Starting phenix.real_space_refine on Fri Mar 22 00:23:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ua2_20704/03_2024/6ua2_20704_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ua2_20704/03_2024/6ua2_20704.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ua2_20704/03_2024/6ua2_20704.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ua2_20704/03_2024/6ua2_20704.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ua2_20704/03_2024/6ua2_20704_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ua2_20704/03_2024/6ua2_20704_updated.pdb" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.091 sd= 2.383 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 84 5.49 5 S 176 5.16 5 C 19696 2.51 5 N 5420 2.21 5 O 6284 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 ARG 136": "NH1" <-> "NH2" Residue "A ARG 149": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "B ARG 126": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "B TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "B PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 126": "NH1" <-> "NH2" Residue "C ARG 128": "NH1" <-> "NH2" Residue "C PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 136": "NH1" <-> "NH2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 231": "NH1" <-> "NH2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "C ARG 412": "NH1" <-> "NH2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "C PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 126": "NH1" <-> "NH2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 149": "NH1" <-> "NH2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 182": "NH1" <-> "NH2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "D ARG 231": "NH1" <-> "NH2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 412": "NH1" <-> "NH2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "E ARG 126": "NH1" <-> "NH2" Residue "E ARG 128": "NH1" <-> "NH2" Residue "E ARG 136": "NH1" <-> "NH2" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 149": "NH1" <-> "NH2" Residue "E ARG 153": "NH1" <-> "NH2" Residue "E ARG 182": "NH1" <-> "NH2" Residue "E ARG 203": "NH1" <-> "NH2" Residue "E ARG 231": "NH1" <-> "NH2" Residue "E ARG 356": "NH1" <-> "NH2" Residue "E PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 407": "NH1" <-> "NH2" Residue "E ARG 412": "NH1" <-> "NH2" Residue "E ARG 512": "NH1" <-> "NH2" Residue "F ARG 126": "NH1" <-> "NH2" Residue "F ARG 128": "NH1" <-> "NH2" Residue "F ARG 136": "NH1" <-> "NH2" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 149": "NH1" <-> "NH2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 182": "NH1" <-> "NH2" Residue "F ARG 203": "NH1" <-> "NH2" Residue "F ARG 224": "NH1" <-> "NH2" Residue "F ARG 231": "NH1" <-> "NH2" Residue "F ARG 356": "NH1" <-> "NH2" Residue "F PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 407": "NH1" <-> "NH2" Residue "F TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 412": "NH1" <-> "NH2" Residue "F ARG 512": "NH1" <-> "NH2" Residue "F PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 126": "NH1" <-> "NH2" Residue "G ARG 128": "NH1" <-> "NH2" Residue "G ARG 136": "NH1" <-> "NH2" Residue "G PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 149": "NH1" <-> "NH2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G ARG 182": "NH1" <-> "NH2" Residue "G ARG 203": "NH1" <-> "NH2" Residue "G ARG 231": "NH1" <-> "NH2" Residue "G ARG 356": "NH1" <-> "NH2" Residue "G ARG 407": "NH1" <-> "NH2" Residue "G ARG 412": "NH1" <-> "NH2" Residue "G ARG 512": "NH1" <-> "NH2" Residue "G PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 126": "NH1" <-> "NH2" Residue "H ARG 128": "NH1" <-> "NH2" Residue "H ARG 136": "NH1" <-> "NH2" Residue "H PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 149": "NH1" <-> "NH2" Residue "H ARG 153": "NH1" <-> "NH2" Residue "H ARG 182": "NH1" <-> "NH2" Residue "H ARG 203": "NH1" <-> "NH2" Residue "H ARG 231": "NH1" <-> "NH2" Residue "H ARG 356": "NH1" <-> "NH2" Residue "H PHE 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 412": "NH1" <-> "NH2" Residue "H ARG 512": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 31660 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "B" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "C" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "D" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 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: "E" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "F" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "G" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} Chain breaks: 1 Chain: "H" Number of atoms: 3710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3710 Classifications: {'peptide': 488} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 16, 'TRANS': 470} 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: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna3p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 160 Unusual residues: {'ATP': 3, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {'ATP': 1, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 160 Unusual residues: {'ATP': 3, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "H" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 98 Unusual residues: {'ATP': 1, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 2} Modifications used: {'rna2p': 1} Link IDs: {None: 2} Time building chain proxies: 17.33, per 1000 atoms: 0.55 Number of scatterers: 31660 At special positions: 0 Unit cell: (143.85, 148.05, 142.8, 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 84 15.00 O 6284 8.00 N 5420 7.00 C 19696 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: 13.38 Conformation dependent library (CDL) restraints added in 5.5 seconds 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7280 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 154 helices and 43 sheets defined 30.9% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.20 Creating SS restraints... Processing helix chain 'A' and resid 20 through 26 removed outlier: 4.613A pdb=" N CYS A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 34 No H-bonds generated for 'chain 'A' and resid 32 through 34' 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 135 Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 175 through 177 No H-bonds generated for 'chain 'A' and resid 175 through 177' 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 204 Processing helix chain 'A' and resid 225 through 232 Processing helix chain 'A' and resid 254 through 266 removed outlier: 4.188A pdb=" N ASP A 261 " --> pdb=" O TYR A 258 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LEU A 262 " --> pdb=" O ARG A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.879A pdb=" N ASP A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 343 through 356 removed outlier: 3.824A pdb=" N LYS A 349 " --> pdb=" O THR A 345 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 Processing helix chain 'A' and resid 453 through 455 No H-bonds generated for 'chain 'A' and resid 453 through 455' Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 477 through 484 Processing helix chain 'A' and resid 495 through 501 Processing helix chain 'B' and resid 21 through 24 No H-bonds generated for 'chain 'B' and resid 21 through 24' Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 97 through 107 Processing helix chain 'B' and resid 127 through 135 Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 194 through 204 Processing helix chain 'B' and resid 225 through 232 Processing helix chain 'B' and resid 254 through 266 removed outlier: 4.480A pdb=" N ASP B 261 " --> pdb=" O TYR B 258 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU B 262 " --> pdb=" O ARG B 259 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 263 " --> pdb=" O LEU B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.855A pdb=" N ASP B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 343 through 356 removed outlier: 3.518A pdb=" N SER B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 379 Processing helix chain 'B' and resid 453 through 455 No H-bonds generated for 'chain 'B' and resid 453 through 455' Processing helix chain 'B' and resid 457 through 471 Processing helix chain 'B' and resid 476 through 484 Processing helix chain 'C' and resid 20 through 24 Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' 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 85 removed outlier: 3.565A pdb=" N THR C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 107 Processing helix chain 'C' and resid 127 through 137 removed outlier: 4.019A pdb=" N ARG C 136 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 226 through 228 No H-bonds generated for 'chain 'C' and resid 226 through 228' Processing helix chain 'C' and resid 254 through 266 removed outlier: 4.373A pdb=" N ASP C 261 " --> pdb=" O TYR C 258 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU C 262 " --> pdb=" O ARG C 259 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN C 265 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 291 Processing helix chain 'C' and resid 307 through 314 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 344 through 347 No H-bonds generated for 'chain 'C' and resid 344 through 347' Processing helix chain 'C' and resid 349 through 354 Processing helix chain 'C' and resid 370 through 379 removed outlier: 3.544A pdb=" N LYS C 375 " --> pdb=" O GLY C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 390 No H-bonds generated for 'chain 'C' and resid 388 through 390' Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'C' and resid 453 through 471 removed outlier: 5.909A pdb=" N VAL C 457 " --> pdb=" O HIS C 454 " (cutoff:3.500A) Proline residue: C 458 - end of helix removed outlier: 3.508A pdb=" N ALA C 462 " --> pdb=" O TYR C 459 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE C 471 " --> pdb=" O CYS C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 484 Processing helix chain 'C' and resid 496 through 499 No H-bonds generated for 'chain 'C' and resid 496 through 499' 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 76 through 83 Processing helix chain 'D' and resid 97 through 109 removed outlier: 4.334A pdb=" N LYS D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 133 Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 194 through 204 Processing helix chain 'D' and resid 225 through 228 Processing helix chain 'D' and resid 254 through 265 removed outlier: 3.681A pdb=" N LYS D 257 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASP D 261 " --> pdb=" O TYR D 258 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN D 265 " --> pdb=" O LEU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 293 removed outlier: 3.990A pdb=" N ASP D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 314 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 377 Processing helix chain 'D' and resid 453 through 455 No H-bonds generated for 'chain 'D' and resid 453 through 455' Processing helix chain 'D' and resid 457 through 471 Processing helix chain 'D' and resid 476 through 484 Processing helix chain 'D' and resid 495 through 501 removed outlier: 4.998A pdb=" N GLU D 500 " --> pdb=" O SER D 496 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 6 Processing helix chain 'E' and resid 20 through 26 removed outlier: 4.590A pdb=" N CYS E 26 " --> pdb=" O GLN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' 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 135 Processing helix chain 'E' and resid 160 through 162 No H-bonds generated for 'chain 'E' and resid 160 through 162' Processing helix chain 'E' and resid 175 through 177 No H-bonds generated for 'chain 'E' and resid 175 through 177' 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 204 Processing helix chain 'E' and resid 225 through 232 Processing helix chain 'E' and resid 254 through 266 removed outlier: 4.240A pdb=" N ASP E 261 " --> pdb=" O TYR E 258 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N LEU E 262 " --> pdb=" O ARG E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 293 removed outlier: 3.862A pdb=" N ASP E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS E 293 " --> pdb=" O TYR E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 314 Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 343 through 356 removed outlier: 3.946A pdb=" N LYS E 349 " --> pdb=" O THR E 345 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 378 Processing helix chain 'E' and resid 453 through 455 No H-bonds generated for 'chain 'E' and resid 453 through 455' Processing helix chain 'E' and resid 457 through 471 Processing helix chain 'E' and resid 477 through 484 Processing helix chain 'E' and resid 495 through 501 Processing helix chain 'F' and resid 21 through 24 No H-bonds generated for 'chain 'F' and resid 21 through 24' Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 76 through 84 Processing helix chain 'F' and resid 97 through 107 Processing helix chain 'F' and resid 127 through 135 Processing helix chain 'F' and resid 160 through 162 No H-bonds generated for 'chain 'F' and resid 160 through 162' Processing helix chain 'F' and resid 194 through 204 Processing helix chain 'F' and resid 225 through 232 Processing helix chain 'F' and resid 254 through 266 removed outlier: 4.480A pdb=" N ASP F 261 " --> pdb=" O TYR F 258 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU F 262 " --> pdb=" O ARG F 259 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU F 263 " --> pdb=" O LEU F 260 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 293 removed outlier: 3.880A pdb=" N ASP F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS F 293 " --> pdb=" O TYR F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 316 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 356 removed outlier: 3.502A pdb=" N SER F 351 " --> pdb=" O VAL F 347 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 379 Processing helix chain 'F' and resid 453 through 455 No H-bonds generated for 'chain 'F' and resid 453 through 455' Processing helix chain 'F' and resid 457 through 471 Processing helix chain 'F' and resid 476 through 484 Processing helix chain 'G' and resid 20 through 24 Processing helix chain 'G' and resid 32 through 34 No H-bonds generated for 'chain 'G' and resid 32 through 34' 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 85 removed outlier: 3.633A pdb=" N THR G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 107 Processing helix chain 'G' and resid 127 through 137 removed outlier: 3.861A pdb=" N ARG G 136 " --> pdb=" O GLU G 132 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N HIS G 137 " --> pdb=" O ALA G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 204 Processing helix chain 'G' and resid 226 through 228 No H-bonds generated for 'chain 'G' and resid 226 through 228' Processing helix chain 'G' and resid 254 through 266 removed outlier: 4.359A pdb=" N ASP G 261 " --> pdb=" O TYR G 258 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU G 262 " --> pdb=" O ARG G 259 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN G 265 " --> pdb=" O LEU G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 293 removed outlier: 4.355A pdb=" N ASP G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS G 293 " --> pdb=" O TYR G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 314 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 344 through 354 removed outlier: 4.833A pdb=" N LYS G 349 " --> pdb=" O THR G 345 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER G 351 " --> pdb=" O VAL G 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 379 removed outlier: 3.551A pdb=" N LYS G 375 " --> pdb=" O GLY G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 390 No H-bonds generated for 'chain 'G' and resid 388 through 390' Processing helix chain 'G' and resid 417 through 419 No H-bonds generated for 'chain 'G' and resid 417 through 419' Processing helix chain 'G' and resid 453 through 471 removed outlier: 5.870A pdb=" N VAL G 457 " --> pdb=" O HIS G 454 " (cutoff:3.500A) Proline residue: G 458 - end of helix removed outlier: 3.511A pdb=" N ALA G 462 " --> pdb=" O TYR G 459 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE G 471 " --> pdb=" O CYS G 468 " (cutoff:3.500A) Processing helix chain 'G' and resid 476 through 484 Processing helix chain 'G' and resid 496 through 499 No H-bonds generated for 'chain 'G' and resid 496 through 499' 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 76 through 83 Processing helix chain 'H' and resid 97 through 108 Processing helix chain 'H' and resid 128 through 136 removed outlier: 4.844A pdb=" N ALA H 135 " --> pdb=" O PHE H 131 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N ARG H 136 " --> pdb=" O GLU H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 162 No H-bonds generated for 'chain 'H' and resid 160 through 162' Processing helix chain 'H' and resid 175 through 177 No H-bonds generated for 'chain 'H' and resid 175 through 177' Processing helix chain 'H' and resid 194 through 204 Processing helix chain 'H' and resid 225 through 229 Processing helix chain 'H' and resid 254 through 266 removed outlier: 3.710A pdb=" N LYS H 257 " --> pdb=" O GLU H 254 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP H 261 " --> pdb=" O TYR H 258 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN H 265 " --> pdb=" O LEU H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 293 removed outlier: 3.983A pdb=" N ASP H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS H 293 " --> pdb=" O TYR H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 314 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 377 Processing helix chain 'H' and resid 453 through 455 No H-bonds generated for 'chain 'H' and resid 453 through 455' Processing helix chain 'H' and resid 457 through 471 Processing helix chain 'H' and resid 476 through 484 Processing helix chain 'H' and resid 495 through 501 removed outlier: 4.951A pdb=" N GLU H 