430 (OUTLIER) cc_final: 0.2596 (tp30) REVERT: G 196 GLU cc_start: 0.7449 (mp0) cc_final: 0.6980 (mt-10) REVERT: G 199 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7110 (mt-10) REVERT: G 203 ARG cc_start: 0.7790 (mpt90) cc_final: 0.7160 (mtp180) REVERT: G 235 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7334 (pp) REVERT: G 274 ASP cc_start: 0.8596 (t0) cc_final: 0.8274 (t0) REVERT: G 330 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.9105 (pp) REVERT: G 408 LEU cc_start: 0.7026 (OUTLIER) cc_final: 0.6626 (pp) REVERT: G 410 LYS cc_start: 0.7477 (pttt) cc_final: 0.6168 (mmtt) REVERT: H 170 GLU cc_start: 0.3484 (OUTLIER) cc_final: 0.2708 (tp30) REVERT: H 196 GLU cc_start: 0.7654 (mp0) cc_final: 0.7223 (mt-10) REVERT: H 217 GLU cc_start: 0.6577 (OUTLIER) cc_final: 0.6056 (tp30) REVERT: H 235 LEU cc_start: 0.7449 (OUTLIER) cc_final: 0.7131 (pp) REVERT: H 408 LEU cc_start: 0.7064 (OUTLIER) cc_final: 0.6631 (pp) REVERT: H 410 LYS cc_start: 0.7490 (pttt) cc_final: 0.6149 (mmtt) outliers start: 116 outliers final: 72 residues processed: 606 average time/residue: 0.3840 time to fit residues: 379.9226 Evaluate side-chains 612 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 510 time to evaluate : 3.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 114 PHE Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 114 PHE Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 309 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 408 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 0.9990 chunk 361 optimal weight: 1.9990 chunk 330 optimal weight: 1.9990 chunk 352 optimal weight: 8.9990 chunk 211 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 chunk 276 optimal weight: 3.9990 chunk 108 optimal weight: 0.2980 chunk 318 optimal weight: 2.9990 chunk 332 optimal weight: 1.9990 chunk 350 optimal weight: 8.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 GLN B 334 GLN ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 309 GLN ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 48 GLN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN G 48 GLN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 GLN G 334 GLN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31920 Z= 0.225 Angle : 0.553 7.411 43288 Z= 0.274 Chirality : 0.044 0.190 4928 Planarity : 0.004 0.047 5424 Dihedral : 16.727 172.210 4910 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.55 % Allowed : 15.69 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -0.81 (0.14), residues: 3960 helix: 0.51 (0.15), residues: 1320 sheet: -0.98 (0.21), residues: 592 loop : -1.06 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS C 137 PHE 0.008 0.001 PHE E 401 TYR 0.023 0.002 TYR G 411 ARG 0.011 0.000 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 543 time to evaluate : 3.509 Fit side-chains revert: symmetry clash REVERT: A 105 ARG cc_start: 0.7477 (mtp-110) cc_final: 0.7067 (ttp80) REVERT: A 170 GLU cc_start: 0.3721 (OUTLIER) cc_final: 0.2900 (tp30) REVERT: A 196 GLU cc_start: 0.7456 (mp0) cc_final: 0.6994 (mt-10) REVERT: A 199 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7120 (mt-10) REVERT: A 203 ARG cc_start: 0.7828 (mpt90) cc_final: 0.7298 (mtp180) REVERT: A 217 GLU cc_start: 0.6087 (tp30) cc_final: 0.5666 (tp30) REVERT: A 235 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7326 (pp) REVERT: A 274 ASP cc_start: 0.8541 (t0) cc_final: 0.8228 (t0) REVERT: A 330 ILE cc_start: 0.9417 (OUTLIER) cc_final: 0.9142 (pp) REVERT: A 408 LEU cc_start: 0.7055 (OUTLIER) cc_final: 0.6634 (pp) REVERT: A 410 LYS cc_start: 0.7533 (pttt) cc_final: 0.6198 (mmtt) REVERT: A 441 GLN cc_start: 0.8455 (mm-40) cc_final: 0.8221 (mm-40) REVERT: B 126 ARG cc_start: 0.5587 (mpt90) cc_final: 0.2466 (mtp85) REVERT: B 196 GLU cc_start: 0.7392 (mp0) cc_final: 0.7002 (mt-10) REVERT: B 199 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7351 (mt-10) REVERT: B 217 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6035 (tp30) REVERT: B 235 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7112 (pp) REVERT: B 330 ILE cc_start: 0.9346 (OUTLIER) cc_final: 0.9125 (pp) REVERT: B 408 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6651 (pp) REVERT: B 410 LYS cc_start: 0.7558 (pttt) cc_final: 0.6112 (mmtt) REVERT: B 441 GLN cc_start: 0.8441 (mm-40) cc_final: 0.8195 (mm-40) REVERT: C 105 ARG cc_start: 0.7442 (mtp-110) cc_final: 0.7008 (ttp80) REVERT: C 112 GLN cc_start: 0.7372 (tp40) cc_final: 0.7125 (tp-100) REVERT: C 126 ARG cc_start: 0.5667 (mpt90) cc_final: 0.2693 (mtp85) REVERT: C 196 GLU cc_start: 0.7248 (mp0) cc_final: 0.6760 (mt-10) REVERT: C 199 GLU cc_start: 0.7416 (mm-30) cc_final: 0.7163 (mt-10) REVERT: C 203 ARG cc_start: 0.7519 (mpt180) cc_final: 0.7307 (mpt180) REVERT: C 235 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7330 (pp) REVERT: C 330 ILE cc_start: 0.9352 (OUTLIER) cc_final: 0.9105 (pp) REVERT: C 408 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6601 (pp) REVERT: C 410 LYS cc_start: 0.7504 (pttt) cc_final: 0.6201 (mmtt) REVERT: C 459 TYR cc_start: 0.8674 (t80) cc_final: 0.8263 (t80) REVERT: D 170 GLU cc_start: 0.3672 (OUTLIER) cc_final: 0.2945 (tp30) REVERT: D 196 GLU cc_start: 0.7394 (mp0) cc_final: 0.6968 (mt-10) REVERT: D 199 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7254 (mt-10) REVERT: D 217 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6001 (tp30) REVERT: D 235 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7080 (pp) REVERT: D 408 LEU cc_start: 0.7124 (OUTLIER) cc_final: 0.6819 (pp) REVERT: D 410 LYS cc_start: 0.7552 (pttt) cc_final: 0.6028 (mmtt) REVERT: D 441 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8204 (mm-40) REVERT: E 170 GLU cc_start: 0.3568 (OUTLIER) cc_final: 0.2640 (tp30) REVERT: E 196 GLU cc_start: 0.7568 (mp0) cc_final: 0.7301 (mp0) REVERT: E 199 GLU cc_start: 0.7391 (mm-30) cc_final: 0.7039 (mt-10) REVERT: E 203 ARG cc_start: 0.7863 (mpt90) cc_final: 0.7078 (mtm110) REVERT: E 235 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7360 (pp) REVERT: E 286 MET cc_start: 0.8917 (tpp) cc_final: 0.8445 (tpt) REVERT: E 330 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9097 (pp) REVERT: E 408 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6571 (pp) REVERT: E 410 LYS cc_start: 0.7472 (pttt) cc_final: 0.6214 (mmtt) REVERT: F 126 ARG cc_start: 0.5574 (mpt90) cc_final: 0.2496 (mtp85) REVERT: F 196 GLU cc_start: 0.7534 (mp0) cc_final: 0.7093 (mt-10) REVERT: F 217 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6153 (tp30) REVERT: F 235 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7133 (pp) REVERT: F 408 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6707 (pp) REVERT: F 410 LYS cc_start: 0.7556 (pttt) cc_final: 0.6086 (mmtt) REVERT: G 170 GLU cc_start: 0.3540 (OUTLIER) cc_final: 0.2682 (tp30) REVERT: G 196 GLU cc_start: 0.7467 (mp0) cc_final: 0.6991 (mt-10) REVERT: G 199 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7133 (mt-10) REVERT: G 203 ARG cc_start: 0.7739 (mpt90) cc_final: 0.7155 (mtp180) REVERT: G 235 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7296 (pp) REVERT: G 274 ASP cc_start: 0.8604 (t0) cc_final: 0.8311 (t0) REVERT: G 330 ILE cc_start: 0.9372 (OUTLIER) cc_final: 0.9114 (pp) REVERT: G 408 LEU cc_start: 0.7053 (OUTLIER) cc_final: 0.6644 (pp) REVERT: G 410 LYS cc_start: 0.7524 (pttt) cc_final: 0.6201 (mmtt) REVERT: H 170 GLU cc_start: 0.3654 (OUTLIER) cc_final: 0.2815 (tp30) REVERT: H 196 GLU cc_start: 0.7676 (mp0) cc_final: 0.7257 (mt-10) REVERT: H 199 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7403 (mt-10) REVERT: H 217 GLU cc_start: 0.6582 (OUTLIER) cc_final: 0.6045 (tp30) REVERT: H 235 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7113 (pp) REVERT: H 408 LEU cc_start: 0.7093 (OUTLIER) cc_final: 0.6676 (pp) REVERT: H 410 LYS cc_start: 0.7495 (pttt) cc_final: 0.6148 (mmtt) outliers start: 116 outliers final: 80 residues processed: 621 average time/residue: 0.4001 time to fit residues: 407.7916 Evaluate side-chains 641 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 531 time to evaluate : 3.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 170 GLU Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 112 GLN Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 331 CYS Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 408 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 3.9990 chunk 372 optimal weight: 2.9990 chunk 227 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 258 optimal weight: 0.7980 chunk 390 optimal weight: 4.9990 chunk 359 optimal weight: 5.9990 chunk 310 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 240 optimal weight: 6.9990 chunk 190 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 GLN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 31920 Z= 0.314 Angle : 0.600 8.291 43288 Z= 0.299 Chirality : 0.045 0.141 4928 Planarity : 0.004 0.044 5424 Dihedral : 16.938 171.412 4910 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.55 % Allowed : 15.90 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -0.90 (0.14), residues: 3960 helix: 0.35 (0.15), residues: 1336 sheet: -1.04 (0.21), residues: 592 loop : -1.06 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 466 PHE 0.017 0.001 PHE D 401 TYR 0.029 0.002 TYR G 110 ARG 0.011 0.001 ARG C 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7920 Ramachandran restraints generated. 