500 " --> pdb=" O SER H 496 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 5 Processing helix chain 'J' and resid 2 through 6 Processing sheet with id= A, first strand: chain 'A' and resid 35 through 37 removed outlier: 3.902A pdb=" N GLU A 491 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 120 through 122 removed outlier: 3.569A pdb=" N ILE A 144 " --> pdb=" O GLY A 156 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 247 through 250 removed outlier: 7.085A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 8.530A pdb=" N ILE A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N VAL A 272 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLN A 298 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 6.498A 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 362 through 364 removed outlier: 7.574A pdb=" N THR A 383 " --> pdb=" O ALA A 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 401 through 403 removed outlier: 3.535A pdb=" N SER A 403 " --> pdb=" O ILE A 406 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 208 through 212 Processing sheet with id= G, first strand: chain 'B' and resid 320 through 322 removed outlier: 7.735A pdb=" N THR B 383 " --> pdb=" O ALA B 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 401 through 403 Processing sheet with id= I, first strand: chain 'B' and resid 142 through 145 Processing sheet with id= J, first strand: chain 'B' and resid 209 through 212 Processing sheet with id= K, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= L, first strand: chain 'C' and resid 120 through 122 Processing sheet with id= M, first strand: chain 'C' and resid 247 through 250 removed outlier: 6.766A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ILE C 250 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N VAL C 272 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLN C 298 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'C' and resid 362 through 364 removed outlier: 6.932A pdb=" N THR C 383 " --> pdb=" O ALA C 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 401 through 403 Processing sheet with id= P, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= Q, first strand: chain 'D' and resid 248 through 250 removed outlier: 6.698A pdb=" N GLN D 298 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'D' and resid 320 through 322 No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'D' and resid 401 through 403 removed outlier: 3.648A pdb=" N LYS D 409 " --> pdb=" O VAL D 447 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL D 447 " --> pdb=" O LYS D 409 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 142 through 145 Processing sheet with id= U, first strand: chain 'D' and resid 209 through 212 Processing sheet with id= V, first strand: chain 'E' and resid 35 through 37 removed outlier: 3.898A pdb=" N GLU E 491 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 120 through 122 removed outlier: 3.610A pdb=" N ILE E 144 " --> pdb=" O GLY E 156 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 187 through 189 removed outlier: 8.278A pdb=" N ALA E 188 " --> pdb=" O LYS E 208 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 247 through 250 removed outlier: 7.130A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 8.560A pdb=" N ILE E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N VAL E 272 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLN E 298 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'E' and resid 362 through 364 removed outlier: 7.479A pdb=" N THR E 383 " --> pdb=" O ALA E 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'E' and resid 401 through 403 removed outlier: 3.531A pdb=" N SER E 403 " --> pdb=" O ILE E 406 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'F' and resid 320 through 322 removed outlier: 7.480A pdb=" N THR F 383 " --> pdb=" O ALA F 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'F' and resid 401 through 403 Processing sheet with id= AD, first strand: chain 'F' and resid 142 through 145 Processing sheet with id= AE, first strand: chain 'F' and resid 209 through 212 Processing sheet with id= AF, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= AG, first strand: chain 'G' and resid 120 through 122 Processing sheet with id= AH, first strand: chain 'G' and resid 248 through 250 removed outlier: 6.853A pdb=" N GLN G 298 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'G' and resid 362 through 364 removed outlier: 6.959A pdb=" N THR G 383 " --> pdb=" O ALA G 363 " (cutoff:3.500A) No H-bonds generated for sheet with id= AI Processing sheet with id= AJ, first strand: chain 'G' and resid 401 through 403 Processing sheet with id= AK, first strand: chain 'G' and resid 209 through 212 removed outlier: 3.615A pdb=" N LEU G 209 " --> pdb=" O ILE G 222 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE G 211 " --> pdb=" O ALA G 220 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AM, first strand: chain 'H' and resid 247 through 250 removed outlier: 7.111A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N ILE H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL H 272 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLN H 298 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AM Processing sheet with id= AN, first strand: chain 'H' and resid 320 through 322 No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain 'H' and resid 401 through 403 removed outlier: 3.656A pdb=" N LYS H 409 " --> pdb=" O VAL H 447 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL H 447 " --> pdb=" O LYS H 409 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'H' and resid 142 through 145 Processing sheet with id= AQ, first strand: chain 'H' and resid 208 through 212 730 hydrogen bonds defined for protein. 1854 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: 9.81 Time building geometry restraints manager: 14.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 5296 1.29 - 1.42: 7667 1.42 - 1.55: 18727 1.55 - 1.68: 222 1.68 - 1.81: 300 Bond restraints: 32212 Sorted by residual: bond pdb=" C2' ATP F 603 " pdb=" C3' ATP F 603 " ideal model delta sigma weight residual 1.531 1.239 0.292 1.20e-02 6.94e+03 5.91e+02 bond pdb=" C2' ATP B 603 " pdb=" C3' ATP B 603 " ideal model delta sigma weight residual 1.531 1.240 0.291 1.20e-02 6.94e+03 5.86e+02 bond pdb=" C2' ATP G 601 " pdb=" C3' ATP G 601 " ideal model delta sigma weight residual 1.531 1.245 0.286 1.20e-02 6.94e+03 5.68e+02 bond pdb=" C2' ATP A 603 " pdb=" C3' ATP A 603 " ideal model delta sigma weight residual 1.531 1.246 0.285 1.20e-02 6.94e+03 5.66e+02 bond pdb=" C2' ATP C 601 " pdb=" C3' ATP C 601 " ideal model delta sigma weight residual 1.531 1.247 0.284 1.20e-02 6.94e+03 5.61e+02 ... (remaining 32207 not shown) Histogram of bond angle deviations from ideal: 93.49 - 103.42: 462 103.42 - 113.35: 18390 113.35 - 123.28: 23258 123.28 - 133.21: 1523 133.21 - 143.14: 79 Bond angle restraints: 43712 Sorted by residual: angle pdb=" PB ATP F 603 " pdb=" O3B ATP F 603 " pdb=" PG ATP F 603 " ideal model delta sigma weight residual 139.87 117.44 22.43 1.00e+00 1.00e+00 5.03e+02 angle pdb=" PB ATP B 603 " pdb=" O3B ATP B 603 " pdb=" PG ATP B 603 " ideal model delta sigma weight residual 139.87 117.74 22.13 1.00e+00 1.00e+00 4.90e+02 angle pdb=" PB ATP H 601 " pdb=" O3B ATP H 601 " pdb=" PG ATP H 601 " ideal model delta sigma weight residual 139.87 118.03 21.84 1.00e+00 1.00e+00 4.77e+02 angle pdb=" PB ATP E 603 " pdb=" O3B ATP E 603 " pdb=" PG ATP E 603 " ideal model delta sigma weight residual 139.87 118.79 21.08 1.00e+00 1.00e+00 4.44e+02 angle pdb=" PA ATP C 605 " pdb=" O3A ATP C 605 " pdb=" PB ATP C 605 " ideal model delta sigma weight residual 136.83 117.23 19.60 1.00e+00 1.00e+00 3.84e+02 ... (remaining 43707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.69: 18923 34.69 - 69.39: 800 69.39 - 104.08: 79 104.08 - 138.78: 17 138.78 - 173.47: 13 Dihedral angle restraints: 19832 sinusoidal: 8424 harmonic: 11408 Sorted by residual: dihedral pdb=" CA SER N 11 " pdb=" C SER N 11 " pdb=" N TYR N 12 " pdb=" CA TYR N 12 " ideal model delta harmonic sigma weight residual 180.00 139.54 40.46 0 5.00e+00 4.00e-02 6.55e+01 dihedral pdb=" CA GLY O 9 " pdb=" C GLY O 9 " pdb=" N THR O 10 " pdb=" CA THR O 10 " ideal model delta harmonic sigma weight residual -180.00 -141.00 -39.00 0 5.00e+00 4.00e-02 6.08e+01 dihedral pdb=" CA GLY K 9 " pdb=" C GLY K 9 " pdb=" N THR K 10 " pdb=" CA THR K 10 " ideal model delta harmonic sigma weight residual 180.00 -141.48 -38.52 0 5.00e+00 4.00e-02 5.94e+01 ... (remaining 19829 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 3845 0.091 - 0.181: 950 0.181 - 0.272: 152 0.272 - 0.362: 29 0.362 - 0.453: 8 Chirality restraints: 4984 Sorted by residual: chirality pdb=" CB ILE F 300 " pdb=" CA ILE F 300 " pdb=" CG1 ILE F 300 " pdb=" CG2 ILE F 300 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.13e+00 chirality pdb=" CB ILE B 300 " pdb=" CA ILE B 300 " pdb=" CG1 ILE B 300 " pdb=" CG2 ILE B 300 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.86e+00 chirality pdb=" CB VAL E 479 " pdb=" CA VAL E 479 " pdb=" CG1 VAL E 479 " pdb=" CG2 VAL E 479 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.62e+00 ... (remaining 4981 not shown) Planarity restraints: 5452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 359 " 0.053 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO B 360 " -0.139 5.00e-02 4.00e+02 pdb=" CA PRO B 360 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO B 360 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 104 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.96e+00 pdb=" C VAL F 104 " -0.055 2.00e-02 2.50e+03 pdb=" O VAL F 104 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG F 105 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 104 " -0.016 2.00e-02 2.50e+03 3.15e-02 9.95e+00 pdb=" C VAL B 104 " 0.055 2.00e-02 2.50e+03 pdb=" O VAL B 104 " -0.020 2.00e-02 2.50e+03 pdb=" N ARG B 105 " -0.018 2.00e-02 2.50e+03 ... (remaining 5449 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 4407 2.73 - 3.27: 33566 3.27 - 3.82: 60223 3.82 - 4.36: 68340 4.36 - 4.90: 105621 Nonbonded interactions: 272157 Sorted by model distance: nonbonded pdb=" O HIS A 504 " pdb=" OG SER B 329 " model vdw 2.191 2.440 nonbonded pdb=" OG SER G 475 " pdb=" OE1 GLN G 478 " model vdw 2.218 2.440 nonbonded pdb=" OG SER C 475 " pdb=" OE1 GLN C 478 " model vdw 2.219 2.440 nonbonded pdb=" OG SER E 475 " pdb=" OE1 GLN E 478 " model vdw 2.229 2.440 nonbonded pdb=" O THR D 393 " pdb=" OH TYR D 400 " model vdw 2.235 2.440 ... (remaining 272152 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' and resid 11 through 514) selection = (chain 'B' and resid 11 through 514) selection = (chain 'C' and resid 11 through 514) selection = (chain 'D' and resid 11 through 514) selection = (chain 'E' and resid 11 through 514) selection = (chain 'F' and resid 11 through 514) selection = (chain 'G' and resid 11 through 514) selection = (chain 'H' and resid 11 through 514) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.720 Check model and map are aligned: 0.430 Set scattering table: 0.270 Process input model: 82.080 Find NCS groups from input model: 2.570 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 98.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 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 : 0.017 0.296 32212 Z= 1.126 Angle : 1.743 22.429 43712 Z= 1.031 Chirality : 0.082 0.453 4984 Planarity : 0.008 0.081 5452 Dihedral : 19.048 173.474 12552 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.27 % Favored : 88.68 % Rotamer: Outliers : 4.10 % Allowed : 15.62 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 1.47 % Twisted General : 0.39 % 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: -4.76 (0.10), residues: 3968 helix: -3.55 (0.10), residues: 1174 sheet: -3.44 (0.21), residues: 404 loop : -3.01 (0.11), residues: 2390 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.004 HIS F 504 PHE 0.038 0.004 PHE E 401 TYR 0.041 0.004 TYR F 233 ARG 0.021 0.002 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1563 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1429 time to evaluate : 3.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.9042 (t70) cc_final: 0.8463 (t70) REVERT: A 32 TYR cc_start: 0.9141 (m-80) cc_final: 0.8534 (m-80) REVERT: A 36 LEU cc_start: 0.9426 (tp) cc_final: 0.8753 (tp) REVERT: A 38 LEU cc_start: 0.9668 (mm) cc_final: 0.9107 (mm) REVERT: A 48 GLN cc_start: 0.9392 (mm-40) cc_final: 0.9108 (mt0) REVERT: A 108 LYS cc_start: 0.9502 (tptp) cc_final: 0.9105 (mmtt) REVERT: A 150 MET cc_start: 0.8262 (tmt) cc_final: 0.8038 (tpt) REVERT: A 194 LEU cc_start: 0.9628 (mm) cc_final: 0.9193 (pp) REVERT: A 224 ARG cc_start: 0.7911 (mmt180) cc_final: 0.7365 (mmt-90) REVERT: A 246 CYS cc_start: 0.9478 (t) cc_final: 0.9276 (t) REVERT: A 256 ASP cc_start: 0.9292 (p0) cc_final: 0.8951 (p0) REVERT: A 262 LEU cc_start: 0.9578 (pt) cc_final: 0.9056 (mt) REVERT: A 269 ASP cc_start: 0.8358 (m-30) cc_final: 0.8048 (m-30) REVERT: A 283 GLN cc_start: 0.9148 (mp-120) cc_final: 0.8817 (mm-40) REVERT: A 284 ILE cc_start: 0.9082 (pp) cc_final: 0.8749 (pp) REVERT: A 288 LYS cc_start: 0.9597 (mtmm) cc_final: 0.9362 (ptpt) REVERT: A 294 TYR cc_start: 0.9471 (m-80) cc_final: 0.8950 (m-80) REVERT: A 297 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8645 (tm) REVERT: A 303 ASN cc_start: 0.7092 (m-40) cc_final: 0.6859 (m-40) REVERT: A 332 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8756 (pp) REVERT: A 334 GLN cc_start: 0.9460 (mp10) cc_final: 0.8636 (mp10) REVERT: A 335 GLU cc_start: 0.8501 (mp0) cc_final: 0.7777 (mp0) REVERT: A 337 LEU cc_start: 0.9161 (tp) cc_final: 0.8717 (tp) REVERT: A 343 GLN cc_start: 0.8888 (pp30) cc_final: 0.7975 (pp30) REVERT: A 352 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8740 (tm-30) REVERT: A 355 ARG cc_start: 0.8861 (ptt90) cc_final: 0.8511 (ptm-80) REVERT: A 364 ASP cc_start: 0.8004 (m-30) cc_final: 0.6502 (m-30) REVERT: A 369 ASN cc_start: 0.9037 (p0) cc_final: 0.8339 (p0) REVERT: A 372 HIS cc_start: 0.9313 (m170) cc_final: 0.8501 (m-70) REVERT: A 375 LYS cc_start: 0.9581 (pttm) cc_final: 0.9315 (pttm) REVERT: A 385 MET cc_start: 0.8543 (ttp) cc_final: 0.7981 (ttp) REVERT: A 386 MET cc_start: 0.8706 (ppp) cc_final: 0.8345 (ppp) REVERT: A 389 LEU cc_start: 0.9621 (OUTLIER) cc_final: 0.9380 (pp) REVERT: A 420 MET cc_start: 0.8395 (mtm) cc_final: 0.7996 (mtp) REVERT: A 448 GLN cc_start: 0.8774 (mp10) cc_final: 0.8434 (mp10) REVERT: A 482 MET cc_start: 0.8752 (tmt) cc_final: 0.8473 (tmt) REVERT: A 507 HIS cc_start: 0.8837 (t-90) cc_final: 0.8618 (t70) REVERT: B 18 LEU cc_start: 0.9439 (OUTLIER) cc_final: 0.9051 (tm) REVERT: B 62 LYS cc_start: 0.8856 (pttt) cc_final: 0.8521 (pttt) REVERT: B 70 MET cc_start: 0.8424 (tpp) cc_final: 0.7647 (tpp) REVERT: B 71 ASP cc_start: 0.7986 (OUTLIER) cc_final: 0.7756 (m-30) REVERT: B 98 GLU cc_start: 0.9717 (mp0) cc_final: 0.9429 (mp0) REVERT: B 108 LYS cc_start: 0.9475 (pmtt) cc_final: 0.8460 (tptt) REVERT: B 131 PHE cc_start: 0.9214 (m-10) cc_final: 0.8789 (m-80) REVERT: B 132 GLU cc_start: 0.9503 (pt0) cc_final: 0.9095 (pp20) REVERT: B 166 LEU cc_start: 0.9323 (mm) cc_final: 0.8906 (tp) REVERT: B 176 GLU cc_start: 0.8262 (mp0) cc_final: 0.7903 (mp0) REVERT: B 177 GLU cc_start: 0.8753 (pm20) cc_final: 0.8251 (pm20) REVERT: B 183 GLU cc_start: 0.9106 (pm20) cc_final: 0.8652 (pm20) REVERT: B 216 ASP cc_start: 0.9502 (t70) cc_final: 0.9254 (t0) REVERT: B 224 ARG cc_start: 0.8975 (ttt-90) cc_final: 0.8766 (ttt180) REVERT: B 243 GLN cc_start: 0.9450 (mm110) cc_final: 0.9093 (mm110) REVERT: B 244 LEU cc_start: 0.9215 (tp) cc_final: 0.8985 (tp) REVERT: B 311 LYS cc_start: 0.9244 (ptmm) cc_final: 0.8894 (tmmt) REVERT: B 334 GLN cc_start: 0.9146 (mt0) cc_final: 0.8865 (mm-40) REVERT: B 337 LEU cc_start: 0.9491 (mm) cc_final: 0.9252 (mm) REVERT: B 343 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8074 (tm-30) REVERT: B 355 ARG cc_start: 0.8222 (ppt170) cc_final: 0.7984 (ttp-170) REVERT: B 417 LEU cc_start: 0.9604 (OUTLIER) cc_final: 0.9394 (pp) REVERT: B 466 HIS cc_start: 0.8665 (t-170) cc_final: 0.8354 (t-90) REVERT: B 478 GLN cc_start: 0.9256 (tt0) cc_final: 0.8606 (tt0) REVERT: B 491 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8218 (tm-30) REVERT: B 493 ARG cc_start: 0.8424 (pmt-80) cc_final: 0.8041 (pmt-80) REVERT: C 32 TYR cc_start: 0.9090 (m-10) cc_final: 0.8638 (m-10) REVERT: C 43 ASP cc_start: 0.8524 (m-30) cc_final: 0.8294 (m-30) REVERT: C 47 ASP cc_start: 0.9598 (m-30) cc_final: 0.9078 (p0) REVERT: C 55 LEU cc_start: 0.8024 (mm) cc_final: 0.7726 (mm) REVERT: C 78 MET cc_start: 0.9314 (mmm) cc_final: 0.9096 (mmm) REVERT: C 82 MET cc_start: 0.9630 (tpp) cc_final: 0.9310 (tpp) REVERT: C 111 GLU cc_start: 0.9215 (tp30) cc_final: 0.8851 (mp0) REVERT: C 112 GLN cc_start: 0.9245 (tm-30) cc_final: 0.8996 (tm-30) REVERT: C 199 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8674 (tp30) REVERT: C 200 ILE cc_start: 0.9147 (mm) cc_final: 0.8907 (mm) REVERT: C 216 ASP cc_start: 0.9473 (m-30) cc_final: 0.9087 (t0) REVERT: C 229 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8769 (mmmt) REVERT: C 244 LEU cc_start: 0.9282 (tm) cc_final: 0.9075 (tm) REVERT: C 274 ASP cc_start: 0.9258 (t0) cc_final: 0.8892 (t0) REVERT: C 289 TYR cc_start: 0.9421 (t80) cc_final: 0.9018 (t80) REVERT: C 331 CYS cc_start: 0.8929 (t) cc_final: 0.8721 (t) REVERT: C 333 THR cc_start: 0.9751 (p) cc_final: 0.9273 (p) REVERT: C 334 GLN cc_start: 0.9277 (mp10) cc_final: 0.8807 (mp10) REVERT: C 335 GLU cc_start: 0.8732 (tm-30) cc_final: 0.8116 (tm-30) REVERT: C 336 VAL cc_start: 0.9555 (m) cc_final: 0.8889 (m) REVERT: C 492 LYS cc_start: 0.8581 (pptt) cc_final: 0.8377 (pptt) REVERT: C 500 GLU cc_start: 0.9309 (pp20) cc_final: 0.8706 (pp20) REVERT: C 504 HIS cc_start: 0.8354 (p90) cc_final: 0.7907 (p-80) REVERT: D 21 GLN cc_start: 0.8958 (tm-30) cc_final: 0.8670 (tm-30) REVERT: D 32 TYR cc_start: 0.9128 (m-80) cc_final: 0.8700 (m-80) REVERT: D 33 ASN cc_start: 0.9173 (t0) cc_final: 0.8666 (t0) REVERT: D 51 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9215 (pp) REVERT: D 91 ILE cc_start: 0.9258 (tp) cc_final: 0.9036 (tp) REVERT: D 140 CYS cc_start: 0.8415 (m) cc_final: 0.7930 (m) REVERT: D 157 ILE cc_start: 0.8764 (mm) cc_final: 0.8543 (pt) REVERT: D 215 ASP cc_start: 0.9490 (m-30) cc_final: 0.9040 (p0) REVERT: D 286 MET cc_start: 0.9700 (tpt) cc_final: 0.9412 (tpt) REVERT: D 289 TYR cc_start: 0.9501 (t80) cc_final: 0.9251 (t80) REVERT: D 311 LYS cc_start: 0.9247 (ttpp) cc_final: 0.8888 (ttpp) REVERT: D 341 ARG cc_start: 0.8321 (ptp-110) cc_final: 0.7982 (ptp-170) REVERT: D 352 GLU cc_start: 0.9255 (tm-30) cc_final: 0.8932 (tm-30) REVERT: D 379 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9234 (tm) REVERT: D 385 MET cc_start: 0.8457 (tpt) cc_final: 0.7290 (tpt) REVERT: D 386 MET cc_start: 0.8682 (ptm) cc_final: 0.8155 (ptm) REVERT: D 399 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7715 (tm-30) REVERT: D 410 LYS cc_start: 0.9444 (mptp) cc_final: 0.9022 (mmtm) REVERT: D 418 ASP cc_start: 0.9426 (t70) cc_final: 0.9115 (t70) REVERT: D 465 GLN cc_start: 0.8959 (pp30) cc_final: 0.8380 (pp30) REVERT: D 482 MET cc_start: 0.9177 (tpt) cc_final: 0.8832 (tpp) REVERT: E 28 ASP cc_start: 0.9108 (t70) cc_final: 0.8496 (t70) REVERT: E 32 TYR cc_start: 0.9304 (m-80) cc_final: 0.8884 (m-80) REVERT: E 36 LEU cc_start: 0.9428 (tp) cc_final: 0.8755 (tp) REVERT: E 38 LEU cc_start: 0.9659 (mm) cc_final: 0.9055 (mm) REVERT: E 48 GLN cc_start: 0.9353 (mm-40) cc_final: 0.9125 (mt0) REVERT: E 82 MET cc_start: 0.9259 (ttp) cc_final: 0.9040 (tmm) REVERT: E 137 HIS cc_start: 0.9431 (m90) cc_final: 0.8971 (m90) REVERT: E 142 ILE cc_start: 0.8518 (tp) cc_final: 0.8202 (tp) REVERT: E 150 MET cc_start: 0.8092 (tmt) cc_final: 0.7748 (tpt) REVERT: E 158 ILE cc_start: 0.8556 (mm) cc_final: 0.8063 (tp) REVERT: E 165 PHE cc_start: 0.8681 (p90) cc_final: 0.8322 (p90) REVERT: E 228 LYS cc_start: 0.9535 (OUTLIER) cc_final: 0.9296 (ptmt) REVERT: E 231 ARG cc_start: 0.9192 (ptp-170) cc_final: 0.8951 (mtm-85) REVERT: E 288 LYS cc_start: 0.9602 (mtmm) cc_final: 0.9286 (ptpp) REVERT: E 294 TYR cc_start: 0.9427 (m-80) cc_final: 0.8915 (m-80) REVERT: E 297 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8786 (tm) REVERT: E 332 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8458 (pp) REVERT: E 334 GLN cc_start: 0.9405 (mp10) cc_final: 0.8550 (mp10) REVERT: E 335 GLU cc_start: 0.8513 (mp0) cc_final: 0.7689 (mp0) REVERT: E 337 LEU cc_start: 0.9193 (tp) cc_final: 0.8768 (tp) REVERT: E 352 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8725 (tm-30) REVERT: E 355 ARG cc_start: 0.8814 (ptt90) cc_final: 0.8490 (ptm-80) REVERT: E 364 ASP cc_start: 0.8115 (m-30) cc_final: 0.6451 (m-30) REVERT: E 372 HIS cc_start: 0.9324 (m170) cc_final: 0.8370 (m170) REVERT: E 385 MET cc_start: 0.8241 (ttp) cc_final: 0.7756 (ttp) REVERT: E 386 MET cc_start: 0.8682 (ppp) cc_final: 0.8417 (ppp) REVERT: E 389 LEU cc_start: 0.9631 (OUTLIER) cc_final: 0.9375 (pp) REVERT: E 420 MET cc_start: 0.8371 (mtm) cc_final: 0.7961 (mtp) REVERT: E 448 GLN cc_start: 0.8803 (mp10) cc_final: 0.8446 (mp10) REVERT: E 482 MET cc_start: 0.8715 (tmt) cc_final: 0.8422 (tmt) REVERT: E 507 HIS cc_start: 0.8992 (t-90) cc_final: 0.8787 (t70) REVERT: E 509 TYR cc_start: 0.9177 (p90) cc_final: 0.8669 (p90) REVERT: E 513 LEU cc_start: 0.9271 (mp) cc_final: 0.8989 (mp) REVERT: F 18 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9155 (tm) REVERT: F 62 LYS cc_start: 0.8988 (pttt) cc_final: 0.8706 (pttt) REVERT: F 70 MET cc_start: 0.8098 (tpp) cc_final: 0.5247 (tpp) REVERT: F 102 ASN cc_start: 0.9522 (t0) cc_final: 0.9279 (t0) REVERT: F 103 GLU cc_start: 0.9658 (tp30) cc_final: 0.9339 (tp30) REVERT: F 108 LYS cc_start: 0.9472 (pmtt) cc_final: 0.8649 (tppt) REVERT: F 131 PHE cc_start: 0.9199 (m-10) cc_final: 0.8836 (m-80) REVERT: F 132 GLU cc_start: 0.9440 (pt0) cc_final: 0.9085 (pp20) REVERT: F 136 ARG cc_start: 0.9364 (mmp-170) cc_final: 0.9074 (mmm160) REVERT: F 166 LEU cc_start: 0.9396 (mm) cc_final: 0.8311 (tp) REVERT: F 176 GLU cc_start: 0.8278 (mp0) cc_final: 0.7986 (mp0) REVERT: F 183 GLU cc_start: 0.9136 (pm20) cc_final: 0.8707 (pm20) REVERT: F 216 ASP cc_start: 0.9441 (t70) cc_final: 0.9212 (t0) REVERT: F 243 GLN cc_start: 0.9421 (mm110) cc_final: 0.9157 (mm110) REVERT: F 244 LEU cc_start: 0.9246 (tp) cc_final: 0.8975 (tp) REVERT: F 262 LEU cc_start: 0.9460 (pt) cc_final: 0.9224 (pt) REVERT: F 265 GLN cc_start: 0.9391 (pm20) cc_final: 0.9184 (pm20) REVERT: F 311 LYS cc_start: 0.9244 (ptmm) cc_final: 0.8895 (tmmt) REVERT: F 334 GLN cc_start: 0.9181 (mt0) cc_final: 0.8864 (mm-40) REVERT: F 335 GLU cc_start: 0.8639 (tm-30) cc_final: 0.8161 (tm-30) REVERT: F 336 VAL cc_start: 0.9663 (p) cc_final: 0.9114 (p) REVERT: F 337 LEU cc_start: 0.9493 (mm) cc_final: 0.9271 (mm) REVERT: F 343 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8072 (tm-30) REVERT: F 348 TYR cc_start: 0.9293 (t80) cc_final: 0.9092 (t80) REVERT: F 355 ARG cc_start: 0.8371 (ppt170) cc_final: 0.8106 (ttp-170) REVERT: F 399 GLU cc_start: 0.8584 (pm20) cc_final: 0.8286 (pm20) REVERT: F 455 LYS cc_start: 0.9350 (pttp) cc_final: 0.9005 (ptmm) REVERT: F 466 HIS cc_start: 0.8650 (t-170) cc_final: 0.8344 (t-90) REVERT: F 478 GLN cc_start: 0.9296 (tt0) cc_final: 0.8555 (tt0) REVERT: F 491 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8156 (tm-30) REVERT: F 493 ARG cc_start: 0.8374 (pmt-80) cc_final: 0.7781 (pmt-80) REVERT: F 507 HIS cc_start: 0.8766 (t-90) cc_final: 0.8490 (t-90) REVERT: G 32 TYR cc_start: 0.9111 (m-10) cc_final: 0.8596 (m-10) REVERT: G 43 ASP cc_start: 0.8507 (m-30) cc_final: 0.8241 (m-30) REVERT: G 55 LEU cc_start: 0.8039 (mm) cc_final: 0.7779 (mm) REVERT: G 67 SER cc_start: 0.9569 (p) cc_final: 0.9245 (p) REVERT: G 78 MET cc_start: 0.9562 (tpp) cc_final: 0.9214 (tpp) REVERT: G 82 MET cc_start: 0.9644 (tpp) cc_final: 0.9378 (tpp) REVERT: G 106 LYS cc_start: 0.7962 (mttp) cc_final: 0.7536 (mttm) REVERT: G 112 GLN cc_start: 0.9232 (tm-30) cc_final: 0.8916 (tm-30) REVERT: G 199 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8681 (tp30) REVERT: G 200 ILE cc_start: 0.9179 (mm) cc_final: 0.8964 (mm) REVERT: G 216 ASP cc_start: 0.9474 (m-30) cc_final: 0.9100 (t70) REVERT: G 229 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8779 (mmmt) REVERT: G 274 ASP cc_start: 0.9308 (t0) cc_final: 0.8953 (t0) REVERT: G 289 TYR cc_start: 0.9419 (t80) cc_final: 0.8905 (t80) REVERT: G 331 CYS cc_start: 0.9090 (t) cc_final: 0.8816 (t) REVERT: G 333 THR cc_start: 0.9759 (p) cc_final: 0.9270 (p) REVERT: G 334 GLN cc_start: 0.9328 (mp10) cc_final: 0.8849 (mp10) REVERT: G 335 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8053 (tm-30) REVERT: G 336 VAL cc_start: 0.9558 (m) cc_final: 0.8667 (m) REVERT: G 339 CYS cc_start: 0.8908 (t) cc_final: 0.8472 (t) REVERT: G 410 LYS cc_start: 0.9175 (tmmm) cc_final: 0.8689 (tppt) REVERT: G 411 TYR cc_start: 0.9533 (t80) cc_final: 0.9270 (t80) REVERT: G 418 ASP cc_start: 0.9420 (t70) cc_final: 0.9063 (t70) REVERT: G 444 SER cc_start: 0.8733 (t) cc_final: 0.8290 (t) REVERT: G 482 MET cc_start: 0.9265 (tpp) cc_final: 0.8778 (tpp) REVERT: G 487 GLU cc_start: 0.9051 (pm20) cc_final: 0.8761 (pm20) REVERT: G 492 LYS cc_start: 0.8547 (pptt) cc_final: 0.8307 (pptt) REVERT: G 500 GLU cc_start: 0.9292 (pp20) cc_final: 0.8696 (pp20) REVERT: H 21 GLN cc_start: 0.8939 (tm-30) cc_final: 0.8647 (tm-30) REVERT: H 32 TYR cc_start: 0.9136 (m-80) cc_final: 0.8690 (m-80) REVERT: H 33 ASN cc_start: 0.9179 (t0) cc_final: 0.8645 (t0) REVERT: H 91 ILE cc_start: 0.9200 (tp) cc_final: 0.8969 (tp) REVERT: H 93 HIS cc_start: 0.9263 (p-80) cc_final: 0.8762 (p-80) REVERT: H 108 LYS cc_start: 0.8909 (tptm) cc_final: 0.8303 (tptt) REVERT: H 112 GLN cc_start: 0.9122 (tm-30) cc_final: 0.8870 (tm-30) REVERT: H 150 MET cc_start: 0.6933 (ttt) cc_final: 0.6724 (tmm) REVERT: H 203 ARG cc_start: 0.9149 (tpp-160) cc_final: 0.8889 (ttm110) REVERT: H 208 LYS cc_start: 0.8013 (tppp) cc_final: 0.7629 (tmtt) REVERT: H 215 ASP cc_start: 0.9506 (m-30) cc_final: 0.8982 (p0) REVERT: H 258 TYR cc_start: 0.9529 (t80) cc_final: 0.9307 (t80) REVERT: H 286 MET cc_start: 0.9701 (tpt) cc_final: 0.9362 (tpt) REVERT: H 289 TYR cc_start: 0.9519 (t80) cc_final: 0.9292 (t80) REVERT: H 341 ARG cc_start: 0.8393 (ptp-110) cc_final: 0.8086 (ptp-170) REVERT: H 352 GLU cc_start: 0.9266 (tm-30) cc_final: 0.8942 (tm-30) REVERT: H 362 ILE cc_start: 0.9477 (tp) cc_final: 0.9224 (tp) REVERT: H 379 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9212 (tm) REVERT: H 385 MET cc_start: 0.8394 (tpt) cc_final: 0.7367 (tpt) REVERT: H 386 MET cc_start: 0.8577 (ptm) cc_final: 0.8010 (ptm) REVERT: H 399 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7799 (tm-30) REVERT: H 410 LYS cc_start: 0.9391 (mptp) cc_final: 0.8956 (mmtm) REVERT: H 418 ASP cc_start: 0.9402 (t70) cc_final: 0.9029 (t70) REVERT: H 465 GLN cc_start: 0.8968 (pp30) cc_final: 0.8414 (pp30) REVERT: H 482 MET cc_start: 0.9069 (tpt) cc_final: 0.8401 (tpt) REVERT: H 487 GLU cc_start: 0.9102 (pm20) cc_final: 0.8851 (pm20) outliers start: 134 outliers final: 41 residues processed: 1481 average time/residue: 0.4042 time to fit residues: 949.4201 Evaluate side-chains 1186 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 1129 time to evaluate : 3.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 4.9990 chunk 297 optimal weight: 7.9990 chunk 164 optimal weight: 0.0870 chunk 101 optimal weight: 6.9990 chunk 200 optimal weight: 0.9980 chunk 158 optimal weight: 6.9990 chunk 307 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 228 optimal weight: 0.9990 chunk 355 optimal weight: 7.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 25 ASN ** A 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 ASN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN B 507 HIS ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 ASN C 303 ASN C 454 HIS C 465 GLN D 25 ASN D 265 GLN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN ** D 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 ASN ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 GLN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 448 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 HIS ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 ASN G 303 ASN G 454 HIS G 465 GLN H 25 ASN ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 283 GLN ** H 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 32212 Z= 0.272 Angle : 0.849 10.652 43712 Z= 0.431 Chirality : 0.051 0.319 4984 Planarity : 0.008 0.333 5452 Dihedral : 18.904 177.911 5344 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 26.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.22 % Favored : 91.68 % Rotamer: Outliers : 0.43 % Allowed : 7.46 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.74 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.11), residues: 3968 helix: -2.51 (0.12), residues: 1206 sheet: -3.20 (0.22), residues: 424 loop : -2.57 (0.11), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS G 92 PHE 0.022 0.002 PHE C 131 TYR 0.022 0.002 TYR F 110 ARG 0.007 0.001 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1474 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1460 time to evaluate : 3.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8906 (t70) cc_final: 0.8594 (t70) REVERT: A 32 TYR cc_start: 0.8904 (m-80) cc_final: 0.8672 (m-80) REVERT: A 36 LEU cc_start: 0.9090 (tp) cc_final: 0.8346 (tp) REVERT: A 38 LEU cc_start: 0.9618 (mm) cc_final: 0.8780 (mm) REVERT: A 105 ARG cc_start: 0.9130 (mmm160) cc_final: 0.8656 (tpm170) REVERT: A 108 LYS cc_start: 0.9539 (tptp) cc_final: 0.8991 (mmtt) REVERT: A 125 ASP cc_start: 0.9356 (p0) cc_final: 0.9150 (p0) REVERT: A 269 ASP cc_start: 0.8112 (m-30) cc_final: 0.7844 (m-30) REVERT: A 294 TYR cc_start: 0.9303 (m-80) cc_final: 0.9030 (m-80) REVERT: A 334 GLN cc_start: 0.9335 (mp10) cc_final: 0.8504 (mp10) REVERT: A 343 GLN cc_start: 0.8669 (pp30) cc_final: 0.7942 (pp30) REVERT: A 352 GLU cc_start: 0.9084 (tm-30) cc_final: 0.8764 (tm-30) REVERT: A 372 HIS cc_start: 0.9230 (m170) cc_final: 0.8304 (m170) REVERT: A 385 MET cc_start: 0.8528 (ttp) cc_final: 0.7989 (ttp) REVERT: A 386 MET cc_start: 0.8850 (ppp) cc_final: 0.8471 (ppp) REVERT: A 414 MET cc_start: 0.8333 (ptt) cc_final: 0.7948 (ptt) REVERT: A 420 MET cc_start: 0.8441 (mtm) cc_final: 0.7892 (mtp) REVERT: A 448 GLN cc_start: 0.8693 (mp10) cc_final: 0.8381 (mp10) REVERT: A 460 LEU cc_start: 0.9697 (mp) cc_final: 0.9377 (mp) REVERT: A 498 GLN cc_start: 0.9075 (pm20) cc_final: 0.8864 (pm20) REVERT: A 509 TYR cc_start: 0.9124 (p90) cc_final: 0.8861 (p90) REVERT: B 18 LEU cc_start: 0.9494 (tp) cc_final: 0.9259 (tp) REVERT: B 34 ASP cc_start: 0.8192 (m-30) cc_final: 0.7932 (m-30) REVERT: B 36 LEU cc_start: 0.9353 (tp) cc_final: 0.9042 (tp) REVERT: B 37 ILE cc_start: 0.9214 (mm) cc_final: 0.8752 (mm) REVERT: B 62 LYS cc_start: 0.8855 (pttt) cc_final: 0.8477 (ptpp) REVERT: B 106 LYS cc_start: 0.9330 (mtpt) cc_final: 0.9099 (mtpt) REVERT: B 108 LYS cc_start: 0.9391 (pttm) cc_final: 0.8856 (tttt) REVERT: B 129 ASP cc_start: 0.9751 (m-30) cc_final: 0.9506 (m-30) REVERT: B 131 PHE cc_start: 0.9197 (m-10) cc_final: 0.8299 (m-80) REVERT: B 132 GLU cc_start: 0.9536 (pt0) cc_final: 0.9056 (pp20) REVERT: B 172 ASP cc_start: 0.8810 (t0) cc_final: 0.8538 (t0) REVERT: B 224 ARG cc_start: 0.8844 (ttt-90) cc_final: 0.8530 (ttt180) REVERT: B 238 LYS cc_start: 0.9010 (mmmm) cc_final: 0.8727 (tppt) REVERT: B 287 ILE cc_start: 0.9589 (pt) cc_final: 0.9345 (pt) REVERT: B 290 ILE cc_start: 0.9774 (pt) cc_final: 0.9559 (pt) REVERT: B 291 LYS cc_start: 0.9507 (mmmt) cc_final: 0.8920 (tppt) REVERT: B 334 GLN cc_start: 0.9211 (mt0) cc_final: 0.8908 (mm-40) REVERT: B 343 GLN cc_start: 0.8386 (tm-30) cc_final: 0.7703 (tm-30) REVERT: B 355 ARG cc_start: 0.8153 (ppt170) cc_final: 0.7882 (ttp-170) REVERT: B 404 ASP cc_start: 0.8619 (t0) cc_final: 0.8341 (t0) REVERT: B 491 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8070 (tm-30) REVERT: C 32 TYR cc_start: 0.9037 (m-10) cc_final: 0.8652 (m-10) REVERT: C 47 ASP cc_start: 0.9648 (m-30) cc_final: 0.8993 (p0) REVERT: C 65 LEU cc_start: 0.9372 (tt) cc_final: 0.9128 (tt) REVERT: C 82 MET cc_start: 0.9640 (tpp) cc_final: 0.9248 (tpp) REVERT: C 90 PHE cc_start: 0.9064 (m-80) cc_final: 0.8835 (m-80) REVERT: C 110 TYR cc_start: 0.9136 (t80) cc_final: 0.8853 (t80) REVERT: C 111 GLU cc_start: 0.9251 (tp30) cc_final: 0.8905 (mp0) REVERT: C 150 MET cc_start: 0.8839 (tpp) cc_final: 0.8616 (tpp) REVERT: C 175 LEU cc_start: 0.9012 (mt) cc_final: 0.8790 (mt) REVERT: C 199 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8630 (tp30) REVERT: C 200 ILE cc_start: 0.9283 (mm) cc_final: 0.8674 (mm) REVERT: C 201 LEU cc_start: 0.8857 (tt) cc_final: 0.8656 (tp) REVERT: C 203 ARG cc_start: 0.8584 (mtm-85) cc_final: 0.7752 (ptt90) REVERT: C 229 LYS cc_start: 0.9409 (ptpp) cc_final: 0.9050 (mmmt) REVERT: C 274 ASP cc_start: 0.9193 (t0) cc_final: 0.8870 (t70) REVERT: C 289 TYR cc_start: 0.9444 (t80) cc_final: 0.9084 (t80) REVERT: C 290 ILE cc_start: 0.9489 (pt) cc_final: 0.9233 (pt) REVERT: C 291 LYS cc_start: 0.9111 (ptpp) cc_final: 0.8882 (pttt) REVERT: C 331 CYS cc_start: 0.8745 (t) cc_final: 0.8432 (t) REVERT: C 333 THR cc_start: 0.9719 (p) cc_final: 0.9386 (p) REVERT: C 334 GLN cc_start: 0.9189 (mp10) cc_final: 0.8594 (mp10) REVERT: C 335 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8053 (tm-30) REVERT: C 336 VAL cc_start: 0.9598 (m) cc_final: 0.8821 (m) REVERT: C 482 MET cc_start: 0.9253 (tpp) cc_final: 0.8724 (tpp) REVERT: C 487 GLU cc_start: 0.8534 (pm20) cc_final: 0.8228 (pm20) REVERT: C 492 LYS cc_start: 0.8539 (pptt) cc_final: 0.8276 (pptt) REVERT: C 500 GLU cc_start: 0.9255 (pp20) cc_final: 0.8570 (pp20) REVERT: C 504 HIS cc_start: 0.8369 (p90) cc_final: 0.8085 (p90) REVERT: D 12 TYR cc_start: 0.8117 (t80) cc_final: 0.6755 (m-80) REVERT: D 16 ASP cc_start: 0.8466 (m-30) cc_final: 0.8254 (m-30) REVERT: D 21 GLN cc_start: 0.8918 (tm-30) cc_final: 0.8408 (tm-30) REVERT: D 25 ASN cc_start: 0.8718 (m110) cc_final: 0.8145 (m110) REVERT: D 32 TYR cc_start: 0.8960 (m-80) cc_final: 0.8664 (m-80) REVERT: D 71 ASP cc_start: 0.9386 (t0) cc_final: 0.8920 (t70) REVERT: D 91 ILE cc_start: 0.9293 (tp) cc_final: 0.9086 (tp) REVERT: D 111 GLU cc_start: 0.9076 (mp0) cc_final: 0.8838 (mp0) REVERT: D 112 GLN cc_start: 0.9211 (tm-30) cc_final: 0.8879 (tm-30) REVERT: D 114 PHE cc_start: 0.9199 (m-10) cc_final: 0.8859 (m-10) REVERT: D 192 ILE cc_start: 0.7796 (tp) cc_final: 0.7487 (tt) REVERT: D 215 ASP cc_start: 0.9481 (m-30) cc_final: 0.8988 (p0) REVERT: D 257 LYS cc_start: 0.9827 (ptpp) cc_final: 0.9569 (mmtm) REVERT: D 258 TYR cc_start: 0.9592 (t80) cc_final: 0.9341 (t80) REVERT: D 286 MET cc_start: 0.9669 (tpt) cc_final: 0.9371 (tpt) REVERT: D 289 TYR cc_start: 0.9491 (t80) cc_final: 0.9076 (t80) REVERT: D 290 ILE cc_start: 0.9770 (pt) cc_final: 0.9483 (pt) REVERT: D 311 LYS cc_start: 0.9217 (ttpp) cc_final: 0.8847 (ttpp) REVERT: D 349 LYS cc_start: 0.9610 (mmtp) cc_final: 0.9385 (mmmm) REVERT: D 352 GLU cc_start: 0.9175 (tm-30) cc_final: 0.8857 (tm-30) REVERT: D 385 MET cc_start: 0.8417 (tpt) cc_final: 0.7386 (tpt) REVERT: D 386 MET cc_start: 0.8742 (ptm) cc_final: 0.8338 (ptm) REVERT: D 418 ASP cc_start: 0.9372 (t70) cc_final: 0.9103 (t0) REVERT: D 482 MET cc_start: 0.9151 (tpt) cc_final: 0.8766 (tpt) REVERT: P 1 MET cc_start: 0.8532 (mpp) cc_final: 0.8021 (pmm) REVERT: E 28 ASP cc_start: 0.8866 (t70) cc_final: 0.8547 (t70) REVERT: E 32 TYR cc_start: 0.9366 (m-80) cc_final: 0.8893 (m-80) REVERT: E 38 LEU cc_start: 0.9641 (mm) cc_final: 0.8833 (mm) REVERT: E 69 PRO cc_start: 0.9561 (Cg_endo) cc_final: 0.9247 (Cg_exo) REVERT: E 82 MET cc_start: 0.9376 (ttp) cc_final: 0.9139 (ptm) REVERT: E 105 ARG cc_start: 0.9074 (mmm160) cc_final: 0.8675 (tpm170) REVERT: E 108 LYS cc_start: 0.9495 (tppt) cc_final: 0.9013 (mmtt) REVERT: E 142 ILE cc_start: 0.8696 (tp) cc_final: 0.8402 (tp) REVERT: E 158 ILE cc_start: 0.8720 (mm) cc_final: 0.8154 (tp) REVERT: E 165 PHE cc_start: 0.8653 (p90) cc_final: 0.8365 (p90) REVERT: E 179 MET cc_start: 