3960 Oldfield, 0 Emsley, 3960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 545 time to evaluate : 3.760 Fit side-chains revert: symmetry clash REVERT: A 105 ARG cc_start: 0.7459 (mtp-110) cc_final: 0.6889 (ttt-90) REVERT: A 170 GLU cc_start: 0.3739 (OUTLIER) cc_final: 0.2847 (tp30) REVERT: A 196 GLU cc_start: 0.7528 (mp0) cc_final: 0.7048 (mt-10) REVERT: A 199 GLU cc_start: 0.7601 (mm-30) cc_final: 0.7108 (mt-10) REVERT: A 203 ARG cc_start: 0.7862 (mpt90) cc_final: 0.7362 (mtp180) REVERT: A 235 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7286 (pp) REVERT: A 274 ASP cc_start: 0.8640 (t0) cc_final: 0.8355 (t0) REVERT: A 286 MET cc_start: 0.8840 (tpp) cc_final: 0.8339 (tpt) REVERT: A 330 ILE cc_start: 0.9435 (OUTLIER) cc_final: 0.9182 (pp) REVERT: A 408 LEU cc_start: 0.7182 (OUTLIER) cc_final: 0.6740 (pp) REVERT: A 410 LYS cc_start: 0.7537 (pttt) cc_final: 0.6216 (mmtt) REVERT: A 441 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8255 (mm-40) REVERT: B 126 ARG cc_start: 0.5768 (mpt90) cc_final: 0.2528 (mtp85) REVERT: B 165 PHE cc_start: 0.8366 (m-80) cc_final: 0.8139 (m-80) REVERT: B 196 GLU cc_start: 0.7462 (mp0) cc_final: 0.7099 (mt-10) REVERT: B 199 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7412 (mt-10) REVERT: B 217 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6067 (tp30) REVERT: B 235 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7002 (pp) REVERT: B 286 MET cc_start: 0.8866 (tpp) cc_final: 0.8413 (tpt) REVERT: B 330 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9138 (pp) REVERT: B 408 LEU cc_start: 0.7202 (OUTLIER) cc_final: 0.6722 (pp) REVERT: B 410 LYS cc_start: 0.7578 (pttt) cc_final: 0.6098 (mmtt) REVERT: B 441 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8227 (mm-40) REVERT: C 126 ARG cc_start: 0.5639 (mpt90) cc_final: 0.2604 (mtp85) REVERT: C 199 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7155 (mt-10) REVERT: C 235 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7311 (pp) REVERT: C 286 MET cc_start: 0.8903 (tpp) cc_final: 0.8216 (tpt) REVERT: C 330 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9130 (pp) REVERT: C 408 LEU cc_start: 0.7108 (OUTLIER) cc_final: 0.6670 (pp) REVERT: C 410 LYS cc_start: 0.7576 (pttt) cc_final: 0.6157 (mmtt) REVERT: D 170 GLU cc_start: 0.3722 (OUTLIER) cc_final: 0.2907 (tp30) REVERT: D 196 GLU cc_start: 0.7355 (mp0) cc_final: 0.6961 (mt-10) REVERT: D 199 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7123 (mt-10) REVERT: D 203 ARG cc_start: 0.7563 (mpt180) cc_final: 0.7206 (mtp180) REVERT: D 217 GLU cc_start: 0.6637 (OUTLIER) cc_final: 0.6066 (tp30) REVERT: D 235 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7047 (pp) REVERT: D 408 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6819 (pp) REVERT: D 410 LYS cc_start: 0.7588 (pttt) cc_final: 0.6038 (mmtt) REVERT: D 441 GLN cc_start: 0.8519 (mm-40) cc_final: 0.8252 (mm-40) REVERT: E 126 ARG cc_start: 0.5636 (mpt90) cc_final: 0.2490 (mtp85) REVERT: E 196 GLU cc_start: 0.7628 (mp0) cc_final: 0.7302 (mp0) REVERT: E 199 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7174 (mt-10) REVERT: E 203 ARG cc_start: 0.7901 (mpt90) cc_final: 0.7152 (mtm110) REVERT: E 221 ILE cc_start: 0.7887 (mp) cc_final: 0.7629 (tt) REVERT: E 235 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7239 (pp) REVERT: E 286 MET cc_start: 0.8923 (tpp) cc_final: 0.8421 (tpt) REVERT: E 330 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9118 (pp) REVERT: E 408 LEU cc_start: 0.7069 (OUTLIER) cc_final: 0.6627 (pp) REVERT: E 410 LYS cc_start: 0.7644 (pttt) cc_final: 0.6361 (mmtt) REVERT: F 126 ARG cc_start: 0.5767 (mpt90) cc_final: 0.2579 (mtp85) REVERT: F 196 GLU cc_start: 0.7556 (mp0) cc_final: 0.7112 (mt-10) REVERT: F 217 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.6149 (tp30) REVERT: F 235 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7105 (pp) REVERT: F 408 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6799 (pp) REVERT: F 410 LYS cc_start: 0.7617 (pttt) cc_final: 0.6152 (mmtt) REVERT: G 165 PHE cc_start: 0.8277 (m-80) cc_final: 0.8071 (m-80) REVERT: G 170 GLU cc_start: 0.3535 (OUTLIER) cc_final: 0.2638 (tp30) REVERT: G 196 GLU cc_start: 0.7551 (mp0) cc_final: 0.7070 (mt-10) REVERT: G 199 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7130 (mt-10) REVERT: G 203 ARG cc_start: 0.7790 (mpt90) cc_final: 0.7265 (mtm110) REVERT: G 235 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7308 (pp) REVERT: G 274 ASP cc_start: 0.8646 (t0) cc_final: 0.8355 (t0) REVERT: G 330 ILE cc_start: 0.9404 (OUTLIER) cc_final: 0.9159 (pp) REVERT: G 408 LEU cc_start: 0.7165 (OUTLIER) cc_final: 0.6737 (pp) REVERT: G 410 LYS cc_start: 0.7575 (pttt) cc_final: 0.6250 (mmtt) REVERT: H 170 GLU cc_start: 0.3978 (OUTLIER) cc_final: 0.3072 (tp30) REVERT: H 196 GLU cc_start: 0.7705 (mp0) cc_final: 0.7273 (mt-10) REVERT: H 217 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6181 (tp30) REVERT: H 235 LEU cc_start: 0.7420 (OUTLIER) cc_final: 0.6992 (pp) REVERT: H 286 MET cc_start: 0.8852 (tpp) cc_final: 0.8411 (tpt) REVERT: H 408 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6732 (pp) REVERT: H 410 LYS cc_start: 0.7658 (pttt) cc_final: 0.6257 (mmtt) outliers start: 116 outliers final: 82 residues processed: 624 average time/residue: 0.4091 time to fit residues: 419.1471 Evaluate side-chains 640 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 529 time to evaluate : 3.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 331 CYS Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 193 THR Chi-restraints excluded: chain B residue 217 GLU Chi-restraints excluded: chain B residue 225 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 74 THR Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 268 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 280 SER Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 331 CYS Chi-restraints excluded: chain C residue 408 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 193 THR Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 217 GLU Chi-restraints excluded: chain D residue 225 THR Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 329 SER Chi-restraints excluded: chain D residue 331 CYS Chi-restraints excluded: chain D residue 408 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 74 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 268 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 329 SER Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 331 CYS Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 408 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 74 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 170 GLU Chi-restraints excluded: chain G residue 201 LEU Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 331 CYS Chi-restraints excluded: chain G residue 408 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 170 GLU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 268 VAL Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 408 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 0.6980 chunk 331 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 286 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 311 optimal weight: 3.9990 chunk 130 optimal weight: 0.2980 chunk 319 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 GLN B 334 GLN ** C 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 277 GLN G 48 GLN ** G 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 GLN G 334 GLN ** H 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.152113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.115094 restraints weight = 36239.999| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.36 r_work: 0.3165 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 31920 Z= 0.169 Angle : 0.534 7.246 43288 Z= 0.265 Chirality : 0.043 0.138 4928 Planarity : 0.004 0.046 5424 Dihedral : 16.659 172.365 4906 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.25 % Allowed : 16.45 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -0.78 (0.14), residues: 3960 helix: 0.49 (0.15), residues: 1336 sheet: -0.97 (0.21), residues: 592 loop : -1.01 (0.14), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 137 PHE 0.016 0.001 PHE D 401 TYR 0.023 0.001 TYR G 110 ARG 0.011 0.000 ARG C 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8461.67 seconds wall clock time: 153 minutes 4.99 seconds (9184.99 seconds total)