0.7269 (pmm) cc_final: 0.6815 (pmm) REVERT: E 246 CYS cc_start: 0.9492 (t) cc_final: 0.9277 (t) REVERT: E 250 ILE cc_start: 0.9414 (pt) cc_final: 0.9156 (pt) REVERT: E 273 LEU cc_start: 0.9178 (tt) cc_final: 0.8914 (tt) REVERT: E 274 ASP cc_start: 0.8500 (t0) cc_final: 0.8265 (t0) REVERT: E 288 LYS cc_start: 0.9624 (mtmm) cc_final: 0.9350 (mttt) REVERT: E 294 TYR cc_start: 0.9324 (m-80) cc_final: 0.8923 (m-80) REVERT: E 334 GLN cc_start: 0.9291 (mp10) cc_final: 0.8422 (mp10) REVERT: E 352 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8742 (tm-30) REVERT: E 364 ASP cc_start: 0.7864 (m-30) cc_final: 0.6160 (m-30) REVERT: E 368 GLN cc_start: 0.8838 (mm-40) cc_final: 0.8583 (mm-40) REVERT: E 385 MET cc_start: 0.8391 (ttp) cc_final: 0.7797 (ttp) REVERT: E 386 MET cc_start: 0.8858 (ppp) cc_final: 0.8449 (ppp) REVERT: E 420 MET cc_start: 0.8400 (mtm) cc_final: 0.7847 (mtp) REVERT: E 448 GLN cc_start: 0.8730 (mp10) cc_final: 0.8403 (mp10) REVERT: E 460 LEU cc_start: 0.9674 (mp) cc_final: 0.9431 (mp) REVERT: E 469 GLN cc_start: 0.9370 (tp40) cc_final: 0.8797 (tt0) REVERT: E 483 MET cc_start: 0.9628 (tmm) cc_final: 0.9265 (tmm) REVERT: E 507 HIS cc_start: 0.8879 (t-90) cc_final: 0.8594 (t70) REVERT: E 509 TYR cc_start: 0.9173 (p90) cc_final: 0.8874 (p90) REVERT: F 34 ASP cc_start: 0.8258 (m-30) cc_final: 0.7985 (m-30) REVERT: F 37 ILE cc_start: 0.9310 (mm) cc_final: 0.8812 (mm) REVERT: F 70 MET cc_start: 0.7919 (tpp) cc_final: 0.7094 (tpt) REVERT: F 106 LYS cc_start: 0.9412 (mtpt) cc_final: 0.9163 (mtpt) REVERT: F 108 LYS cc_start: 0.9369 (pttm) cc_final: 0.8218 (tppt) REVERT: F 131 PHE cc_start: 0.9186 (m-10) cc_final: 0.8240 (m-80) REVERT: F 132 GLU cc_start: 0.9455 (pt0) cc_final: 0.9026 (pt0) REVERT: F 136 ARG cc_start: 0.9370 (mmp-170) cc_final: 0.8892 (mmm160) REVERT: F 144 ILE cc_start: 0.9505 (tp) cc_final: 0.9228 (tp) REVERT: F 244 LEU cc_start: 0.9026 (tp) cc_final: 0.8814 (tp) REVERT: F 287 ILE cc_start: 0.9561 (pt) cc_final: 0.9336 (pt) REVERT: F 290 ILE cc_start: 0.9770 (pt) cc_final: 0.9549 (pt) REVERT: F 291 LYS cc_start: 0.9495 (mmmt) cc_final: 0.8899 (tppt) REVERT: F 312 ASN cc_start: 0.9106 (p0) cc_final: 0.8870 (p0) REVERT: F 333 THR cc_start: 0.9616 (p) cc_final: 0.9209 (t) REVERT: F 335 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8097 (tm-30) REVERT: F 336 VAL cc_start: 0.9624 (p) cc_final: 0.9161 (p) REVERT: F 337 LEU cc_start: 0.9467 (mm) cc_final: 0.8919 (mm) REVERT: F 343 GLN cc_start: 0.8417 (tm-30) cc_final: 0.7758 (tm-30) REVERT: F 348 TYR cc_start: 0.9304 (t80) cc_final: 0.8951 (t80) REVERT: F 355 ARG cc_start: 0.8296 (ppt170) cc_final: 0.7971 (ttp-170) REVERT: F 372 HIS cc_start: 0.9119 (m170) cc_final: 0.8530 (m170) REVERT: F 404 ASP cc_start: 0.8576 (t0) cc_final: 0.8314 (t0) REVERT: F 482 MET cc_start: 0.9039 (ttp) cc_final: 0.8793 (mtm) REVERT: F 491 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8138 (tm-30) REVERT: F 506 LEU cc_start: 0.9112 (pp) cc_final: 0.8905 (pt) REVERT: F 507 HIS cc_start: 0.8667 (t-90) cc_final: 0.8368 (t-90) REVERT: G 32 TYR cc_start: 0.9049 (m-10) cc_final: 0.8660 (m-10) REVERT: G 43 ASP cc_start: 0.8500 (m-30) cc_final: 0.7624 (m-30) REVERT: G 47 ASP cc_start: 0.9639 (m-30) cc_final: 0.9005 (p0) REVERT: G 78 MET cc_start: 0.9548 (tpp) cc_final: 0.9272 (tpp) REVERT: G 82 MET cc_start: 0.9670 (tpp) cc_final: 0.9431 (tpp) REVERT: G 92 HIS cc_start: 0.8167 (p90) cc_final: 0.7958 (p90) REVERT: G 106 LYS cc_start: 0.7893 (mttp) cc_final: 0.7676 (mttm) REVERT: G 150 MET cc_start: 0.9002 (tpp) cc_final: 0.8787 (tpp) REVERT: G 175 LEU cc_start: 0.9086 (mt) cc_final: 0.8837 (mt) REVERT: G 181 LYS cc_start: 0.8839 (mptt) cc_final: 0.8610 (mmmt) REVERT: G 199 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8643 (tp30) REVERT: G 200 ILE cc_start: 0.9239 (mm) cc_final: 0.8934 (mm) REVERT: G 203 ARG cc_start: 0.8615 (mtm-85) cc_final: 0.8204 (mtm110) REVERT: G 216 ASP cc_start: 0.9360 (m-30) cc_final: 0.9123 (t0) REVERT: G 229 LYS cc_start: 0.9407 (ptpp) cc_final: 0.9056 (mmmt) REVERT: G 274 ASP cc_start: 0.9270 (t0) cc_final: 0.8925 (t70) REVERT: G 287 ILE cc_start: 0.9709 (OUTLIER) cc_final: 0.9398 (tt) REVERT: G 289 TYR cc_start: 0.9437 (t80) cc_final: 0.8973 (t80) REVERT: G 290 ILE cc_start: 0.9441 (pt) cc_final: 0.9189 (pt) REVERT: G 291 LYS cc_start: 0.9146 (ptpp) cc_final: 0.8874 (pttt) REVERT: G 331 CYS cc_start: 0.8995 (t) cc_final: 0.8648 (t) REVERT: G 333 THR cc_start: 0.9718 (p) cc_final: 0.9375 (p) REVERT: G 334 GLN cc_start: 0.9170 (mp10) cc_final: 0.8626 (mp10) REVERT: G 335 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8059 (tm-30) REVERT: G 336 VAL cc_start: 0.9596 (m) cc_final: 0.8732 (m) REVERT: G 482 MET cc_start: 0.9256 (tpp) cc_final: 0.8644 (tpp) REVERT: G 487 GLU cc_start: 0.8845 (pm20) cc_final: 0.8570 (pm20) REVERT: G 492 LYS cc_start: 0.8556 (pptt) cc_final: 0.8275 (pptt) REVERT: G 500 GLU cc_start: 0.9244 (pp20) cc_final: 0.8625 (pp20) REVERT: H 16 ASP cc_start: 0.8387 (m-30) cc_final: 0.8143 (m-30) REVERT: H 21 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8178 (tm-30) REVERT: H 25 ASN cc_start: 0.8734 (m110) cc_final: 0.8126 (m110) REVERT: H 91 ILE cc_start: 0.9222 (tp) cc_final: 0.8925 (tp) REVERT: H 93 HIS cc_start: 0.9098 (p-80) cc_final: 0.8846 (p-80) REVERT: H 108 LYS cc_start: 0.8878 (tptm) cc_final: 0.8468 (tptt) REVERT: H 112 GLN cc_start: 0.9195 (tm-30) cc_final: 0.8872 (tm-30) REVERT: H 192 ILE cc_start: 0.7449 (tp) cc_final: 0.7011 (tt) REVERT: H 203 ARG cc_start: 0.9142 (tpp-160) cc_final: 0.8899 (ttm110) REVERT: H 215 ASP cc_start: 0.9454 (m-30) cc_final: 0.9016 (p0) REVERT: H 257 LYS cc_start: 0.9824 (ptpp) cc_final: 0.9576 (mmtm) REVERT: H 258 TYR cc_start: 0.9510 (t80) cc_final: 0.9196 (t80) REVERT: H 286 MET cc_start: 0.9690 (tpt) cc_final: 0.9352 (tpt) REVERT: H 289 TYR cc_start: 0.9495 (t80) cc_final: 0.9095 (t80) REVERT: H 290 ILE cc_start: 0.9771 (pt) cc_final: 0.9469 (pt) REVERT: H 349 LYS cc_start: 0.9628 (mmtp) cc_final: 0.9392 (mmmm) REVERT: H 352 GLU cc_start: 0.9196 (tm-30) cc_final: 0.8883 (tm-30) REVERT: H 385 MET cc_start: 0.8239 (tpt) cc_final: 0.7084 (tpt) REVERT: H 386 MET cc_start: 0.8562 (ptm) cc_final: 0.8168 (ptm) REVERT: H 418 ASP cc_start: 0.9368 (t70) cc_final: 0.9058 (t70) REVERT: H 465 GLN cc_start: 0.8684 (pp30) cc_final: 0.8228 (tt0) REVERT: H 482 MET cc_start: 0.9048 (tpt) cc_final: 0.8596 (tpt) REVERT: L 1 MET cc_start: 0.8482 (mpp) cc_final: 0.8025 (pmm) outliers start: 14 outliers final: 2 residues processed: 1464 average time/residue: 0.4093 time to fit residues: 956.2418 Evaluate side-chains 1183 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1180 time to evaluate : 3.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 30.0000 chunk 296 optimal weight: 7.9990 chunk 242 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 356 optimal weight: 9.9990 chunk 385 optimal weight: 0.0570 chunk 317 optimal weight: 9.9990 chunk 353 optimal weight: 8.9990 chunk 121 optimal weight: 0.8980 chunk 286 optimal weight: 0.9980 overall best weight: 1.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 GLN A 465 GLN A 466 HIS B 25 ASN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 HIS ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 ASN ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 283 GLN ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 448 GLN E 465 GLN E 466 HIS ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 504 HIS ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN ** G 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 32212 Z= 0.278 Angle : 0.817 10.184 43712 Z= 0.413 Chirality : 0.050 0.268 4984 Planarity : 0.005 0.133 5452 Dihedral : 17.776 178.854 5344 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 25.78 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.55 % Favored : 90.40 % Rotamer: Outliers : 0.34 % Allowed : 7.40 % Favored : 92.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.74 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.12), residues: 3968 helix: -2.08 (0.13), residues: 1212 sheet: -2.77 (0.24), residues: 378 loop : -2.36 (0.12), residues: 2378 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS G 92 PHE 0.019 0.002 PHE D 165 TYR 0.025 0.002 TYR A 353 ARG 0.011 0.001 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1411 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1400 time to evaluate : 3.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8901 (t70) cc_final: 0.8564 (t70) REVERT: A 32 TYR cc_start: 0.8882 (m-80) cc_final: 0.8557 (m-10) REVERT: A 36 LEU cc_start: 0.9153 (tp) cc_final: 0.8431 (tp) REVERT: A 38 LEU cc_start: 0.9625 (mm) cc_final: 0.8734 (mm) REVERT: A 48 GLN cc_start: 0.9250 (mt0) cc_final: 0.8869 (mt0) REVERT: A 105 ARG cc_start: 0.9135 (mmm160) cc_final: 0.8828 (tpp80) REVERT: A 108 LYS cc_start: 0.9540 (tptp) cc_final: 0.9316 (tppt) REVERT: A 246 CYS cc_start: 0.9494 (t) cc_final: 0.8618 (p) REVERT: A 294 TYR cc_start: 0.9338 (m-80) cc_final: 0.9032 (m-80) REVERT: A 334 GLN cc_start: 0.9334 (mp10) cc_final: 0.8504 (mp10) REVERT: A 343 GLN cc_start: 0.8620 (pp30) cc_final: 0.7809 (pp30) REVERT: A 352 GLU cc_start: 0.9213 (tm-30) cc_final: 0.8707 (tm-30) REVERT: A 355 ARG cc_start: 0.8831 (ptm-80) cc_final: 0.8548 (ptt90) REVERT: A 372 HIS cc_start: 0.9304 (m170) cc_final: 0.8469 (m170) REVERT: A 385 MET cc_start: 0.8644 (ttp) cc_final: 0.8037 (ttp) REVERT: A 386 MET cc_start: 0.8725 (ppp) cc_final: 0.8016 (ppp) REVERT: A 390 LEU cc_start: 0.9145 (pt) cc_final: 0.8925 (pt) REVERT: A 414 MET cc_start: 0.8346 (ptt) cc_final: 0.8135 (ptt) REVERT: A 420 MET cc_start: 0.8434 (mtm) cc_final: 0.7943 (mtp) REVERT: A 448 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8316 (mp10) REVERT: A 509 TYR cc_start: 0.9101 (p90) cc_final: 0.8798 (p90) REVERT: B 16 ASP cc_start: 0.7936 (t0) cc_final: 0.6659 (t0) REVERT: B 34 ASP cc_start: 0.8123 (m-30) cc_final: 0.7746 (m-30) REVERT: B 36 LEU cc_start: 0.9357 (tp) cc_final: 0.9131 (tp) REVERT: B 37 ILE cc_start: 0.9069 (mm) cc_final: 0.8625 (mm) REVERT: B 82 MET cc_start: 0.9348 (ttt) cc_final: 0.8990 (tmm) REVERT: B 103 GLU cc_start: 0.9506 (tp30) cc_final: 0.9186 (tp30) REVERT: B 108 LYS cc_start: 0.9338 (pttm) cc_final: 0.8708 (tttt) REVERT: B 132 GLU cc_start: 0.9517 (pt0) cc_final: 0.9169 (pt0) REVERT: B 181 LYS cc_start: 0.9129 (tppt) cc_final: 0.8747 (tppt) REVERT: B 224 ARG cc_start: 0.8798 (ttt-90) cc_final: 0.8486 (ttt180) REVERT: B 238 LYS cc_start: 0.8902 (mmmm) cc_final: 0.8628 (tppt) REVERT: B 250 ILE cc_start: 0.9270 (mp) cc_final: 0.8708 (tp) REVERT: B 334 GLN cc_start: 0.9204 (mt0) cc_final: 0.8898 (mm-40) REVERT: B 335 GLU cc_start: 0.8511 (tm-30) cc_final: 0.8242 (tm-30) REVERT: B 343 GLN cc_start: 0.8334 (tm-30) cc_final: 0.7567 (tm-30) REVERT: B 355 ARG cc_start: 0.8181 (ppt170) cc_final: 0.7904 (ttp-170) REVERT: B 372 HIS cc_start: 0.8998 (m170) cc_final: 0.8476 (m170) REVERT: B 403 SER cc_start: 0.9348 (t) cc_final: 0.9145 (t) REVERT: B 404 ASP cc_start: 0.8707 (t0) cc_final: 0.8410 (t0) REVERT: B 491 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8059 (tm-30) REVERT: C 32 TYR cc_start: 0.9016 (m-10) cc_final: 0.8594 (m-10) REVERT: C 43 ASP cc_start: 0.8302 (m-30) cc_final: 0.8077 (m-30) REVERT: C 47 ASP cc_start: 0.9664 (m-30) cc_final: 0.9009 (p0) REVERT: C 65 LEU cc_start: 0.9384 (tt) cc_final: 0.9170 (tt) REVERT: C 82 MET cc_start: 0.9620 (tpp) cc_final: 0.9257 (tpp) REVERT: C 90 PHE cc_start: 0.9063 (m-80) cc_final: 0.8757 (m-80) REVERT: C 111 GLU cc_start: 0.9298 (tp30) cc_final: 0.9049 (mp0) REVERT: C 175 LEU cc_start: 0.9016 (mt) cc_final: 0.8728 (mt) REVERT: C 199 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8688 (tp30) REVERT: C 200 ILE cc_start: 0.9302 (mm) cc_final: 0.8889 (mm) REVERT: C 203 ARG cc_start: 0.8659 (mtm-85) cc_final: 0.7970 (mtm110) REVERT: C 229 LYS cc_start: 0.9407 (ptpp) cc_final: 0.9126 (mmmt) REVERT: C 274 ASP cc_start: 0.9013 (t0) cc_final: 0.8663 (t70) REVERT: C 277 GLN cc_start: 0.8355 (tm-30) cc_final: 0.8108 (tm-30) REVERT: C 289 TYR cc_start: 0.9468 (t80) cc_final: 0.9230 (t80) REVERT: C 290 ILE cc_start: 0.9473 (pt) cc_final: 0.9190 (pt) REVERT: C 321 LEU cc_start: 0.9323 (tp) cc_final: 0.9114 (tp) REVERT: C 331 CYS cc_start: 0.8824 (t) cc_final: 0.8620 (t) REVERT: C 333 THR cc_start: 0.9667 (p) cc_final: 0.9308 (p) REVERT: C 334 GLN cc_start: 0.9149 (mp10) cc_final: 0.8549 (mp10) REVERT: C 335 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8084 (tm-30) REVERT: C 336 VAL cc_start: 0.9612 (m) cc_final: 0.8831 (m) REVERT: C 390 LEU cc_start: 0.9416 (pt) cc_final: 0.9002 (pt) REVERT: C 414 MET cc_start: 0.9187 (pmm) cc_final: 0.8928 (pmm) REVERT: C 482 MET cc_start: 0.9310 (tpp) cc_final: 0.8854 (tpp) REVERT: C 487 GLU cc_start: 0.8530 (pm20) cc_final: 0.8204 (pm20) REVERT: C 492 LYS cc_start: 0.8552 (pptt) cc_final: 0.8302 (pptt) REVERT: C 500 GLU cc_start: 0.9233 (pp20) cc_final: 0.8535 (pp20) REVERT: C 504 HIS cc_start: 0.8453 (p90) cc_final: 0.8116 (p90) REVERT: D 12 TYR cc_start: 0.8314 (t80) cc_final: 0.7051 (m-80) REVERT: D 16 ASP cc_start: 0.8381 (m-30) cc_final: 0.8153 (m-30) REVERT: D 21 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8242 (tm-30) REVERT: D 25 ASN cc_start: 0.8608 (m110) cc_final: 0.8151 (m110) REVERT: D 33 ASN cc_start: 0.8744 (t0) cc_final: 0.8325 (t0) REVERT: D 51 LEU cc_start: 0.9484 (pp) cc_final: 0.9180 (pp) REVERT: D 71 ASP cc_start: 0.9423 (t0) cc_final: 0.9111 (t70) REVERT: D 91 ILE cc_start: 0.9273 (tp) cc_final: 0.9070 (tp) REVERT: D 112 GLN cc_start: 0.9169 (tm-30) cc_final: 0.8764 (tm-30) REVERT: D 114 PHE cc_start: 0.9278 (m-10) cc_final: 0.8966 (m-10) REVERT: D 192 ILE cc_start: 0.7917 (tp) cc_final: 0.7618 (tt) REVERT: D 215 ASP cc_start: 0.9443 (m-30) cc_final: 0.8980 (p0) REVERT: D 257 LYS cc_start: 0.9841 (ptpp) cc_final: 0.9558 (mmtm) REVERT: D 258 TYR cc_start: 0.9594 (t80) cc_final: 0.9359 (t80) REVERT: D 286 MET cc_start: 0.9666 (tpt) cc_final: 0.9369 (tpt) REVERT: D 289 TYR cc_start: 0.9482 (t80) cc_final: 0.9047 (t80) REVERT: D 290 ILE cc_start: 0.9771 (pt) cc_final: 0.9465 (pt) REVERT: D 311 LYS cc_start: 0.9214 (ttpp) cc_final: 0.8839 (ttpp) REVERT: D 352 GLU cc_start: 0.9222 (tm-30) cc_final: 0.8903 (tm-30) REVERT: D 385 MET cc_start: 0.8588 (tpt) cc_final: 0.7857 (tpt) REVERT: D 386 MET cc_start: 0.8812 (ptm) cc_final: 0.8524 (ptm) REVERT: D 418 ASP cc_start: 0.9393 (t70) cc_final: 0.9108 (t70) REVERT: D 465 GLN cc_start: 0.9118 (tt0) cc_final: 0.8525 (tm-30) REVERT: D 468 CYS cc_start: 0.9128 (t) cc_final: 0.8849 (t) REVERT: D 478 GLN cc_start: 0.9440 (mt0) cc_final: 0.8907 (mt0) REVERT: D 482 MET cc_start: 0.9200 (tpt) cc_final: 0.8886 (tpt) REVERT: P 1 MET cc_start: 0.8501 (mpp) cc_final: 0.8083 (pmm) REVERT: E 28 ASP cc_start: 0.8752 (t70) cc_final: 0.8423 (t70) REVERT: E 32 TYR cc_start: 0.9350 (m-80) cc_final: 0.8819 (m-80) REVERT: E 36 LEU cc_start: 0.9056 (tp) cc_final: 0.8715 (tp) REVERT: E 38 LEU cc_start: 0.9628 (mm) cc_final: 0.8841 (mm) REVERT: E 48 GLN cc_start: 0.9249 (mt0) cc_final: 0.8855 (mt0) REVERT: E 69 PRO cc_start: 0.9525 (Cg_endo) cc_final: 0.9130 (Cg_exo) REVERT: E 82 MET cc_start: 0.9447 (ttp) cc_final: 0.9115 (ptm) REVERT: E 105 ARG cc_start: 0.9090 (mmm160) cc_final: 0.8649 (tpm170) REVERT: E 108 LYS cc_start: 0.9538 (tppt) cc_final: 0.9044 (mmtt) REVERT: E 142 ILE cc_start: 0.8740 (tp) cc_final: 0.8479 (tp) REVERT: E 158 ILE cc_start: 0.8726 (mm) cc_final: 0.8424 (tp) REVERT: E 165 PHE cc_start: 0.8664 (p90) cc_final: 0.8405 (p90) REVERT: E 231 ARG cc_start: 0.9340 (ptm160) cc_final: 0.9063 (ptm160) REVERT: E 246 CYS cc_start: 0.9519 (t) cc_final: 0.9168 (t) REVERT: E 262 LEU cc_start: 0.9548 (pp) cc_final: 0.9348 (pp) REVERT: E 273 LEU cc_start: 0.9233 (tt) cc_final: 0.8996 (tt) REVERT: E 288 LYS cc_start: 0.9634 (mtmm) cc_final: 0.9362 (mttt) REVERT: E 294 TYR cc_start: 0.9327 (m-80) cc_final: 0.8987 (m-80) REVERT: E 334 GLN cc_start: 0.9342 (mp10) cc_final: 0.8560 (mp10) REVERT: E 352 GLU cc_start: 0.9227 (tm-30) cc_final: 0.8703 (tm-30) REVERT: E 353 TYR cc_start: 0.8847 (t80) cc_final: 0.8550 (t80) REVERT: E 355 ARG cc_start: 0.8805 (ptm-80) cc_final: 0.8408 (ptm-80) REVERT: E 364 ASP cc_start: 0.7825 (m-30) cc_final: 0.7014 (m-30) REVERT: E 372 HIS cc_start: 0.9276 (m170) cc_final: 0.8366 (m170) REVERT: E 386 MET cc_start: 0.8727 (ppp) cc_final: 0.8287 (tmm) REVERT: E 414 MET cc_start: 0.8166 (ptt) cc_final: 0.6942 (ptt) REVERT: E 420 MET cc_start: 0.8409 (mtm) cc_final: 0.7947 (mtp) REVERT: E 448 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8317 (mp10) REVERT: E 480 ARG cc_start: 0.8830 (mpp-170) cc_final: 0.8391 (mpp80) REVERT: E 483 MET cc_start: 0.9562 (tmm) cc_final: 0.9199 (tmm) REVERT: E 507 HIS cc_start: 0.8868 (t-90) cc_final: 0.8595 (t70) REVERT: E 509 TYR cc_start: 0.9161 (p90) cc_final: 0.8888 (p90) REVERT: F 34 ASP cc_start: 0.8185 (m-30) cc_final: 0.7978 (m-30) REVERT: F 37 ILE cc_start: 0.9147 (mm) cc_final: 0.8674 (mm) REVERT: F 70 MET cc_start: 0.7858 (tpp) cc_final: 0.6809 (tpt) REVERT: F 106 LYS cc_start: 0.9383 (mtpt) cc_final: 0.9134 (mtpt) REVERT: F 108 LYS cc_start: 0.9228 (pttm) cc_final: 0.8199 (tppt) REVERT: F 111 GLU cc_start: 0.9047 (mp0) cc_final: 0.8630 (mp0) REVERT: F 132 GLU cc_start: 0.9451 (pt0) cc_final: 0.9151 (pt0) REVERT: F 166 LEU cc_start: 0.9526 (mm) cc_final: 0.8455 (tp) REVERT: F 185 LEU cc_start: 0.8904 (mt) cc_final: 0.8414 (mt) REVERT: F 238 LYS cc_start: 0.8905 (mmmm) cc_final: 0.8556 (tppt) REVERT: F 334 GLN cc_start: 0.9284 (mt0) cc_final: 0.8916 (mm-40) REVERT: F 335 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8158 (tm-30) REVERT: F 336 VAL cc_start: 0.9608 (p) cc_final: 0.9164 (p) REVERT: F 337 LEU cc_start: 0.9481 (mm) cc_final: 0.9221 (mm) REVERT: F 343 GLN cc_start: 0.8398 (tm-30) cc_final: 0.7661 (tm-30) REVERT: F 355 ARG cc_start: 0.8353 (ppt170) cc_final: 0.8011 (ttp-170) REVERT: F 372 HIS cc_start: 0.9144 (m170) cc_final: 0.8571 (m170) REVERT: F 404 ASP cc_start: 0.8658 (t0) cc_final: 0.8383 (t0) REVERT: F 491 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8277 (tm-30) REVERT: F 507 HIS cc_start: 0.8654 (t-90) cc_final: 0.8415 (t-90) REVERT: G 32 TYR cc_start: 0.9050 (m-10) cc_final: 0.8544 (m-10) REVERT: G 43 ASP cc_start: 0.8460 (m-30) cc_final: 0.8194 (m-30) REVERT: G 78 MET cc_start: 0.9557 (tpp) cc_final: 0.9272 (tpp) REVERT: G 82 MET cc_start: 0.9685 (tpp) cc_final: 0.9417 (tpp) REVERT: G 175 LEU cc_start: 0.9059 (mt) cc_final: 0.8845 (mt) REVERT: G 199 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8847 (tp30) REVERT: G 216 ASP cc_start: 0.9318 (m-30) cc_final: 0.9071 (t70) REVERT: G 229 LYS cc_start: 0.9408 (ptpp) cc_final: 0.9120 (mmmt) REVERT: G 274 ASP cc_start: 0.9079 (t0) cc_final: 0.8735 (t70) REVERT: G 287 ILE cc_start: 0.9703 (OUTLIER) cc_final: 0.9341 (tt) REVERT: G 289 TYR cc_start: 0.9468 (t80) cc_final: 0.9090 (t80) REVERT: G 290 ILE cc_start: 0.9416 (pt) cc_final: 0.9210 (pt) REVERT: G 291 LYS cc_start: 0.9132 (ptpp) cc_final: 0.8819 (pttm) REVERT: G 331 CYS cc_start: 0.8942 (t) cc_final: 0.8629 (t) REVERT: G 333 THR cc_start: 0.9684 (p) cc_final: 0.9317 (p) REVERT: G 334 GLN cc_start: 0.9132 (mp10) cc_final: 0.8540 (mp10) REVERT: G 335 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8016 (tm-30) REVERT: G 336 VAL cc_start: 0.9588 (m) cc_final: 0.8684 (m) REVERT: G 386 MET cc_start: 0.8972 (tmm) cc_final: 0.8693 (tmm) REVERT: G 395 GLU cc_start: 0.8757 (mp0) cc_final: 0.8446 (mp0) REVERT: G 414 MET cc_start: 0.9184 (pmm) cc_final: 0.8929 (pmm) REVERT: G 482 MET cc_start: 0.9308 (tpp) cc_final: 0.8760 (tpp) REVERT: G 487 GLU cc_start: 0.8836 (pm20) cc_final: 0.8555 (pm20) REVERT: G 492 LYS cc_start: 0.8645 (pptt) cc_final: 0.8362 (pptt) REVERT: G 500 GLU cc_start: 0.9240 (pp20) cc_final: 0.8635 (pp20) REVERT: G 507 HIS cc_start: 0.8581 (t70) cc_final: 0.8243 (t-90) REVERT: H 16 ASP cc_start: 0.8400 (m-30) cc_final: 0.8174 (m-30) REVERT: H 51 LEU cc_start: 0.9474 (pp) cc_final: 0.9260 (pp) REVERT: H 91 ILE cc_start: 0.9324 (tp) cc_final: 0.9007 (tp) REVERT: H 108 LYS cc_start: 0.9018 (tptm) cc_final: 0.8553 (tptp) REVERT: H 112 GLN cc_start: 0.9267 (tm-30) cc_final: 0.8965 (tm-30) REVERT: H 150 MET cc_start: 0.6882 (tmm) cc_final: 0.6541 (tmm) REVERT: H 158 ILE cc_start: 0.7124 (tp) cc_final: 0.6882 (tp) REVERT: H 179 MET cc_start: 0.7418 (ppp) cc_final: 0.7054 (ppp) REVERT: H 203 ARG cc_start: 0.9150 (tpp-160) cc_final: 0.8900 (ttm110) REVERT: H 208 LYS cc_start: 0.7768 (tppp) cc_final: 0.7236 (tmtt) REVERT: H 258 TYR cc_start: 0.9528 (t80) cc_final: 0.9284 (t80) REVERT: H 286 MET cc_start: 0.9685 (tpt) cc_final: 0.9283 (tpt) REVERT: H 290 ILE cc_start: 0.9786 (pt) cc_final: 0.9493 (pt) REVERT: H 352 GLU cc_start: 0.9231 (tm-30) cc_final: 0.8910 (tm-30) REVERT: H 385 MET cc_start: 0.8731 (tpt) cc_final: 0.8082 (tpt) REVERT: H 400 TYR cc_start: 0.7869 (m-80) cc_final: 0.7664 (m-80) REVERT: H 418 ASP cc_start: 0.9418 (t70) cc_final: 0.9121 (t0) REVERT: H 465 GLN cc_start: 0.8639 (pp30) cc_final: 0.8195 (tt0) REVERT: H 478 GLN cc_start: 0.9406 (mt0) cc_final: 0.8878 (mt0) REVERT: H 482 MET cc_start: 0.9057 (tpt) cc_final: 0.8685 (tpt) REVERT: J 5 LEU cc_start: 0.9473 (mt) cc_final: 0.9096 (mt) REVERT: L 1 MET cc_start: 0.8424 (mpp) cc_final: 0.8038 (pmm) outliers start: 11 outliers final: 2 residues processed: 1402 average time/residue: 0.4076 time to fit residues: 921.1916 Evaluate side-chains 1143 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1138 time to evaluate : 3.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 0.9980 chunk 268 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 170 optimal weight: 4.9990 chunk 239 optimal weight: 1.9990 chunk 357 optimal weight: 0.4980 chunk 378 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 339 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 466 HIS ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN B 507 HIS ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 GLN D 94 ASN ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 HIS ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN G 469 GLN ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32212 Z= 0.212 Angle : 0.798 10.064 43712 Z= 0.396 Chirality : 0.050 0.274 4984 Planarity : 0.005 0.193 5452 Dihedral : 17.061 176.110 5344 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 23.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.59 % Favored : 91.36 % Rotamer: Outliers : 0.21 % Allowed : 5.50 % Favored : 94.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.12), residues: 3968 helix: -1.91 (0.13), residues: 1200 sheet: -2.58 (0.24), residues: 374 loop : -2.21 (0.12), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.001 HIS D 466 PHE 0.025 0.002 PHE B 131 TYR 0.028 0.002 TYR G 348 ARG 0.017 0.001 ARG H 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1443 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1436 time to evaluate : 3.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8976 (t70) cc_final: 0.8589 (t70) REVERT: A 36 LEU cc_start: 0.9190 (tp) cc_final: 0.8526 (tp) REVERT: A 38 LEU cc_start: 0.9621 (mm) cc_final: 0.8787 (mm) REVERT: A 48 GLN cc_start: 0.9206 (mt0) cc_final: 0.8860 (mt0) REVERT: A 58 LYS cc_start: 0.9319 (mttm) cc_final: 0.8906 (mttm) REVERT: A 68 SER cc_start: 0.9330 (t) cc_final: 0.8643 (t) REVERT: A 98 GLU cc_start: 0.9178 (mp0) cc_final: 0.8976 (mp0) REVERT: A 105 ARG cc_start: 0.9104 (mmm160) cc_final: 0.8814 (tpp80) REVERT: A 108 LYS cc_start: 0.9517 (tptp) cc_final: 0.9303 (tppt) REVERT: A 246 CYS cc_start: 0.9423 (t) cc_final: 0.8659 (p) REVERT: A 294 TYR cc_start: 0.9315 (m-80) cc_final: 0.8985 (m-80) REVERT: A 334 GLN cc_start: 0.9272 (mp10) cc_final: 0.9031 (mp10) REVERT: A 343 GLN cc_start: 0.8569 (pp30) cc_final: 0.8281 (pp30) REVERT: A 352 GLU cc_start: 0.9189 (tm-30) cc_final: 0.8768 (tm-30) REVERT: A 372 HIS cc_start: 0.9264 (m170) cc_final: 0.8348 (m170) REVERT: A 385 MET cc_start: 0.8568 (ttp) cc_final: 0.8072 (ttp) REVERT: A 386 MET cc_start: 0.8781 (ppp) cc_final: 0.8414 (ppp) REVERT: A 420 MET cc_start: 0.8345 (mtm) cc_final: 0.7914 (mtp) REVERT: A 482 MET cc_start: 0.9026 (ttt) cc_final: 0.8803 (ttt) REVERT: A 509 TYR cc_start: 0.9106 (p90) cc_final: 0.8829 (p90) REVERT: B 34 ASP cc_start: 0.8221 (m-30) cc_final: 0.7876 (m-30) REVERT: B 36 LEU cc_start: 0.9404 (tp) cc_final: 0.9189 (tp) REVERT: B 37 ILE cc_start: 0.9141 (mm) cc_final: 0.8724 (mm) REVERT: B 41 TYR cc_start: 0.9173 (t80) cc_final: 0.8969 (t80) REVERT: B 103 GLU cc_start: 0.9479 (tp30) cc_final: 0.9249 (tp30) REVERT: B 108 LYS cc_start: 0.9267 (pttm) cc_final: 0.8538 (tttt) REVERT: B 129 ASP cc_start: 0.9710 (m-30) cc_final: 0.9458 (m-30) REVERT: B 131 PHE cc_start: 0.9156 (m-80) cc_final: 0.8684 (m-80) REVERT: B 132 GLU cc_start: 0.9515 (pt0) cc_final: 0.9133 (pp20) REVERT: B 134 LYS cc_start: 0.9718 (pttm) cc_final: 0.9367 (tttp) REVERT: B 181 LYS cc_start: 0.9158 (tppt) cc_final: 0.8788 (tppt) REVERT: B 185 LEU cc_start: 0.8800 (mt) cc_final: 0.8443 (mt) REVERT: B 224 ARG cc_start: 0.8756 (ttt-90) cc_final: 0.8469 (ttt180) REVERT: B 287 ILE cc_start: 0.9522 (pt) cc_final: 0.9311 (pt) REVERT: B 291 LYS cc_start: 0.9443 (mmmt) cc_final: 0.8968 (tppt) REVERT: B 294 TYR cc_start: 0.9348 (m-80) cc_final: 0.9085 (m-80) REVERT: B 334 GLN cc_start: 0.9191 (mt0) cc_final: 0.8771 (mm-40) REVERT: B 335 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8119 (tm-30) REVERT: B 343 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8093 (tm-30) REVERT: B 348 TYR cc_start: 0.9110 (t80) cc_final: 0.8829 (t80) REVERT: B 355 ARG cc_start: 0.8252 (ppt170) cc_final: 0.7862 (ttp-170) REVERT: B 372 HIS cc_start: 0.8920 (m170) cc_final: 0.8451 (m90) REVERT: B 404 ASP cc_start: 0.8673 (t0) cc_final: 0.8387 (t0) REVERT: B 441 GLN cc_start: 0.9015 (mt0) cc_final: 0.8681 (mt0) REVERT: B 449 ASP cc_start: 0.8312 (t70) cc_final: 0.8101 (t70) REVERT: B 491 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8191 (tm-30) REVERT: C 32 TYR cc_start: 0.8918 (m-10) cc_final: 0.8507 (m-10) REVERT: C 43 ASP cc_start: 0.8527 (m-30) cc_final: 0.8279 (m-30) REVERT: C 47 ASP cc_start: 0.9654 (m-30) cc_final: 0.9001 (p0) REVERT: C 65 LEU cc_start: 0.9415 (tt) cc_final: 0.9160 (tt) REVERT: C 82 MET cc_start: 0.9628 (tpp) cc_final: 0.9304 (tpp) REVERT: C 90 PHE cc_start: 0.9107 (m-80) cc_final: 0.8690 (m-80) REVERT: C 111 GLU cc_start: 0.9299 (tp30) cc_final: 0.9034 (mp0) REVERT: C 175 LEU cc_start: 0.9023 (mt) cc_final: 0.8774 (mt) REVERT: C 199 GLU cc_start: 0.9198 (mt-10) cc_final: 0.8638 (tp30) REVERT: C 200 ILE cc_start: 0.9329 (mm) cc_final: 0.8899 (mm) REVERT: C 203 ARG cc_start: 0.8663 (mtm-85) cc_final: 0.7918 (mtm180) REVERT: C 229 LYS cc_start: 0.9371 (ptpp) cc_final: 0.9098 (mmmt) REVERT: C 274 ASP cc_start: 0.8980 (t0) cc_final: 0.8665 (t70) REVERT: C 289 TYR cc_start: 0.9478 (t80) cc_final: 0.9271 (t80) REVERT: C 290 ILE cc_start: 0.9499 (pt) cc_final: 0.9230 (pt) REVERT: C 291 LYS cc_start: 0.9080 (ptpp) cc_final: 0.8858 (pttm) REVERT: C 311 LYS cc_start: 0.8753 (tttt) cc_final: 0.8485 (ttmt) REVERT: C 331 CYS cc_start: 0.8825 (t) cc_final: 0.8616 (t) REVERT: C 333 THR cc_start: 0.9730 (p) cc_final: 0.9387 (p) REVERT: C 334 GLN cc_start: 0.9023 (mp10) cc_final: 0.8567 (mp10) REVERT: C 335 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8085 (tm-30) REVERT: C 336 VAL cc_start: 0.9596 (m) cc_final: 0.8829 (m) REVERT: C 349 LYS cc_start: 0.8810 (mtpt) cc_final: 0.8381 (mtpt) REVERT: C 482 MET cc_start: 0.9338 (tpp) cc_final: 0.8791 (mmm) REVERT: C 500 GLU cc_start: 0.9215 (pp20) cc_final: 0.8501 (pp20) REVERT: C 504 HIS cc_start: 0.8343 (p90) cc_final: 0.8103 (p90) REVERT: D 12 TYR cc_start: 0.8416 (t80) cc_final: 0.7099 (m-80) REVERT: D 21 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8445 (tm-30) REVERT: D 33 ASN cc_start: 0.8934 (t0) cc_final: 0.8621 (t0) REVERT: D 51 LEU cc_start: 0.9464 (pp) cc_final: 0.9242 (pp) REVERT: D 71 ASP cc_start: 0.9429 (t0) cc_final: 0.8854 (t0) REVERT: D 91 ILE cc_start: 0.9271 (tp) cc_final: 0.9058 (tp) REVERT: D 215 ASP cc_start: 0.9443 (m-30) cc_final: 0.8972 (p0) REVERT: D 257 LYS cc_start: 0.9835 (ptpp) cc_final: 0.9597 (mmtm) REVERT: D 258 TYR cc_start: 0.9607 (t80) cc_final: 0.9407 (t80) REVERT: D 286 MET cc_start: 0.9661 (tpt) cc_final: 0.9355 (tpt) REVERT: D 289 TYR cc_start: 0.9486 (t80) cc_final: 0.9140 (t80) REVERT: D 290 ILE cc_start: 0.9781 (pt) cc_final: 0.9480 (pt) REVERT: D 311 LYS cc_start: 0.9123 (ttpp) cc_final: 0.8687 (ttpp) REVERT: D 352 GLU cc_start: 0.9206 (tm-30) cc_final: 0.8883 (tm-30) REVERT: D 385 MET cc_start: 0.8550 (tpt) cc_final: 0.7872 (tpt) REVERT: D 418 ASP cc_start: 0.9359 (t70) cc_final: 0.9124 (t0) REVERT: D 465 GLN cc_start: 0.9130 (tt0) cc_final: 0.8803 (tt0) REVERT: D 478 GLN cc_start: 0.9403 (mt0) cc_final: 0.9173 (mt0) REVERT: D 482 MET cc_start: 0.9117 (tpt) cc_final: 0.8780 (tpt) REVERT: D 489 LYS cc_start: 0.8841 (ptpt) cc_final: 0.8361 (ptpt) REVERT: D 491 GLU cc_start: 0.9131 (tp30) cc_final: 0.8843 (tm-30) REVERT: P 1 MET cc_start: 0.8493 (mpp) cc_final: 0.8108 (pmm) REVERT: E 28 ASP cc_start: 0.8924 (t70) cc_final: 0.8605 (t70) REVERT: E 32 TYR cc_start: 0.9308 (m-80) cc_final: 0.8782 (m-80) REVERT: E 36 LEU cc_start: 0.8915 (tp) cc_final: 0.8580 (tp) REVERT: E 38 LEU cc_start: 0.9624 (mm) cc_final: 0.8857 (mm) REVERT: E 48 GLN cc_start: 0.9262 (mt0) cc_final: 0.8899 (mt0) REVERT: E 82 MET cc_start: 0.9428 (ttp) cc_final: 0.9134 (ptm) REVERT: E 105 ARG cc_start: 0.9082 (mmm160) cc_final: 0.8467 (tpp-160) REVERT: E 108 LYS cc_start: 0.9485 (tppt) cc_final: 0.8715 (mmtt) REVERT: E 109 LYS cc_start: 0.9537 (ptpp) cc_final: 0.9240 (mtmt) REVERT: E 142 ILE cc_start: 0.8729 (tp) cc_final: 0.8429 (tp) REVERT: E 158 ILE cc_start: 0.8770 (mm) cc_final: 0.8204 (tp) REVERT: E 165 PHE cc_start: 0.8557 (p90) cc_final: 0.8287 (p90) REVERT: E 179 MET cc_start: 0.7391 (pmm) cc_final: 0.6845 (pmm) REVERT: E 224 ARG cc_start: 0.7460 (mmt180) cc_final: 0.7171 (mmt180) REVERT: E 246 CYS cc_start: 0.9513 (t) cc_final: 0.9176 (t) REVERT: E 273 LEU cc_start: 0.9213 (tt) cc_final: 0.8976 (tt) REVERT: E 294 TYR cc_start: 0.9292 (m-80) cc_final: 0.8950 (m-80) REVERT: E 352 GLU cc_start: 0.9195 (tm-30) cc_final: 0.8660 (tm-30) REVERT: E 353 TYR cc_start: 0.8783 (t80) cc_final: 0.8540 (t80) REVERT: E 355 ARG cc_start: 0.8704 (ptm-80) cc_final: 0.8351 (ptm-80) REVERT: E 375 LYS cc_start: 0.9668 (pttt) cc_final: 0.9355 (pttt) REVERT: E 385 MET cc_start: 0.8610 (ttp) cc_final: 0.7803 (ttp) REVERT: E 386 MET cc_start: 0.8736 (ppp) cc_final: 0.8205 (tmm) REVERT: E 420 MET cc_start: 0.8352 (mtm) cc_final: 0.7872 (mtp) REVERT: E 469 GLN cc_start: 0.8846 (tp40) cc_final: 0.8629 (tt0) REVERT: E 480 ARG cc_start: 0.8932 (mpp-170) cc_final: 0.8566 (mpp80) REVERT: E 482 MET cc_start: 0.8936 (ttt) cc_final: 0.8725 (ttt) REVERT: E 483 MET cc_start: 0.9452 (tmm) cc_final: 0.9021 (tmm) REVERT: E 498 GLN cc_start: 0.8966 (pm20) cc_final: 0.8698 (pm20) REVERT: E 507 HIS cc_start: 0.8844 (t-90) cc_final: 0.8586 (t70) REVERT: E 509 TYR cc_start: 0.9126 (p90) cc_final: 0.8894 (p90) REVERT: F 34 ASP cc_start: 0.8346 (m-30) cc_final: 0.8022 (m-30) REVERT: F 37 ILE cc_start: 0.9068 (mm) cc_final: 0.8656 (mm) REVERT: F 70 MET cc_start: 0.7857 (tpp) cc_final: 0.6727 (tpt) REVERT: F 75 GLU cc_start: 0.8162 (pm20) cc_final: 0.7857 (pm20) REVERT: F 82 MET cc_start: 0.9423 (ttt) cc_final: 0.8932 (tmm) REVERT: F 103 GLU cc_start: 0.9510 (tp30) cc_final: 0.9166 (tp30) REVERT: F 106 LYS cc_start: 0.9379 (mtpt) cc_final: 0.8916 (mtpt) REVERT: F 108 LYS cc_start: 0.9268 (pttm) cc_final: 0.8072 (tppt) REVERT: F 111 GLU cc_start: 0.9091 (mp0) cc_final: 0.8764 (mp0) REVERT: F 131 PHE cc_start: 0.9343 (m-80) cc_final: 0.8809 (m-80) REVERT: F 132 GLU cc_start: 0.9476 (pt0) cc_final: 0.9184 (pt0) REVERT: F 134 LYS cc_start: 0.9485 (ptpp) cc_final: 0.9084 (pttt) REVERT: F 176 GLU cc_start: 0.8184 (mp0) cc_final: 0.7941 (mp0) REVERT: F 185 LEU cc_start: 0.8802 (mt) cc_final: 0.8222 (mt) REVERT: F 238 LYS cc_start: 0.8855 (mmmm) cc_final: 0.8452 (tppt) REVERT: F 287 ILE cc_start: 0.9501 (pt) cc_final: 0.9298 (pt) REVERT: F 291 LYS cc_start: 0.9439 (mmmt) cc_final: 0.8965 (tppt) REVERT: F 334 GLN cc_start: 0.9280 (mt0) cc_final: 0.8888 (mm-40) REVERT: F 335 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8175 (tm-30) REVERT: F 336 VAL cc_start: 0.9582 (p) cc_final: 0.9142 (p) REVERT: F 337 LEU cc_start: 0.9483 (mm) cc_final: 0.9155 (mm) REVERT: F 343 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8052 (tm-30) REVERT: F 349 LYS cc_start: 0.9084 (mmmm) cc_final: 0.8762 (mmtp) REVERT: F 352 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8037 (pm20) REVERT: F 355 ARG cc_start: 0.8252 (ppt170) cc_final: 0.7845 (ttp-170) REVERT: F 372 HIS cc_start: 0.9090 (m170) cc_final: 0.8517 (m170) REVERT: F 404 ASP cc_start: 0.8690 (t0) cc_final: 0.8370 (t0) REVERT: F 441 GLN cc_start: 0.9154 (mt0) cc_final: 0.8903 (mt0) REVERT: F 449 ASP cc_start: 0.8316 (t70) cc_final: 0.8101 (t70) REVERT: F 491 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8252 (tm-30) REVERT: F 507 HIS cc_start: 0.8594 (t-90) cc_final: 0.8359 (t-90) REVERT: G 32 TYR cc_start: 0.8977 (m-10) cc_final: 0.8522 (m-10) REVERT: G 47 ASP cc_start: 0.9664 (m-30) cc_final: 0.9037 (p0) REVERT: G 78 MET cc_start: 0.9584 (tpp) cc_final: 0.9254 (tpp) REVERT: G 82 MET cc_start: 0.9685 (tpp) cc_final: 0.9451 (tpp) REVERT: G 199 GLU cc_start: 0.9210 (mt-10) cc_final: 0.8695 (tp30) REVERT: G 200 ILE cc_start: 0.9346 (mm) cc_final: 0.9087 (mm) REVERT: G 203 ARG cc_start: 0.8613 (mtm-85) cc_final: 0.8349 (mtm110) REVERT: G 216 ASP cc_start: 0.9317 (m-30) cc_final: 0.9075 (t70) REVERT: G 229 LYS cc_start: 0.9368 (ptpp) cc_final: 0.9097 (mmmt) REVERT: G 274 ASP cc_start: 0.9065 (t0) cc_final: 0.8685 (t70) REVERT: G 287 ILE cc_start: 0.9694 (OUTLIER) cc_final: 0.9424 (tt) REVERT: G 289 TYR cc_start: 0.9476 (t80) cc_final: 0.9135 (t80) REVERT: G 290 ILE cc_start: 0.9440 (pt) cc_final: 0.9214 (pt) REVERT: G 291 LYS cc_start: 0.9082 (ptpp) cc_final: 0.8818 (pttm) REVERT: G 331 CYS cc_start: 0.8985 (t) cc_final: 0.8710 (t) REVERT: G 333 THR cc_start: 0.9728 (p) cc_final: 0.9381 (p) REVERT: G 334 GLN cc_start: 0.8959 (mp10) cc_final: 0.8544 (mp10) REVERT: G 335 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8016 (tm-30) REVERT: G 336 VAL cc_start: 0.9522 (m) cc_final: 0.8560 (m) REVERT: G 395 GLU cc_start: 0.8777 (mp0) cc_final: 0.8539 (mp0) REVERT: G 414 MET cc_start: 0.9188 (pmm) cc_final: 0.8772 (ptt) REVERT: G 441 GLN cc_start: 0.8350 (mp-120) cc_final: 0.7975 (mp-120) REVERT: G 482 MET cc_start: 0.9344 (tpp) cc_final: 0.8822 (tpp) REVERT: G 487 GLU cc_start: 0.8851 (pm20) cc_final: 0.8602 (pm20) REVERT: H 21 GLN cc_start: 0.8915 (tp40) cc_final: 0.8457 (tp40) REVERT: H 25 ASN cc_start: 0.8546 (m110) cc_final: 0.7823 (m110) REVERT: H 51 LEU cc_start: 0.9443 (pp) cc_final: 0.9236 (pp) REVERT: H 91 ILE cc_start: 0.9261 (tp) cc_final: 0.8918 (tp) REVERT: H 108 LYS cc_start: 0.9063 (tptm) cc_final: 0.8678 (tptt) REVERT: H 112 GLN cc_start: 0.9253 (tm-30) cc_final: 0.8968 (tm-30) REVERT: H 144 ILE cc_start: 0.8796 (mm) cc_final: 0.8581 (tp) REVERT: H 158 ILE cc_start: 0.7163 (tp) cc_final: 0.6939 (tp) REVERT: H 164 ASP cc_start: 0.8861 (t0) cc_final: 0.8655 (t0) REVERT: H 179 MET cc_start: 0.7499 (ppp) cc_final: 0.7170 (ppp) REVERT: H 203 ARG cc_start: 0.9179 (tpp-160) cc_final: 0.8913 (ttm110) REVERT: H 258 TYR cc_start: 0.9542 (t80) cc_final: 0.9283 (t80) REVERT: H 286 MET cc_start: 0.9671 (tpt) cc_final: 0.9256 (tpt) REVERT: H 290 ILE cc_start: 0.9773 (pt) cc_final: 0.9471 (pt) REVERT: H 352 GLU cc_start: 0.9237 (tm-30) cc_final: 0.8944 (tm-30) REVERT: H 385 MET cc_start: 0.7692 (tpt) cc_final: 0.7066 (tpt) REVERT: H 414 MET cc_start: 0.8681 (pmm) cc_final: 0.8474 (pmm) REVERT: H 418 ASP cc_start: 0.9385 (t70) cc_final: 0.9126 (t0) REVERT: H 465 GLN cc_start: 0.8562 (pp30) cc_final: 0.8161 (tt0) REVERT: H 478 GLN cc_start: 0.9384 (mt0) cc_final: 0.9130 (mt0) REVERT: H 482 MET cc_start: 0.9145 (tpp) cc_final: 0.8494 (tpp) REVERT: J 5 LEU cc_start: 0.9495 (mt) cc_final: 0.9004 (mt) REVERT: L 1 MET cc_start: 0.8395 (mpp) cc_final: 0.7970 (pmm) outliers start: 7 outliers final: 0 residues processed: 1437 average time/residue: 0.4048 time to fit residues: 936.1633 Evaluate side-chains 1210 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1208 time to evaluate : 3.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 10.0000 chunk 215 optimal weight: 10.0000 chunk 5 optimal weight: 0.2980 chunk 282 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 chunk 323 optimal weight: 8.9990 chunk 261 optimal weight: 0.0370 chunk 0 optimal weight: 8.9990 chunk 193 optimal weight: 0.0870 chunk 340 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 25 ASN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 HIS B 198 ASN ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 HIS ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 25 ASN ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 HIS ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 GLN ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 32212 Z= 0.272 Angle : 0.811 11.082 43712 Z= 0.405 Chirality : 0.050 0.293 4984 Planarity : 0.005 0.156 5452 Dihedral : 16.589 171.793 5344 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 27.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.63 % Favored : 90.30 % Rotamer: Outliers : 0.06 % Allowed : 4.71 % Favored : 95.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.12), residues: 3968 helix: -1.85 (0.13), residues: 1210 sheet: -2.48 (0.24), residues: 374 loop : -2.11 (0.12), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS G 504 PHE 0.041 0.002 PHE A 456 TYR 0.031 0.002 TYR A 110 ARG 0.015 0.001 ARG H 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1384 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1382 time to evaluate : 3.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8923 (t70) cc_final: 0.8536 (t70) REVERT: A 32 TYR cc_start: 0.8988 (m-10) cc_final: 0.8705 (m-10) REVERT: A 36 LEU cc_start: 0.9261 (tp) cc_final: 0.8504 (tp) REVERT: A 38 LEU cc_start: 0.9616 (mm) cc_final: 0.8721 (mm) REVERT: A 48 GLN cc_start: 0.9250 (mt0) cc_final: 0.8914 (mt0) REVERT: A 68 SER cc_start: 0.9323 (t) cc_final: 0.8694 (t) REVERT: A 105 ARG cc_start: 0.9090 (mmm160) cc_final: 0.8789 (tpp80) REVERT: A 108 LYS cc_start: 0.9502 (tptp) cc_final: 0.9283 (tppt) REVERT: A 109 LYS cc_start: 0.9397 (ptpp) cc_final: 0.9172 (ptpt) REVERT: A 179 MET cc_start: 0.7126 (pmm) cc_final: 0.6897 (pmm) REVERT: A 231 ARG cc_start: 0.9307 (ptm160) cc_final: 0.9054 (ptm-80) REVERT: A 246 CYS cc_start: 0.9433 (t) cc_final: 0.8549 (p) REVERT: A 258 TYR cc_start: 0.9439 (t80) cc_final: 0.9193 (t80) REVERT: A 294 TYR cc_start: 0.9341 (m-80) cc_final: 0.9050 (m-80) REVERT: A 325 MET cc_start: 0.9059 (ptm) cc_final: 0.8628 (ptm) REVERT: A 343 GLN cc_start: 0.8439 (pp30) cc_final: 0.8007 (pp30) REVERT: A 352 GLU cc_start: 0.9205 (tm-30) cc_final: 0.8746 (tm-30) REVERT: A 375 LYS cc_start: 0.9685 (pttt) cc_final: 0.9383 (pttt) REVERT: A 385 MET cc_start: 0.8631 (ttp) cc_final: 0.8067 (ttp) REVERT: A 386 MET cc_start: 0.8648 (ppp) cc_final: 0.7983 (ppp) REVERT: A 390 LEU cc_start: 0.9104 (pt) cc_final: 0.8847 (pt) REVERT: A 420 MET cc_start: 0.8404 (mtm) cc_final: 0.7990 (mtp) REVERT: A 482 MET cc_start: 0.9077 (ttt) cc_final: 0.8864 (ttt) REVERT: A 483 MET cc_start: 0.9625 (tmm) cc_final: 0.9158 (tmm) REVERT: A 509 TYR cc_start: 0.9105 (p90) cc_final: 0.8781 (p90) REVERT: B 18 LEU cc_start: 0.9463 (tp) cc_final: 0.9181 (tp) REVERT: B 34 ASP cc_start: 0.8432 (m-30) cc_final: 0.8060 (m-30) REVERT: B 36 LEU cc_start: 0.9383 (tp) cc_final: 0.9093 (tp) REVERT: B 37 ILE cc_start: 0.9273 (mm) cc_final: 0.8754 (mm) REVERT: B 82 MET cc_start: 0.8955 (tmm) cc_final: 0.8616 (tmm) REVERT: B 103 GLU cc_start: 0.9482 (tp30) cc_final: 0.9119 (tp30) REVERT: B 108 LYS cc_start: 0.9305 (pttm) cc_final: 0.8564 (tttt) REVERT: B 131 PHE cc_start: 0.9192 (m-80) cc_final: 0.8490 (m-80) REVERT: B 132 GLU cc_start: 0.9532 (pt0) cc_final: 0.9235 (pp20) REVERT: B 134 LYS cc_start: 0.9697 (pttm) cc_final: 0.9466 (pttt) REVERT: B 166 LEU cc_start: 0.9479 (mm) cc_final: 0.9003 (tp) REVERT: B 176 GLU cc_start: 0.8229 (mp0) cc_final: 0.8014 (mp0) REVERT: B 181 LYS cc_start: 0.9166 (tppt) cc_final: 0.8763 (tppt) REVERT: B 185 LEU cc_start: 0.8805 (mt) cc_final: 0.8430 (mt) REVERT: B 199 GLU cc_start: 0.9596 (mt-10) cc_final: 0.9328 (mt-10) REVERT: B 224 ARG cc_start: 0.8721 (ttt-90) cc_final: 0.8487 (ttt180) REVERT: B 242 LYS cc_start: 0.8706 (tttt) cc_final: 0.8489 (tptt) REVERT: B 334 GLN cc_start: 0.9183 (mt0) cc_final: 0.8843 (mm-40) REVERT: B 335 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8136 (tm-30) REVERT: B 348 TYR cc_start: 0.9156 (t80) cc_final: 0.8936 (t80) REVERT: B 372 HIS cc_start: 0.9048 (m170) cc_final: 0.8460 (m170) REVERT: B 404 ASP cc_start: 0.8763 (t0) cc_final: 0.8474 (t0) REVERT: B 449 ASP cc_start: 0.8394 (t70) cc_final: 0.8174 (t70) REVERT: B 491 GLU cc_start: 0.8669 (tm-30) cc_final: 0.8212 (tm-30) REVERT: C 32 TYR cc_start: 0.9013 (m-10) cc_final: 0.8548 (m-10) REVERT: C 47 ASP cc_start: 0.9666 (m-30) cc_final: 0.8946 (p0) REVERT: C 65 LEU cc_start: 0.9356 (tt) cc_final: 0.9132 (tt) REVERT: C 82 MET cc_start: 0.9631 (tpp) cc_final: 0.9267 (tpp) REVERT: C 90 PHE cc_start: 0.9117 (m-80) cc_final: 0.8714 (m-80) REVERT: C 111 GLU cc_start: 0.9324 (tp30) cc_final: 0.9071 (mp0) REVERT: C 175 LEU cc_start: 0.9042 (mt) cc_final: 0.8790 (mt) REVERT: C 199 GLU cc_start: 0.9224 (mt-10) cc_final: 0.8707 (tp30) REVERT: C 200 ILE cc_start: 0.9343 (mm) cc_final: 0.8912 (mm) REVERT: C 203 ARG cc_start: 0.8777 (mtm-85) cc_final: 0.8209 (mtm180) REVERT: C 229 LYS cc_start: 0.9367 (ptpp) cc_final: 0.9097 (mmmt) REVERT: C 274 ASP cc_start: 0.8871 (t0) cc_final: 0.8641 (t70) REVERT: C 277 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7721 (tm-30) REVERT: C 290 ILE cc_start: 0.9467 (pt) cc_final: 0.9179 (pt) REVERT: C 291 LYS cc_start: 0.9038 (ptpp) cc_final: 0.8804 (pttm) REVERT: C 333 THR cc_start: 0.9704 (p) cc_final: 0.9329 (p) REVERT: C 334 GLN cc_start: 0.9009 (mp10) cc_final: 0.8542 (mp10) REVERT: C 335 GLU cc_start: 0.8780 (tm-30) cc_final: 0.8140 (tm-30) REVERT: C 336 VAL cc_start: 0.9624 (m) cc_final: 0.8916 (m) REVERT: C 349 LYS cc_start: 0.8943 (mtpt) cc_final: 0.8474 (mtpt) REVERT: C 441 GLN cc_start: 0.8341 (mp-120) cc_final: 0.7965 (mp-120) REVERT: C 482 MET cc_start: 0.9379 (tpp) cc_final: 0.9044 (mmm) REVERT: D 12 TYR cc_start: 0.7895 (t80) cc_final: 0.6930 (m-80) REVERT: D 16 ASP cc_start: 0.8430 (m-30) cc_final: 0.8216 (m-30) REVERT: D 21 GLN cc_start: 0.8756 (tm-30) cc_final: 0.8168 (tm-30) REVERT: D 33 ASN cc_start: 0.9172 (t0) cc_final: 0.8868 (t0) REVERT: D 36 LEU cc_start: 0.9230 (pt) cc_final: 0.9003 (pt) REVERT: D 51 LEU cc_start: 0.9507 (pp) cc_final: 0.9221 (pp) REVERT: D 150 MET cc_start: 0.7139 (tmm) cc_final: 0.6767 (tmm) REVERT: D 164 ASP cc_start: 0.9043 (t0) cc_final: 0.8834 (p0) REVERT: D 215 ASP cc_start: 0.9448 (m-30) cc_final: 0.8975 (p0) REVERT: D 242 LYS cc_start: 0.9366 (mmpt) cc_final: 0.9152 (mmmt) REVERT: D 258 TYR cc_start: 0.9619 (t80) cc_final: 0.9385 (t80) REVERT: D 286 MET cc_start: 0.9625 (tpt) cc_final: 0.9350 (tpt) REVERT: D 289 TYR cc_start: 0.9470 (t80) cc_final: 0.9162 (t80) REVERT: D 290 ILE cc_start: 0.9768 (pt) cc_final: 0.9455 (pt) REVERT: D 311 LYS cc_start: 0.9148 (ttpp) cc_final: 0.8727 (ttpp) REVERT: D 332 ILE cc_start: 0.8970 (tp) cc_final: 0.8238 (tp) REVERT: D 335 GLU cc_start: 0.8817 (tm-30) cc_final: 0.8494 (tm-30) REVERT: D 349 LYS cc_start: 0.9576 (mmmm) cc_final: 0.9314 (mmmm) REVERT: D 352 GLU cc_start: 0.9213 (tm-30) cc_final: 0.8892 (tm-30) REVERT: D 385 MET cc_start: 0.8349 (tpt) cc_final: 0.7648 (tpt) REVERT: D 386 MET cc_start: 0.8678 (ptm) cc_final: 0.8150 (ptm) REVERT: D 399 GLU cc_start: 0.7923 (pp20) cc_final: 0.7577 (pp20) REVERT: D 418 ASP cc_start: 0.9400 (t70) cc_final: 0.9169 (t0) REVERT: D 465 GLN cc_start: 0.9078 (tt0) cc_final: 0.8703 (tt0) REVERT: D 482 MET cc_start: 0.9296 (tpp) cc_final: 0.8221 (tpt) REVERT: D 487 GLU cc_start: 0.9188 (pm20) cc_final: 0.8354 (pm20) REVERT: N 12 TYR cc_start: 0.8888 (t80) cc_final: 0.8503 (t80) REVERT: P 1 MET cc_start: 0.8531 (mpp) cc_final: 0.8134 (pmm) REVERT: E 28 ASP cc_start: 0.8953 (t70) cc_final: 0.8536 (t70) REVERT: E 32 TYR cc_start: 0.9351 (m-80) cc_final: 0.8709 (m-80) REVERT: E 36 LEU cc_start: 0.9083 (tp) cc_final: 0.8673 (tp) REVERT: E 38 LEU cc_start: 0.9615 (mm) cc_final: 0.8803 (mm) REVERT: E 48 GLN cc_start: 0.9205 (mt0) cc_final: 0.8750 (mt0) REVERT: E 82 MET cc_start: 0.9478 (ttp) cc_final: 0.9200 (ttp) REVERT: E 105 ARG cc_start: 0.9083 (mmm160) cc_final: 0.8831 (mmm160) REVERT: E 158 ILE cc_start: 0.8799 (mm) cc_final: 0.8232 (tp) REVERT: E 165 PHE cc_start: 0.8612 (p90) cc_final: 0.8358 (p90) REVERT: E 179 MET cc_start: 0.7656 (pmm) cc_final: 0.7075 (pmm) REVERT: E 246 CYS cc_start: 0.9540 (t) cc_final: 0.8629 (p) REVERT: E 250 ILE cc_start: 0.9465 (pt) cc_final: 0.9257 (pt) REVERT: E 288 LYS cc_start: 0.9537 (mtmm) cc_final: 0.9297 (mttt) REVERT: E 294 TYR cc_start: 0.9336 (m-80) cc_final: 0.9015 (m-80) REVERT: E 325 MET cc_start: 0.9143 (ptm) cc_final: 0.8322 (ptm) REVERT: E 352 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8671 (tm-30) REVERT: E 375 LYS cc_start: 0.9700 (pttt) cc_final: 0.9321 (pttt) REVERT: E 385 MET cc_start: 0.8354 (ttp) cc_final: 0.7650 (ttp) REVERT: E 386 MET cc_start: 0.8566 (ppp) cc_final: 0.8302 (ppp) REVERT: E 420 MET cc_start: 0.8390 (mtm) cc_final: 0.7917 (mtp) REVERT: E 465 GLN cc_start: 0.9339 (tt0) cc_final: 0.9077 (tp40) REVERT: E 480 ARG cc_start: 0.8972 (mpp-170) cc_final: 0.8513 (mpp80) REVERT: E 482 MET cc_start: 0.8972 (ttt) cc_final: 0.8761 (ttt) REVERT: E 483 MET cc_start: 0.9479 (tmm) cc_final: 0.9079 (tmm) REVERT: E 507 HIS cc_start: 0.8847 (t-90) cc_final: 0.8594 (t70) REVERT: E 509 TYR cc_start: 0.9130 (p90) cc_final: 0.8887 (p90) REVERT: F 34 ASP cc_start: 0.8451 (m-30) cc_final: 0.8151 (m-30) REVERT: F 37 ILE cc_start: 0.9242 (mm) cc_final: 0.8778 (mm) REVERT: F 70 MET cc_start: 0.7973 (tpp) cc_final: 0.6875 (tpt) REVERT: F 82 MET cc_start: 0.9487 (ttt) cc_final: 0.8916 (tmm) REVERT: F 103 GLU cc_start: 0.9474 (tp30) cc_final: 0.9096 (tp30) REVERT: F 106 LYS cc_start: 0.9358 (mtpt) cc_final: 0.9027 (mtpt) REVERT: F 108 LYS cc_start: 0.9308 (pttm) cc_final: 0.8189 (tppt) REVERT: F 131 PHE cc_start: 0.9357 (m-80) cc_final: 0.8892 (m-80) REVERT: F 132 GLU cc_start: 0.9503 (pt0) cc_final: 0.9205 (pt0) REVERT: F 134 LYS cc_start: 0.9456 (ptpp) cc_final: 0.9217 (pttp) REVERT: F 179 MET cc_start: 0.6467 (ppp) cc_final: 0.6260 (ppp) REVERT: F 185 LEU cc_start: 0.8702 (mt) cc_final: 0.8215 (mt) REVERT: F 334 GLN cc_start: 0.9262 (mt0) cc_final: 0.8915 (mm-40) REVERT: F 335 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8137 (tm-30) REVERT: F 336 VAL cc_start: 0.9585 (p) cc_final: 0.9147 (p) REVERT: F 337 LEU cc_start: 0.9550 (mm) cc_final: 0.9236 (mm) REVERT: F 352 GLU cc_start: 0.8523 (pm20) cc_final: 0.8264 (pm20) REVERT: F 355 ARG cc_start: 0.8182 (ppt170) cc_final: 0.7392 (ptm-80) REVERT: F 372 HIS cc_start: 0.9111 (m170) cc_final: 0.8558 (m170) REVERT: F 404 ASP cc_start: 0.8753 (t0) cc_final: 0.8441 (t0) REVERT: F 491 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8331 (tm-30) REVERT: F 507 HIS cc_start: 0.8607 (t-90) cc_final: 0.8335 (t-90) REVERT: G 32 TYR cc_start: 0.9067 (m-10) cc_final: 0.8582 (m-10) REVERT: G 47 ASP cc_start: 0.9663 (m-30) cc_final: 0.8983 (p0) REVERT: G 78 MET cc_start: 0.9606 (tpp) cc_final: 0.9243 (tpp) REVERT: G 82 MET cc_start: 0.9706 (tpp) cc_final: 0.9448 (tpp) REVERT: G 150 MET cc_start: 0.8930 (mmp) cc_final: 0.8372 (tpp) REVERT: G 199 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8654 (tp30) REVERT: G 200 ILE cc_start: 0.9367 (mm) cc_final: 0.8974 (mm) REVERT: G 203 ARG cc_start: 0.8691 (mtm-85) cc_final: 0.8297 (mtm110) REVERT: G 216 ASP cc_start: 0.9323 (m-30) cc_final: 0.9077 (t70) REVERT: G 229 LYS cc_start: 0.9365 (ptpp) cc_final: 0.9100 (mmmt) REVERT: G 274 ASP cc_start: 0.8911 (t0) cc_final: 0.8521 (t70) REVERT: G 287 ILE cc_start: 0.9708 (mp) cc_final: 0.9134 (tt) REVERT: G 289 TYR cc_start: 0.9487 (t80) cc_final: 0.9175 (t80) REVERT: G 290 ILE cc_start: 0.9432 (pt) cc_final: 0.9212 (pt) REVERT: G 291 LYS cc_start: 0.9145 (ptpp) cc_final: 0.8755 (pttt) REVERT: G 331 CYS cc_start: 0.8968 (t) cc_final: 0.8455 (t) REVERT: G 333 THR cc_start: 0.9702 (p) cc_final: 0.9368 (p) REVERT: G 334 GLN cc_start: 0.8952 (mp10) cc_final: 0.8517 (mp10) REVERT: G 335 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8054 (tm-30) REVERT: G 336 VAL cc_start: 0.9573 (m) cc_final: 0.8723 (m) REVERT: G 395 GLU cc_start: 0.8767 (mp0) cc_final: 0.8391 (mp0) REVERT: G 441 GLN cc_start: 0.8314 (mp-120) cc_final: 0.7920 (mp-120) REVERT: G 482 MET cc_start: 0.9318 (tpp) cc_final: 0.8764 (mmm) REVERT: H 33 ASN cc_start: 0.9109 (t0) cc_final: 0.8718 (t0) REVERT: H 51 LEU cc_start: 0.9482 (pp) cc_final: 0.9217 (pp) REVERT: H 70 MET cc_start: 0.8540 (mmt) cc_final: 0.8202 (mmp) REVERT: H 91 ILE cc_start: 0.9275 (tp) cc_final: 0.8930 (tp) REVERT: H 112 GLN cc_start: 0.9282 (tm-30) cc_final: 0.8758 (tm-30) REVERT: H 150 MET cc_start: 0.6909 (tmm) cc_final: 0.6556 (tmm) REVERT: H 158 ILE cc_start: 0.6850 (tp) cc_final: 0.6563 (tp) REVERT: H 179 MET cc_start: 0.7338 (ppp) cc_final: 0.6687 (ppp) REVERT: H 203 ARG cc_start: 0.9115 (tpp-160) cc_final: 0.8868 (ttm110) REVERT: H 258 TYR cc_start: 0.9547 (t80) cc_final: 0.9255 (t80) REVERT: H 286 MET cc_start: 0.9664 (tpt) cc_final: 0.9285 (tpt) REVERT: H 290 ILE cc_start: 0.9770 (pt) cc_final: 0.9498 (pt) REVERT: H 311 LYS cc_start: 0.9277 (ttpt) cc_final: 0.8877 (ttpt) REVERT: H 315 ASP cc_start: 0.9575 (m-30) cc_final: 0.9068 (p0) REVERT: H 332 ILE cc_start: 0.8875 (tp) cc_final: 0.8208 (tp) REVERT: H 335 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8626 (tm-30) REVERT: H 352 GLU cc_start: 0.9229 (tm-30) cc_final: 0.8925 (tm-30) REVERT: H 385 MET cc_start: 0.8472 (tpt) cc_final: 0.8247 (tpt) REVERT: H 409 LYS cc_start: 0.8549 (ttmm) cc_final: 0.8159 (tppt) REVERT: H 418 ASP cc_start: 0.9415 (t70) cc_final: 0.9156 (t0) REVERT: H 465 GLN cc_start: 0.8576 (pp30) cc_final: 0.8186 (tt0) REVERT: H 482 MET cc_start: 0.9211 (tpp) cc_final: 0.8919 (tpp) REVERT: J 5 LEU cc_start: 0.9499 (mt) cc_final: 0.9042 (mt) REVERT: L 1 MET cc_start: 0.8349 (mpp) cc_final: 0.8016 (pmm) outliers start: 2 outliers final: 2 residues processed: 1384 average time/residue: 0.4085 time to fit residues: 910.5870 Evaluate side-chains 1174 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1172 time to evaluate : 3.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 1.9990 chunk 341 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 222 optimal weight: 0.9990 chunk 93 optimal weight: 0.9990 chunk 379 optimal weight: 0.0870 chunk 314 optimal weight: 8.9990 chunk 175 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 199 optimal weight: 3.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN A 466 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 HIS ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 HIS F 21 GLN ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 32212 Z= 0.236 Angle : 0.800 9.871 43712 Z= 0.397 Chirality : 0.050 0.294 4984 Planarity : 0.005 0.129 5452 Dihedral : 16.364 166.754 5344 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 25.31 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.07 % Favored : 90.88 % Rotamer: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.12), residues: 3968 helix: -1.75 (0.13), residues: 1200 sheet: -2.52 (0.23), residues: 386 loop : -1.98 (0.12), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS C 92 PHE 0.021 0.002 PHE B 131 TYR 0.021 0.002 TYR F 233 ARG 0.019 0.001 ARG H 322 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1409 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1409 time to evaluate : 3.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.7648 (t80) cc_final: 0.7017 (m-80) REVERT: A 28 ASP cc_start: 0.8909 (t70) cc_final: 0.8624 (t70) REVERT: A 32 TYR cc_start: 0.8950 (m-10) cc_final: 0.8672 (m-10) REVERT: A 36 LEU cc_start: 0.9017 (tp) cc_final: 0.8410 (tp) REVERT: A 38 LEU cc_start: 0.9603 (mm) cc_final: 0.8804 (mm) REVERT: A 48 GLN cc_start: 0.9278 (mt0) cc_final: 0.8909 (mt0) REVERT: A 78 MET cc_start: 0.9277 (tpp) cc_final: 0.8823 (tpp) REVERT: A 98 GLU cc_start: 0.9175 (mp0) cc_final: 0.8940 (mp0) REVERT: A 105 ARG cc_start: 0.9089 (mmm160) cc_final: 0.8336 (tpp80) REVERT: A 108 LYS cc_start: 0.9522 (tptp) cc_final: 0.9072 (tppt) REVERT: A 179 MET cc_start: 0.7117 (pmm) cc_final: 0.6801 (pmm) REVERT: A 231 ARG cc_start: 0.9311 (ptm160) cc_final: 0.8955 (ptm-80) REVERT: A 246 CYS cc_start: 0.9397 (t) cc_final: 0.8529 (p) REVERT: A 254 GLU cc_start: 0.9315 (tp30) cc_final: 0.8933 (pm20) REVERT: A 273 LEU cc_start: 0.9381 (tt) cc_final: 0.8151 (tt) REVERT: A 274 ASP cc_start: 0.8628 (t0) cc_final: 0.7796 (t0) REVERT: A 294 TYR cc_start: 0.9344 (m-80) cc_final: 0.9013 (m-80) REVERT: A 325 MET cc_start: 0.9027 (ptm) cc_final: 0.8653 (ptm) REVERT: A 332 ILE cc_start: 0.9296 (pt) cc_final: 0.9015 (pt) REVERT: A 335 GLU cc_start: 0.8607 (mp0) cc_final: 0.8083 (mp0) REVERT: A 343 GLN cc_start: 0.8414 (pp30) cc_final: 0.7942 (pp30) REVERT: A 352 GLU cc_start: 0.9165 (tm-30) cc_final: 0.8708 (tm-30) REVERT: A 375 LYS cc_start: 0.9653 (pttt) cc_final: 0.9339 (pttt) REVERT: A 386 MET cc_start: 0.8686 (ppp) cc_final: 0.8101 (ppp) REVERT: A 420 MET cc_start: 0.8384 (mtm) cc_final: 0.7954 (mtp) REVERT: A 469 GLN cc_start: 0.8875 (tp40) cc_final: 0.8444 (tt0) REVERT: A 480 ARG cc_start: 0.8819 (mtm110) cc_final: 0.8596 (mtm110) REVERT: A 482 MET cc_start: 0.9054 (ttt) cc_final: 0.8841 (ttt) REVERT: A 483 MET cc_start: 0.9608 (tmm) cc_final: 0.9130 (tmm) REVERT: A 509 TYR cc_start: 0.9082 (p90) cc_final: 0.8774 (p90) REVERT: B 18 LEU cc_start: 0.9450 (tp) cc_final: 0.9232 (tp) REVERT: B 25 ASN cc_start: 0.8872 (m-40) cc_final: 0.8617 (m110) REVERT: B 34 ASP cc_start: 0.8320 (m-30) cc_final: 0.7912 (m-30) REVERT: B 36 LEU cc_start: 0.9391 (tp) cc_final: 0.8986 (tp) REVERT: B 37 ILE cc_start: 0.9277 (mm) cc_final: 0.8790 (mm) REVERT: B 103 GLU cc_start: 0.9480 (tp30) cc_final: 0.9248 (tp30) REVERT: B 131 PHE cc_start: 0.9268 (m-80) cc_final: 0.8606 (m-80) REVERT: B 132 GLU cc_start: 0.9574 (pt0) cc_final: 0.9242 (pp20) REVERT: B 134 LYS cc_start: 0.9686 (pttm) cc_final: 0.9435 (pttt) REVERT: B 166 LEU cc_start: 0.9414 (mm) cc_final: 0.9007 (tp) REVERT: B 167 LYS cc_start: 0.9128 (mppt) cc_final: 0.8899 (mmtt) REVERT: B 181 LYS cc_start: 0.9155 (tppt) cc_final: 0.8782 (tppt) REVERT: B 185 LEU cc_start: 0.8875 (mt) cc_final: 0.8512 (mt) REVERT: B 238 LYS cc_start: 0.9000 (mmmt) cc_final: 0.8520 (tppt) REVERT: B 250 ILE cc_start: 0.9245 (mp) cc_final: 0.8758 (tp) REVERT: B 281 ILE cc_start: 0.9499 (tp) cc_final: 0.9162 (tp) REVERT: B 285 ASN cc_start: 0.9560 (m110) cc_final: 0.9356 (m-40) REVERT: B 334 GLN cc_start: 0.9186 (mt0) cc_final: 0.8715 (mm-40) REVERT: B 335 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8154 (tm-30) REVERT: B 348 TYR cc_start: 0.9135 (t80) cc_final: 0.8635 (t80) REVERT: B 352 GLU cc_start: 0.8530 (pm20) cc_final: 0.7925 (pm20) REVERT: B 355 ARG cc_start: 0.7958 (ttp-170) cc_final: 0.7336 (ttp-170) REVERT: B 372 HIS cc_start: 0.9035 (m170) cc_final: 0.8477 (m170) REVERT: B 399 GLU cc_start: 0.7831 (mp0) cc_final: 0.7617 (pm20) REVERT: B 404 ASP cc_start: 0.8767 (t0) cc_final: 0.8474 (t0) REVERT: B 449 ASP cc_start: 0.8507 (t70) cc_final: 0.8272 (t70) REVERT: B 491 GLU cc_start: 0.8672 (tm-30) cc_final: 0.8197 (tm-30) REVERT: C 32 TYR cc_start: 0.8973 (m-10) cc_final: 0.8564 (m-10) REVERT: C 47 ASP cc_start: 0.9658 (m-30) cc_final: 0.8994 (p0) REVERT: C 74 THR cc_start: 0.6711 (t) cc_final: 0.6493 (t) REVERT: C 82 MET cc_start: 0.9618 (tpp) cc_final: 0.9256 (tpp) REVERT: C 90 PHE cc_start: 0.9186 (m-80) cc_final: 0.8701 (m-80) REVERT: C 111 GLU cc_start: 0.9323 (tp30) cc_final: 0.9079 (mp0) REVERT: C 175 LEU cc_start: 0.9067 (mt) cc_final: 0.8860 (mt) REVERT: C 199 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8697 (tp30) REVERT: C 200 ILE cc_start: 0.9357 (mm) cc_final: 0.8978 (mm) REVERT: C 203 ARG cc_start: 0.8778 (mtm-85) cc_final: 0.8225 (mtm110) REVERT: C 229 LYS cc_start: 0.9383 (ptpp) cc_final: 0.9102 (mmmt) REVERT: C 274 ASP cc_start: 0.9001 (t0) cc_final: 0.8644 (t70) REVERT: C 277 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7674 (tm-30) REVERT: C 290 ILE cc_start: 0.9501 (pt) cc_final: 0.9193 (pt) REVERT: C 291 LYS cc_start: 0.9041 (ptpp) cc_final: 0.8804 (pttm) REVERT: C 333 THR cc_start: 0.9705 (p) cc_final: 0.9294 (p) REVERT: C 334 GLN cc_start: 0.9006 (mp10) cc_final: 0.8479 (mp10) REVERT: C 335 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8087 (tm-30) REVERT: C 336 VAL cc_start: 0.9598 (m) cc_final: 0.8824 (m) REVERT: C 349 LYS cc_start: 0.8954 (mtpt) cc_final: 0.8463 (mtpt) REVERT: C 441 GLN cc_start: 0.8389 (mp-120) cc_final: 0.7986 (mp-120) REVERT: C 482 MET cc_start: 0.9370 (tpp) cc_final: 0.9010 (mmm) REVERT: D 12 TYR cc_start: 0.7988 (t80) cc_final: 0.6961 (m-80) REVERT: D 16 ASP cc_start: 0.8357 (m-30) cc_final: 0.8140 (m-30) REVERT: D 21 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8107 (tm-30) REVERT: D 25 ASN cc_start: 0.8602 (m110) cc_final: 0.8176 (m110) REVERT: D 51 LEU cc_start: 0.9481 (pp) cc_final: 0.9266 (pp) REVERT: D 71 ASP cc_start: 0.9437 (t0) cc_final: 0.9150 (t0) REVERT: D 91 ILE cc_start: 0.9278 (tp) cc_final: 0.9048 (tp) REVERT: D 114 PHE cc_start: 0.9056 (m-10) cc_final: 0.8839 (m-10) REVERT: D 164 ASP cc_start: 0.9075 (t0) cc_final: 0.8866 (p0) REVERT: D 215 ASP cc_start: 0.9460 (m-30) cc_final: 0.8989 (p0) REVERT: D 242 LYS cc_start: 0.9386 (mmpt) cc_final: 0.9174 (mmmt) REVERT: D 289 TYR cc_start: 0.9377 (t80) cc_final: 0.9112 (t80) REVERT: D 290 ILE cc_start: 0.9770 (pt) cc_final: 0.9426 (pt) REVERT: D 332 ILE cc_start: 0.9022 (tp) cc_final: 0.8374 (tp) REVERT: D 335 GLU cc_start: 0.8862 (tm-30) cc_final: 0.8560 (tm-30) REVERT: D 349 LYS cc_start: 0.9567 (mmmm) cc_final: 0.9326 (mmmm) REVERT: D 352 GLU cc_start: 0.9201 (tm-30) cc_final: 0.8908 (tm-30) REVERT: D 385 MET cc_start: 0.8546 (tpt) cc_final: 0.7747 (tpt) REVERT: D 386 MET cc_start: 0.8684 (ptm) cc_final: 0.8294 (ptm) REVERT: D 400 TYR cc_start: 0.7826 (m-80) cc_final: 0.7565 (m-80) REVERT: D 418 ASP cc_start: 0.9390 (t70) cc_final: 0.9188 (t0) REVERT: D 465 GLN cc_start: 0.9086 (tt0) cc_final: 0.8694 (tt0) REVERT: D 478 GLN cc_start: 0.9455 (mt0) cc_final: 0.8999 (mt0) REVERT: D 482 MET cc_start: 0.9316 (tpp) cc_final: 0.8114 (tpt) REVERT: D 487 GLU cc_start: 0.9094 (pm20) cc_final: 0.8079 (pm20) REVERT: P 1 MET cc_start: 0.8487 (mpp) cc_final: 0.8148 (pmm) REVERT: E 12 TYR cc_start: 0.7676 (t80) cc_final: 0.7035 (m-80) REVERT: E 28 ASP cc_start: 0.8913 (t70) cc_final: 0.8600 (t70) REVERT: E 32 TYR cc_start: 0.9307 (m-80) cc_final: 0.8679 (m-80) REVERT: E 36 LEU cc_start: 0.9013 (tp) cc_final: 0.8718 (tp) REVERT: E 38 LEU cc_start: 0.9593 (mm) cc_final: 0.8839 (mm) REVERT: E 48 GLN cc_start: 0.9246 (mt0) cc_final: 0.8810 (mt0) REVERT: E 82 MET cc_start: 0.9501 (ttp) cc_final: 0.9191 (ttp) REVERT: E 100 GLN cc_start: 0.9345 (mp10) cc_final: 0.9093 (mp10) REVERT: E 105 ARG cc_start: 0.9028 (mmm160) cc_final: 0.8174 (tpm170) REVERT: E 109 LYS cc_start: 0.9349 (ptpp) cc_final: 0.9005 (ptpp) REVERT: E 142 ILE cc_start: 0.8699 (tp) cc_final: 0.8470 (tp) REVERT: E 150 MET cc_start: 0.7910 (tpt) cc_final: 0.7632 (tpt) REVERT: E 158 ILE cc_start: 0.8923 (mm) cc_final: 0.8434 (tp) REVERT: E 165 PHE cc_start: 0.8538 (p90) cc_final: 0.8256 (p90) REVERT: E 179 MET cc_start: 0.7611 (pmm) cc_final: 0.6982 (pmm) REVERT: E 228 LYS cc_start: 0.9524 (ptpp) cc_final: 0.9299 (ptpp) REVERT: E 246 CYS cc_start: 0.9487 (t) cc_final: 0.8607 (p) REVERT: E 273 LEU cc_start: 0.9088 (tt) cc_final: 0.8849 (tt) REVERT: E 288 LYS cc_start: 0.9541 (mtmm) cc_final: 0.9300 (mttt) REVERT: E 294 TYR cc_start: 0.9303 (m-80) cc_final: 0.8936 (m-80) REVERT: E 352 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8696 (tm-30) REVERT: E 364 ASP cc_start: 0.8218 (m-30) cc_final: 0.7770 (m-30) REVERT: E 375 LYS cc_start: 0.9704 (pttt) cc_final: 0.9343 (pttt) REVERT: E 385 MET cc_start: 0.8468 (ttp) cc_final: 0.8184 (ttp) REVERT: E 386 MET cc_start: 0.8669 (ppp) cc_final: 0.8415 (ppp) REVERT: E 420 MET cc_start: 0.8376 (mtm) cc_final: 0.7895 (mtp) REVERT: E 465 GLN cc_start: 0.9344 (tt0) cc_final: 0.9112 (tp40) REVERT: E 482 MET cc_start: 0.8998 (ttt) cc_final: 0.8787 (ttt) REVERT: E 483 MET cc_start: 0.9536 (tmm) cc_final: 0.9043 (tmm) REVERT: E 507 HIS cc_start: 0.8804 (t-90) cc_final: 0.8561 (t70) REVERT: E 509 TYR cc_start: 0.9110 (p90) cc_final: 0.8876 (p90) REVERT: F 16 ASP cc_start: 0.6964 (t0) cc_final: 0.6426 (t0) REVERT: F 25 ASN cc_start: 0.8905 (m-40) cc_final: 0.8643 (m110) REVERT: F 34 ASP cc_start: 0.8397 (m-30) cc_final: 0.8073 (m-30) REVERT: F 36 LEU cc_start: 0.9308 (tp) cc_final: 0.9041 (tp) REVERT: F 37 ILE cc_start: 0.9137 (mm) cc_final: 0.8666 (mm) REVERT: F 70 MET cc_start: 0.8078 (tpp) cc_final: 0.7537 (mmm) REVERT: F 82 MET cc_start: 0.9510 (ttt) cc_final: 0.8898 (tmm) REVERT: F 103 GLU cc_start: 0.9412 (tp30) cc_final: 0.9045 (tp30) REVERT: F 106 LYS cc_start: 0.9362 (mtpt) cc_final: 0.9064 (mtpt) REVERT: F 108 LYS cc_start: 0.9228 (pttm) cc_final: 0.8290 (tppt) REVERT: F 132 GLU cc_start: 0.9517 (pt0) cc_final: 0.9218 (pt0) REVERT: F 185 LEU cc_start: 0.8768 (mt) cc_final: 0.8081 (mt) REVERT: F 242 LYS cc_start: 0.8677 (tttt) cc_final: 0.8440 (tptt) REVERT: F 281 ILE cc_start: 0.9492 (tp) cc_final: 0.9146 (tp) REVERT: F 334 GLN cc_start: 0.9275 (mt0) cc_final: 0.8936 (mm-40) REVERT: F 335 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8130 (tm-30) REVERT: F 337 LEU cc_start: 0.9588 (mm) cc_final: 0.9298 (mm) REVERT: F 349 LYS cc_start: 0.9335 (mmtp) cc_final: 0.9005 (mmmm) REVERT: F 355 ARG cc_start: 0.8174 (ppt170) cc_final: 0.7167 (ptm-80) REVERT: F 372 HIS cc_start: 0.9053 (m170) cc_final: 0.8531 (m170) REVERT: F 404 ASP cc_start: 0.8745 (t0) cc_final: 0.8416 (t0) REVERT: F 449 ASP cc_start: 0.8426 (t70) cc_final: 0.8190 (t70) REVERT: F 491 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8283 (tm-30) REVERT: F 507 HIS cc_start: 0.8606 (t-90) cc_final: 0.8346 (t-90) REVERT: G 32 TYR cc_start: 0.8984 (m-10) cc_final: 0.8625 (m-10) REVERT: G 47 ASP cc_start: 0.9667 (m-30) cc_final: 0.8983 (p0) REVERT: G 78 MET cc_start: 0.9602 (tpp) cc_final: 0.9241 (tpp) REVERT: G 82 MET cc_start: 0.9698 (tpp) cc_final: 0.9448 (tpp) REVERT: G 139 PHE cc_start: 0.5870 (p90) cc_final: 0.5547 (p90) REVERT: G 150 MET cc_start: 0.8938 (mmp) cc_final: 0.8433 (tpp) REVERT: G 216 ASP cc_start: 0.9307 (m-30) cc_final: 0.9061 (t70) REVERT: G 229 LYS cc_start: 0.9362 (ptpp) cc_final: 0.9098 (mmmt) REVERT: G 274 ASP cc_start: 0.9056 (t0) cc_final: 0.8637 (t70) REVERT: G 287 ILE cc_start: 0.9705 (mp) cc_final: 0.9347 (tt) REVERT: G 291 LYS cc_start: 0.9089 (ptpp) cc_final: 0.8847 (pttm) REVERT: G 306 THR cc_start: 0.9132 (t) cc_final: 0.8842 (t) REVERT: G 331 CYS cc_start: 0.8956 (t) cc_final: 0.8583 (t) REVERT: G 333 THR cc_start: 0.9689 (p) cc_final: 0.9333 (p) REVERT: G 334 GLN cc_start: 0.8915 (mp10) cc_final: 0.8422 (mp10) REVERT: G 335 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8015 (tm-30) REVERT: G 336 VAL cc_start: 0.9552 (m) cc_final: 0.8674 (m) REVERT: G 357 PHE cc_start: 0.9283 (m-80) cc_final: 0.8953 (m-80) REVERT: G 395 GLU cc_start: 0.8745 (mp0) cc_final: 0.8384 (mp0) REVERT: G 441 GLN cc_start: 0.8396 (mp-120) cc_final: 0.8002 (mp-120) REVERT: G 482 MET cc_start: 0.9333 (tpp) cc_final: 0.8927 (mmm) REVERT: G 504 HIS cc_start: 0.8498 (p90) cc_final: 0.8224 (p90) REVERT: H 21 GLN cc_start: 0.9116 (tp-100) cc_final: 0.8451 (tp40) REVERT: H 25 ASN cc_start: 0.8575 (m110) cc_final: 0.7898 (m110) REVERT: H 32 TYR cc_start: 0.9041 (m-80) cc_final: 0.8514 (m-80) REVERT: H 33 ASN cc_start: 0.9140 (t0) cc_final: 0.8728 (t0) REVERT: H 91 ILE cc_start: 0.9321 (tp) cc_final: 0.8976 (tp) REVERT: H 112 GLN cc_start: 0.9255 (tm-30) cc_final: 0.8718 (tm-30) REVERT: H 158 ILE cc_start: 0.6855 (tp) cc_final: 0.6619 (tp) REVERT: H 179 MET cc_start: 0.7440 (ppp) cc_final: 0.6729 (ppp) REVERT: H 208 LYS cc_start: 0.7997 (tppp) cc_final: 0.7743 (tptp) REVERT: H 258 TYR cc_start: 0.9555 (t80) cc_final: 0.9259 (t80) REVERT: H 286 MET cc_start: 0.9622 (tpt) cc_final: 0.9243 (tpt) REVERT: H 290 ILE cc_start: 0.9769 (pt) cc_final: 0.9494 (pt) REVERT: H 311 LYS cc_start: 0.9218 (ttpt) cc_final: 0.8722 (ttpt) REVERT: H 315 ASP cc_start: 0.9528 (m-30) cc_final: 0.8959 (p0) REVERT: H 352 GLU cc_start: 0.9235 (tm-30) cc_final: 0.8926 (tm-30) REVERT: H 409 LYS cc_start: 0.8426 (ttmm) cc_final: 0.8181 (tppt) REVERT: H 410 LYS cc_start: 0.8929 (mptt) cc_final: 0.8650 (mmtm) REVERT: H 418 ASP cc_start: 0.9383 (t70) cc_final: 0.9145 (t0) REVERT: H 465 GLN cc_start: 0.8579 (pp30) cc_final: 0.8197 (tt0) REVERT: H 482 MET cc_start: 0.9179 (tpp) cc_final: 0.8777 (tpt) REVERT: J 12 TYR cc_start: 0.9064 (t80) cc_final: 0.8401 (t80) REVERT: L 1 MET cc_start: 0.8306 (mpp) cc_final: 0.8001 (pmm) outliers start: 0 outliers final: 0 residues processed: 1409 average time/residue: 0.3981 time to fit residues: 909.7879 Evaluate side-chains 1186 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1186 time to evaluate : 3.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 216 optimal weight: 0.5980 chunk 276 optimal weight: 0.0010 chunk 214 optimal weight: 0.4980 chunk 319 optimal weight: 8.9990 chunk 211 optimal weight: 3.9990 chunk 377 optimal weight: 4.9990 chunk 236 optimal weight: 6.9990 chunk 230 optimal weight: 0.8980 chunk 174 optimal weight: 7.9990 overall best weight: 0.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 466 HIS B 171 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 HIS ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 GLN ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32212 Z= 0.214 Angle : 0.806 10.594 43712 Z= 0.396 Chirality : 0.050 0.310 4984 Planarity : 0.006 0.276 5452 Dihedral : 16.127 167.981 5344 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 23.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.20 % Favored : 90.78 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.12), residues: 3968 helix: -1.70 (0.13), residues: 1178 sheet: -2.48 (0.22), residues: 426 loop : -1.85 (0.13), residues: 2364 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS G 92 PHE 0.022 0.002 PHE H 114 TYR 0.038 0.002 TYR E 110 ARG 0.027 0.001 ARG D 322 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1413 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1413 time to evaluate : 3.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 TYR cc_start: 0.7707 (t80) cc_final: 0.7041 (m-80) REVERT: A 28 ASP cc_start: 0.8924 (t70) cc_final: 0.8618 (t70) REVERT: A 32 TYR cc_start: 0.8921 (m-10) cc_final: 0.8677 (m-10) REVERT: A 36 LEU cc_start: 0.9020 (tp) cc_final: 0.8443 (tp) REVERT: A 38 LEU cc_start: 0.9580 (mm) cc_final: 0.8781 (mm) REVERT: A 48 GLN cc_start: 0.9228 (mt0) cc_final: 0.8802 (mt0) REVERT: A 68 SER cc_start: 0.9351 (t) cc_final: 0.8879 (t) REVERT: A 75 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8162 (mm-30) REVERT: A 78 MET cc_start: 0.9253 (tpp) cc_final: 0.8825 (tpp) REVERT: A 179 MET cc_start: 0.7151 (pmm) cc_final: 0.6941 (pmm) REVERT: A 231 ARG cc_start: 0.9334 (ptm160) cc_final: 0.8984 (ptm-80) REVERT: A 246 CYS cc_start: 0.9421 (t) cc_final: 0.8645 (p) REVERT: A 254 GLU cc_start: 0.9325 (tp30) cc_final: 0.9004 (pm20) REVERT: A 273 LEU cc_start: 0.9345 (tt) cc_final: 0.8640 (tt) REVERT: A 284 ILE cc_start: 0.9391 (pt) cc_final: 0.9187 (pt) REVERT: A 288 LYS cc_start: 0.9538 (mtmm) cc_final: 0.9319 (ptpt) REVERT: A 294 TYR cc_start: 0.9350 (m-80) cc_final: 0.9011 (m-80) REVERT: A 332 ILE cc_start: 0.9242 (pt) cc_final: 0.8953 (pt) REVERT: A 335 GLU cc_start: 0.8565 (mp0) cc_final: 0.8019 (mp0) REVERT: A 343 GLN cc_start: 0.8438 (pp30) cc_final: 0.8015 (pp30) REVERT: A 353 TYR cc_start: 0.8869 (t80) cc_final: 0.8444 (t80) REVERT: A 357 PHE cc_start: 0.9311 (m-80) cc_final: 0.8920 (m-10) REVERT: A 375 LYS cc_start: 0.9611 (pttt) cc_final: 0.9304 (pttt) REVERT: A 385 MET cc_start: 0.8770 (ttp) cc_final: 0.8276 (ttp) REVERT: A 386 MET cc_start: 0.8760 (ppp) cc_final: 0.8206 (ppp) REVERT: A 420 MET cc_start: 0.8387 (mtm) cc_final: 0.7956 (mtp) REVERT: A 465 GLN cc_start: 0.9299 (tt0) cc_final: 0.9007 (tp40) REVERT: A 469 GLN cc_start: 0.8888 (tp40) cc_final: 0.8468 (tt0) REVERT: A 482 MET cc_start: 0.9045 (ttt) cc_final: 0.8832 (ttt) REVERT: A 483 MET cc_start: 0.9591 (tmm) cc_final: 0.9108 (tmm) REVERT: A 509 TYR cc_start: 0.9065 (p90) cc_final: 0.8764 (p90) REVERT: B 25 ASN cc_start: 0.8803 (m-40) cc_final: 0.8542 (m110) REVERT: B 34 ASP cc_start: 0.8311 (m-30) cc_final: 0.7915 (m-30) REVERT: B 36 LEU cc_start: 0.9452 (tp) cc_final: 0.9180 (tp) REVERT: B 37 ILE cc_start: 0.9288 (mm) cc_final: 0.8764 (mm) REVERT: B 41 TYR cc_start: 0.9182 (t80) cc_final: 0.8889 (t80) REVERT: B 103 GLU cc_start: 0.9403 (mm-30) cc_final: 0.9042 (tp30) REVERT: B 108 LYS cc_start: 0.9282 (pttm) cc_final: 0.8137 (tppt) REVERT: B 131 PHE cc_start: 0.9266 (m-80) cc_final: 0.8646 (m-80) REVERT: B 134 LYS cc_start: 0.9687 (pttm) cc_final: 0.9457 (pttt) REVERT: B 167 LYS cc_start: 0.9143 (mppt) cc_final: 0.8895 (mmtt) REVERT: B 176 GLU cc_start: 0.8291 (mp0) cc_final: 0.7930 (mp0) REVERT: B 181 LYS cc_start: 0.9099 (tppt) cc_final: 0.8734 (tppt) REVERT: B 185 LEU cc_start: 0.8876 (mt) cc_final: 0.8418 (mt) REVERT: B 238 LYS cc_start: 0.9001 (mmmt) cc_final: 0.8509 (tppt) REVERT: B 250 ILE cc_start: 0.9257 (mp) cc_final: 0.8871 (tp) REVERT: B 281 ILE cc_start: 0.9487 (tp) cc_final: 0.9134 (tp) REVERT: B 289 TYR cc_start: 0.9532 (t80) cc_final: 0.9194 (t80) REVERT: B 334 GLN cc_start: 0.9160 (mt0) cc_final: 0.8709 (mm-40) REVERT: B 335 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8203 (tm-30) REVERT: B 355 ARG cc_start: 0.8005 (ttp-170) cc_final: 0.7579 (ttp-170) REVERT: B 372 HIS cc_start: 0.8948 (m170) cc_final: 0.8584 (m90) REVERT: B 399 GLU cc_start: 0.7968 (mp0) cc_final: 0.7729 (pm20) REVERT: B 404 ASP cc_start: 0.8739 (t0) cc_final: 0.8460 (t0) REVERT: B 449 ASP cc_start: 0.8575 (t70) cc_final: 0.8149 (t70) REVERT: B 482 MET cc_start: 0.8793 (ptp) cc_final: 0.8515 (ptp) REVERT: B 491 GLU cc_start: 0.8686 (tm-30) cc_final: 0.8246 (tm-30) REVERT: C 32 TYR cc_start: 0.8975 (m-10) cc_final: 0.8621 (m-10) REVERT: C 47 ASP cc_start: 0.9654 (m-30) cc_final: 0.9006 (p0) REVERT: C 78 MET cc_start: 0.9227 (mmp) cc_final: 0.8814 (mmt) REVERT: C 82 MET cc_start: 0.9618 (tpp) cc_final: 0.9263 (tpp) REVERT: C 90 PHE cc_start: 0.9173 (m-80) cc_final: 0.8616 (m-80) REVERT: C 111 GLU cc_start: 0.9321 (tp30) cc_final: 0.9113 (mp0) REVERT: C 199 GLU cc_start: 0.9248 (mt-10) cc_final: 0.8741 (tp30) REVERT: C 200 ILE cc_start: 0.9363 (mm) cc_final: 0.8974 (mm) REVERT: C 203 ARG cc_start: 0.8798 (mtm-85) cc_final: 0.8236 (mtm110) REVERT: C 229 LYS cc_start: 0.9393 (ptpp) cc_final: 0.9069 (mmmt) REVERT: C 274 ASP cc_start: 0.8997 (t0) cc_final: 0.8620 (t70) REVERT: C 277 GLN cc_start: 0.7976 (tm-30) cc_final: 0.7737 (tm-30) REVERT: C 290 ILE cc_start: 0.9496 (pt) cc_final: 0.9180 (pt) REVERT: C 291 LYS cc_start: 0.8999 (ptpp) cc_final: 0.8760 (pttm) REVERT: C 333 THR cc_start: 0.9687 (p) cc_final: 0.9271 (p) REVERT: C 334 GLN cc_start: 0.8970 (mp10) cc_final: 0.8422 (mp10) REVERT: C 335 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8053 (tm-30) REVERT: C 349 LYS cc_start: 0.8972 (mtpt) cc_final: 0.8468 (mtpt) REVERT: C 441 GLN cc_start: 0.8278 (mp-120) cc_final: 0.7889 (mp-120) REVERT: C 482 MET cc_start: 0.9366 (tpp) cc_final: 0.9130 (mmm) REVERT: D 12 TYR cc_start: 0.8043 (t80) cc_final: 0.7034 (m-80) REVERT: D 21 GLN cc_start: 0.8751 (tm-30) cc_final: 0.8054 (tm-30) REVERT: D 25 ASN cc_start: 0.8616 (m110) cc_final: 0.8193 (m110) REVERT: D 32 TYR cc_start: 0.8804 (m-80) cc_final: 0.8308 (m-10) REVERT: D 63 THR cc_start: 0.7925 (t) cc_final: 0.7724 (t) REVERT: D 71 ASP cc_start: 0.9460 (t0) cc_final: 0.9129 (t0) REVERT: D 91 ILE cc_start: 0.9268 (tp) cc_final: 0.9052 (tp) REVERT: D 158 ILE cc_start: 0.7429 (tp) cc_final: 0.7203 (tp) REVERT: D 164 ASP cc_start: 0.8994 (t0) cc_final: 0.8780 (p0) REVERT: D 179 MET cc_start: 0.8577 (pmm) cc_final: 0.8265 (pmm) REVERT: D 215 ASP cc_start: 0.9498 (m-30) cc_final: 0.9025 (p0) REVERT: D 242 LYS cc_start: 0.9383 (mmpt) cc_final: 0.9157 (mmmt) REVERT: D 258 TYR cc_start: 0.9537 (t80) cc_final: 0.9329 (t80) REVERT: D 286 MET cc_start: 0.9597 (tpt) cc_final: 0.9374 (tpt) REVERT: D 289 TYR cc_start: 0.9380 (t80) cc_final: 0.9128 (t80) REVERT: D 290 ILE cc_start: 0.9777 (pt) cc_final: 0.9393 (pt) REVERT: D 315 ASP cc_start: 0.9497 (m-30) cc_final: 0.8927 (p0) REVERT: D 332 ILE cc_start: 0.9016 (tp) cc_final: 0.8385 (tp) REVERT: D 335 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8561 (tm-30) REVERT: D 349 LYS cc_start: 0.9542 (mmmm) cc_final: 0.9301 (mmmm) REVERT: D 352 GLU cc_start: 0.9190 (tm-30) cc_final: 0.8898 (tm-30) REVERT: D 385 MET cc_start: 0.8610 (tpt) cc_final: 0.7905 (tpt) REVERT: D 400 TYR cc_start: 0.7776 (m-80) cc_final: 0.7486 (m-80) REVERT: D 465 GLN cc_start: 0.9091 (tt0) cc_final: 0.8743 (tt0) REVERT: D 478 GLN cc_start: 0.9452 (mt0) cc_final: 0.8982 (mt0) REVERT: D 482 MET cc_start: 0.9293 (tpp) cc_final: 0.8864 (tpt) REVERT: P 1 MET cc_start: 0.8475 (mpp) cc_final: 0.8187 (pmm) REVERT: E 12 TYR cc_start: 0.7704 (t80) cc_final: 0.7082 (m-80) REVERT: E 28 ASP cc_start: 0.8916 (t70) cc_final: 0.8596 (t70) REVERT: E 32 TYR cc_start: 0.9289 (m-80) cc_final: 0.8607 (m-80) REVERT: E 36 LEU cc_start: 0.9074 (tp) cc_final: 0.8653 (tp) REVERT: E 38 LEU cc_start: 0.9581 (mm) cc_final: 0.8752 (mm) REVERT: E 48 GLN cc_start: 0.9270 (mt0) cc_final: 0.8841 (mt0) REVERT: E 82 MET cc_start: 0.9490 (ttp) cc_final: 0.9151 (ttp) REVERT: E 105 ARG cc_start: 0.9047 (mmm160) cc_final: 0.8157 (tpm170) REVERT: E 109 LYS cc_start: 0.9331 (ptpp) cc_final: 0.8859 (ptpp) REVERT: E 142 ILE cc_start: 0.8732 (tp) cc_final: 0.8526 (tp) REVERT: E 150 MET cc_start: 0.7895 (tpt) cc_final: 0.7660 (tpt) REVERT: E 158 ILE cc_start: 0.8861 (mm) cc_final: 0.8371 (tp) REVERT: E 165 PHE cc_start: 0.8472 (p90) cc_final: 0.8206 (p90) REVERT: E 179 MET cc_start: 0.7655 (pmm) cc_final: 0.7104 (pmm) REVERT: E 228 LYS cc_start: 0.9514 (ptpp) cc_final: 0.9283 (ptpp) REVERT: E 246 CYS cc_start: 0.9477 (t) cc_final: 0.8635 (p) REVERT: E 250 ILE cc_start: 0.9413 (pt) cc_final: 0.9198 (pt) REVERT: E 273 LEU cc_start: 0.9045 (tt) cc_final: 0.8809 (tt) REVERT: E 294 TYR cc_start: 0.9302 (m-80) cc_final: 0.8934 (m-80) REVERT: E 332 ILE cc_start: 0.9318 (pt) cc_final: 0.8997 (pt) REVERT: E 335 GLU cc_start: 0.8638 (mp0) cc_final: 0.8057 (mp0) REVERT: E 364 ASP cc_start: 0.8321 (m-30) cc_final: 0.7907 (m-30) REVERT: E 375 LYS cc_start: 0.9640 (pttt) cc_final: 0.9233 (pttt) REVERT: E 385 MET cc_start: 0.8447 (ttp) cc_final: 0.8235 (ttp) REVERT: E 386 MET cc_start: 0.8719 (ppp) cc_final: 0.8386 (ppp) REVERT: E 420 MET cc_start: 0.8421 (mtm) cc_final: 0.7900 (mtp) REVERT: E 449 ASP cc_start: 0.7876 (t0) cc_final: 0.6402 (t0) REVERT: E 480 ARG cc_start: 0.8922 (mpp-170) cc_final: 0.8539 (mpp80) REVERT: E 482 MET cc_start: 0.8958 (ttt) cc_final: 0.8729 (ttt) REVERT: E 483 MET cc_start: 0.9511 (tmm) cc_final: 0.9046 (tmm) REVERT: E 507 HIS cc_start: 0.8801 (t-90) cc_final: 0.8570 (t70) REVERT: E 509 TYR cc_start: 0.9096 (p90) cc_final: 0.8888 (p90) REVERT: F 16 ASP cc_start: 0.6952 (t0) cc_final: 0.6048 (t0) REVERT: F 25 ASN cc_start: 0.8891 (m-40) cc_final: 0.8618 (m110) REVERT: F 34 ASP cc_start: 0.8412 (m-30) cc_final: 0.8039 (m-30) REVERT: F 36 LEU cc_start: 0.9291 (tp) cc_final: 0.9048 (tp) REVERT: F 37 ILE cc_start: 0.9041 (mm) cc_final: 0.8603 (mm) REVERT: F 70 MET cc_start: 0.8013 (tpp) cc_final: 0.7012 (tpt) REVERT: F 82 MET cc_start: 0.9495 (ttt) cc_final: 0.9095 (tmm) REVERT: F 102 ASN cc_start: 0.9468 (t0) cc_final: 0.9248 (t0) REVERT: F 103 GLU cc_start: 0.9417 (tp30) cc_final: 0.8915 (tp30) REVERT: F 106 LYS cc_start: 0.9380 (mtpt) cc_final: 0.8965 (mtpt) REVERT: F 108 LYS cc_start: 0.9185 (pttm) cc_final: 0.7916 (tppt) REVERT: F 131 PHE cc_start: 0.9512 (m-80) cc_final: 0.8426 (m-80) REVERT: F 132 GLU cc_start: 0.9485 (pt0) cc_final: 0.9154 (pt0) REVERT: F 134 LYS cc_start: 0.9499 (pttm) cc_final: 0.9188 (tttt) REVERT: F 179 MET cc_start: 0.6553 (ppp) cc_final: 0.6250 (ppp) REVERT: F 185 LEU cc_start: 0.8826 (mt) cc_final: 0.8322 (mt) REVERT: F 238 LYS cc_start: 0.9076 (mmmm) cc_final: 0.8711 (tppt) REVERT: F 281 ILE cc_start: 0.9510 (tp) cc_final: 0.9170 (tp) REVERT: F 285 ASN cc_start: 0.9508 (m110) cc_final: 0.9307 (m110) REVERT: F 334 GLN cc_start: 0.9207 (mt0) cc_final: 0.8844 (mm-40) REVERT: F 337 LEU cc_start: 0.9573 (mm) cc_final: 0.9340 (mm) REVERT: F 352 GLU cc_start: 0.8545 (pm20) cc_final: 0.8344 (pm20) REVERT: F 355 ARG cc_start: 0.8247 (ppt170) cc_final: 0.7912 (ttt180) REVERT: F 372 HIS cc_start: 0.9038 (m170) cc_final: 0.8501 (m170) REVERT: F 388 SER cc_start: 0.8929 (p) cc_final: 0.8678 (p) REVERT: F 404 ASP cc_start: 0.8640 (t0) cc_final: 0.8329 (t0) REVERT: F 414 MET cc_start: 0.9163 (mpp) cc_final: 0.8958 (mpp) REVERT: F 449 ASP cc_start: 0.8493 (t70) cc_final: 0.8251 (t70) REVERT: F 491 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8216 (tm-30) REVERT: F 493 ARG cc_start: 0.8876 (ptt-90) cc_final: 0.8602 (ptt-90) REVERT: F 507 HIS cc_start: 0.8591 (t-90) cc_final: 0.8335 (t-90) REVERT: G 47 ASP cc_start: 0.9661 (m-30) cc_final: 0.9055 (p0) REVERT: G 78 MET cc_start: 0.9603 (tpp) cc_final: 0.9174 (tpp) REVERT: G 82 MET cc_start: 0.9699 (tpp) cc_final: 0.9452 (tpp) REVERT: G 111 GLU cc_start: 0.9384 (tp30) cc_final: 0.9056 (mp0) REVERT: G 115 ILE cc_start: 0.8676 (pt) cc_final: 0.8454 (pt) REVERT: G 150 MET cc_start: 0.8954 (mmp) cc_final: 0.8425 (tpp) REVERT: G 216 ASP cc_start: 0.9320 (m-30) cc_final: 0.9071 (t70) REVERT: G 229 LYS cc_start: 0.9369 (ptpp) cc_final: 0.9097 (mmmt) REVERT: G 274 ASP cc_start: 0.8997 (t0) cc_final: 0.8618 (t70) REVERT: G 287 ILE cc_start: 0.9634 (mp) cc_final: 0.9120 (tt) REVERT: G 291 LYS cc_start: 0.9047 (ptpp) cc_final: 0.8685 (pttm) REVERT: G 331 CYS cc_start: 0.8977 (t) cc_final: 0.8557 (t) REVERT: G 333 THR cc_start: 0.9667 (p) cc_final: 0.9305 (p) REVERT: G 334 GLN cc_start: 0.8931 (mp10) cc_final: 0.8375 (mp10) REVERT: G 335 GLU cc_start: 0.8677 (tm-30) cc_final: 0.7944 (tm-30) REVERT: G 336 VAL cc_start: 0.9515 (m) cc_final: 0.8616 (m) REVERT: G 349 LYS cc_start: 0.8850 (mtpt) cc_final: 0.8598 (mtmt) REVERT: G 386 MET cc_start: 0.8980 (tmm) cc_final: 0.8500 (tmm) REVERT: G 395 GLU cc_start: 0.8746 (mp0) cc_final: 0.8370 (mp0) REVERT: G 411 TYR cc_start: 0.9616 (t80) cc_final: 0.9347 (t80) REVERT: G 441 GLN cc_start: 0.8382 (mp-120) cc_final: 0.7987 (mp-120) REVERT: G 469 GLN cc_start: 0.9336 (tp40) cc_final: 0.9127 (tp40) REVERT: G 482 MET cc_start: 0.9354 (tpp) cc_final: 0.8952 (mmm) REVERT: G 504 HIS cc_start: 0.8516 (p90) cc_final: 0.8252 (p90) REVERT: H 21 GLN cc_start: 0.9117 (tp-100) cc_final: 0.8479 (tp-100) REVERT: H 25 ASN cc_start: 0.8575 (m110) cc_final: 0.7893 (m110) REVERT: H 32 TYR cc_start: 0.8980 (m-80) cc_final: 0.8536 (m-10) REVERT: H 33 ASN cc_start: 0.9124 (t0) cc_final: 0.8313 (t0) REVERT: H 70 MET cc_start: 0.9483 (mpp) cc_final: 0.8784 (mpp) REVERT: H 91 ILE cc_start: 0.9257 (tp) cc_final: 0.8885 (tp) REVERT: H 108 LYS cc_start: 0.9134 (tptm) cc_final: 0.8399 (tptt) REVERT: H 112 GLN cc_start: 0.9243 (tm-30) cc_final: 0.8698 (tm-30) REVERT: H 158 ILE cc_start: 0.6974 (tp) cc_final: 0.6688 (tp) REVERT: H 179 MET cc_start: 0.7406 (ppp) cc_final: 0.6656 (ppp) REVERT: H 208 LYS cc_start: 0.8094 (tppp) cc_final: 0.7888 (tptt) REVERT: H 286 MET cc_start: 0.9621 (tpt) cc_final: 0.9329 (tpt) REVERT: H 311 LYS cc_start: 0.9150 (ttpt) cc_final: 0.8663 (ttpt) REVERT: H 315 ASP cc_start: 0.9493 (m-30) cc_final: 0.8924 (p0) REVERT: H 335 GLU cc_start: 0.8906 (tm-30) cc_final: 0.8666 (tm-30) REVERT: H 352 GLU cc_start: 0.9211 (tm-30) cc_final: 0.8925 (tm-30) REVERT: H 385 MET cc_start: 0.8064 (tpt) cc_final: 0.7227 (tpt) REVERT: H 386 MET cc_start: 0.7267 (ptm) cc_final: 0.6851 (ppp) REVERT: H 409 LYS cc_start: 0.8247 (ttmm) cc_final: 0.7980 (tppt) REVERT: H 410 LYS cc_start: 0.8879 (mptt) cc_final: 0.8629 (mmtm) REVERT: H 414 MET cc_start: 0.8991 (pmm) cc_final: 0.8544 (pmm) REVERT: H 418 ASP cc_start: 0.9377 (t70) cc_final: 0.9169 (t0) REVERT: H 465 GLN cc_start: 0.8522 (pp30) cc_final: 0.8174 (tt0) REVERT: H 478 GLN cc_start: 0.9451 (mt0) cc_final: 0.9012 (mt0) REVERT: H 482 MET cc_start: 0.9123 (tpp) cc_final: 0.8741 (tpt) REVERT: J 5 LEU cc_start: 0.9401 (mt) cc_final: 0.9106 (mt) REVERT: J 11 SER cc_start: 0.8799 (m) cc_final: 0.8563 (p) REVERT: J 12 TYR cc_start: 0.8914 (t80) cc_final: 0.7955 (t80) REVERT: L 1 MET cc_start: 0.8259 (mpp) cc_final: 0.8012 (pmm) outliers start: 0 outliers final: 0 residues processed: 1413 average time/residue: 0.4030 time to fit residues: 923.0922 Evaluate side-chains 1203 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1203 time to evaluate : 3.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 225 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 240 optimal weight: 5.9990 chunk 257 optimal weight: 2.9990 chunk 186 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 296 optimal weight: 8.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 HIS ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 HIS ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 92 HIS ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 32212 Z= 0.329 Angle : 0.855 9.761 43712 Z= 0.429 Chirality : 0.052 0.417 4984 Planarity : 0.005 0.142 5452 Dihedral : 15.748 170.701 5344 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 29.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.26 % Favored : 89.74 % Rotamer: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.88 (0.12), residues: 3968 helix: -1.74 (0.13), residues: 1204 sheet: -2.64 (0.22), residues: 406 loop : -1.89 (0.13), residues: 2358 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS G 504 PHE 0.020 0.002 PHE C 131 TYR 0.026 0.002 TYR G 110 ARG 0.033 0.001 ARG D 322 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1359 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1359 time to evaluate : 3.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8987 (t70) cc_final: 0.8682 (t70) REVERT: A 32 TYR cc_start: 0.8931 (m-10) cc_final: 0.8677 (m-10) REVERT: A 36 LEU cc_start: 0.9056 (tp) cc_final: 0.8627 (tp) REVERT: A 38 LEU cc_start: 0.9659 (mm) cc_final: 0.8876 (mm) REVERT: A 48 GLN cc_start: 0.9249 (mt0) cc_final: 0.8847 (mt0) REVERT: A 78 MET cc_start: 0.9225 (tpp) cc_final: 0.8793 (tpp) REVERT: A 231 ARG cc_start: 0.9338 (ptm160) cc_final: 0.9079 (ptm-80) REVERT: A 246 CYS cc_start: 0.9425 (t) cc_final: 0.8556 (p) REVERT: A 254 GLU cc_start: 0.9392 (tp30) cc_final: 0.9078 (pm20) REVERT: A 273 LEU cc_start: 0.9500 (tt) cc_final: 0.9109 (tt) REVERT: A 284 ILE cc_start: 0.9448 (pt) cc_final: 0.9233 (pt) REVERT: A 288 LYS cc_start: 0.9508 (mtmm) cc_final: 0.9263 (ptpt) REVERT: A 294 TYR cc_start: 0.9360 (m-80) cc_final: 0.9075 (m-80) REVERT: A 325 MET cc_start: 0.9034 (ptm) cc_final: 0.8726 (ptm) REVERT: A 332 ILE cc_start: 0.9331 (pt) cc_final: 0.9063 (pt) REVERT: A 335 GLU cc_start: 0.8582 (mp0) cc_final: 0.8038 (mp0) REVERT: A 343 GLN cc_start: 0.8359 (pp30) cc_final: 0.7908 (pp30) REVERT: A 375 LYS cc_start: 0.9659 (pttt) cc_final: 0.9331 (pttt) REVERT: A 385 MET cc_start: 0.8829 (ttp) cc_final: 0.8377 (ttp) REVERT: A 420 MET cc_start: 0.8427 (mtm) cc_final: 0.8024 (mtp) REVERT: A 469 GLN cc_start: 0.8943 (tp40) cc_final: 0.8612 (tt0) REVERT: A 482 MET cc_start: 0.9122 (ttt) cc_final: 0.8891 (ttt) REVERT: A 483 MET cc_start: 0.9628 (tmm) cc_final: 0.9063 (tmm) REVERT: A 488 LEU cc_start: 0.9238 (pt) cc_final: 0.9027 (pp) REVERT: A 509 TYR cc_start: 0.9091 (p90) cc_final: 0.8209 (p90) REVERT: B 34 ASP cc_start: 0.8401 (m-30) cc_final: 0.7929 (m-30) REVERT: B 36 LEU cc_start: 0.9349 (tp) cc_final: 0.9025 (tp) REVERT: B 37 ILE cc_start: 0.9348 (mm) cc_final: 0.8887 (mm) REVERT: B 41 TYR cc_start: 0.9196 (t80) cc_final: 0.8915 (t80) REVERT: B 103 GLU cc_start: 0.9441 (mm-30) cc_final: 0.9077 (tp30) REVERT: B 106 LYS cc_start: 0.9380 (mtpt) cc_final: 0.9164 (mtpt) REVERT: B 108 LYS cc_start: 0.9345 (pttm) cc_final: 0.8621 (tptt) REVERT: B 129 ASP cc_start: 0.9728 (m-30) cc_final: 0.9526 (m-30) REVERT: B 131 PHE cc_start: 0.9289 (m-80) cc_final: 0.8695 (m-80) REVERT: B 132 GLU cc_start: 0.9600 (pt0) cc_final: 0.9302 (pp20) REVERT: B 134 LYS cc_start: 0.9683 (pttm) cc_final: 0.9457 (pmtt) REVERT: B 166 LEU cc_start: 0.9379 (mm) cc_final: 0.8779 (tp) REVERT: B 181 LYS cc_start: 0.9083 (tppt) cc_final: 0.8763 (tppt) REVERT: B 185 LEU cc_start: 0.8868 (mt) cc_final: 0.8497 (mt) REVERT: B 199 GLU cc_start: 0.9476 (pp20) cc_final: 0.8982 (pp20) REVERT: B 200 ILE cc_start: 0.9687 (mt) cc_final: 0.9427 (mm) REVERT: B 250 ILE cc_start: 0.9254 (mp) cc_final: 0.8748 (tp) REVERT: B 334 GLN cc_start: 0.9207 (mt0) cc_final: 0.8890 (mm-40) REVERT: B 335 GLU cc_start: 0.8624 (tm-30) cc_final: 0.8217 (tm-30) REVERT: B 372 HIS cc_start: 0.9079 (m170) cc_final: 0.8605 (m170) REVERT: B 399 GLU cc_start: 0.8093 (mp0) cc_final: 0.7849 (pm20) REVERT: B 404 ASP cc_start: 0.8818 (t0) cc_final: 0.8555 (t0) REVERT: B 491 GLU cc_start: 0.8627 (tm-30) cc_final: 0.8156 (tm-30) REVERT: C 32 TYR cc_start: 0.9084 (m-10) cc_final: 0.8678 (m-10) REVERT: C 47 ASP cc_start: 0.9677 (m-30) cc_final: 0.9049 (p0) REVERT: C 50 ASP cc_start: 0.8718 (t70) cc_final: 0.8509 (t0) REVERT: C 78 MET cc_start: 0.9261 (mmp) cc_final: 0.8885 (mmt) REVERT: C 82 MET cc_start: 0.9579 (tpp) cc_final: 0.9192 (tpp) REVERT: C 90 PHE cc_start: 0.9183 (m-80) cc_final: 0.8629 (m-80) REVERT: C 111 GLU cc_start: 0.9369 (tp30) cc_final: 0.9100 (mp0) REVERT: C 199 GLU cc_start: 0.9249 (mt-10) cc_final: 0.8865 (tp30) REVERT: C 200 ILE cc_start: 0.9358 (mm) cc_final: 0.9139 (mm) REVERT: C 229 LYS cc_start: 0.9365 (ptpp) cc_final: 0.9019 (mmmt) REVERT: C 274 ASP cc_start: 0.8832 (t0) cc_final: 0.8445 (t70) REVERT: C 290 ILE cc_start: 0.9498 (pt) cc_final: 0.9175 (pt) REVERT: C 331 CYS cc_start: 0.8954 (t) cc_final: 0.8646 (t) REVERT: C 333 THR cc_start: 0.9684 (p) cc_final: 0.9298 (p) REVERT: C 334 GLN cc_start: 0.9005 (mp10) cc_final: 0.8461 (mp10) REVERT: C 335 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8221 (tm-30) REVERT: C 349 LYS cc_start: 0.8996 (mtpt) cc_final: 0.8448 (mtpt) REVERT: C 482 MET cc_start: 0.9345 (tpp) cc_final: 0.8936 (tpp) REVERT: C 487 GLU cc_start: 0.8463 (pm20) cc_final: 0.8199 (pm20) REVERT: D 12 TYR cc_start: 0.8034 (t80) cc_final: 0.7173 (m-80) REVERT: D 21 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8180 (tm-30) REVERT: D 32 TYR cc_start: 0.8832 (m-80) cc_final: 0.8510 (m-10) REVERT: D 63 THR cc_start: 0.8068 (t) cc_final: 0.7853 (t) REVERT: D 71 ASP cc_start: 0.9534 (t0) cc_final: 0.9072 (t0) REVERT: D 164 ASP cc_start: 0.9009 (t0) cc_final: 0.8806 (p0) REVERT: D 179 MET cc_start: 0.8428 (pmm) cc_final: 0.8206 (pmm) REVERT: D 208 LYS cc_start: 0.8658 (tmtt) cc_final: 0.8270 (mmtm) REVERT: D 215 ASP cc_start: 0.9467 (m-30) cc_final: 0.8998 (p0) REVERT: D 242 LYS cc_start: 0.9382 (mmpt) cc_final: 0.9169 (mmmt) REVERT: D 289 TYR cc_start: 0.9402 (t80) cc_final: 0.9147 (t80) REVERT: D 290 ILE cc_start: 0.9771 (pt) cc_final: 0.9398 (pt) REVERT: D 332 ILE cc_start: 0.9011 (tp) cc_final: 0.8444 (tp) REVERT: D 335 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8639 (tm-30) REVERT: D 349 LYS cc_start: 0.9546 (mmmm) cc_final: 0.9288 (mmmm) REVERT: D 352 GLU cc_start: 0.9202 (tm-30) cc_final: 0.8926 (tm-30) REVERT: D 385 MET cc_start: 0.8712 (tpt) cc_final: 0.7957 (tpt) REVERT: D 386 MET cc_start: 0.8737 (ptm) cc_final: 0.8454 (ptm) REVERT: D 400 TYR cc_start: 0.7962 (m-80) cc_final: 0.7551 (m-80) REVERT: D 414 MET cc_start: 0.8740 (pmm) cc_final: 0.8524 (pmm) REVERT: D 441 GLN cc_start: 0.7483 (mp-120) cc_final: 0.7116 (mp-120) REVERT: D 465 GLN cc_start: 0.9116 (tt0) cc_final: 0.8747 (tt0) REVERT: D 482 MET cc_start: 0.9372 (tpp) cc_final: 0.8525 (tpt) REVERT: D 487 GLU cc_start: 0.9024 (pm20) cc_final: 0.8381 (pm20) REVERT: N 12 TYR cc_start: 0.8925 (t80) cc_final: 0.8005 (t80) REVERT: O 1 MET cc_start: 0.8270 (mmm) cc_final: 0.8006 (tpp) REVERT: P 1 MET cc_start: 0.8455 (mpp) cc_final: 0.8206 (pmm) REVERT: E 32 TYR cc_start: 0.9366 (m-80) cc_final: 0.8617 (m-80) REVERT: E 38 LEU cc_start: 0.9616 (mm) cc_final: 0.8883 (mm) REVERT: E 48 GLN cc_start: 0.9226 (mt0) cc_final: 0.8711 (mt0) REVERT: E 82 MET cc_start: 0.9527 (ttp) cc_final: 0.9151 (ttp) REVERT: E 105 ARG cc_start: 0.9063 (mmm160) cc_final: 0.8529 (tpm170) REVERT: E 142 ILE cc_start: 0.8706 (tp) cc_final: 0.8457 (tp) REVERT: E 150 MET cc_start: 0.7880 (tpt) cc_final: 0.7658 (tpt) REVERT: E 158 ILE cc_start: 0.8856 (mm) cc_final: 0.8371 (tp) REVERT: E 165 PHE cc_start: 0.8599 (p90) cc_final: 0.8317 (p90) REVERT: E 179 MET cc_start: 0.7716 (pmm) cc_final: 0.7088 (pmm) REVERT: E 228 LYS cc_start: 0.9509 (ptpp) cc_final: 0.9284 (ptpp) REVERT: E 246 CYS cc_start: 0.9456 (t) cc_final: 0.8498 (p) REVERT: E 273 LEU cc_start: 0.9093 (tt) cc_final: 0.8833 (tt) REVERT: E 288 LYS cc_start: 0.9481 (mtmm) cc_final: 0.9238 (mttt) REVERT: E 294 TYR cc_start: 0.9325 (m-80) cc_final: 0.8996 (m-80) REVERT: E 306 THR cc_start: 0.9476 (p) cc_final: 0.8894 (p) REVERT: E 332 ILE cc_start: 0.9430 (pt) cc_final: 0.9123 (pt) REVERT: E 335 GLU cc_start: 0.8631 (mp0) cc_final: 0.8081 (mp0) REVERT: E 352 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8763 (tm-30) REVERT: E 356 ARG cc_start: 0.9020 (mtt180) cc_final: 0.8636 (mtt-85) REVERT: E 375 LYS cc_start: 0.9687 (pttt) cc_final: 0.9301 (pttt) REVERT: E 385 MET cc_start: 0.8482 (ttp) cc_final: 0.7847 (ttp) REVERT: E 386 MET cc_start: 0.8475 (ppp) cc_final: 0.7969 (ppp) REVERT: E 420 MET cc_start: 0.8392 (mtm) cc_final: 0.7927 (mtp) REVERT: E 454 HIS cc_start: 0.8839 (m90) cc_final: 0.8538 (m90) REVERT: E 482 MET cc_start: 0.9034 (ttt) cc_final: 0.8793 (ttt) REVERT: E 483 MET cc_start: 0.9505 (tmm) cc_final: 0.8991 (tmm) REVERT: E 488 LEU cc_start: 0.9222 (pt) cc_final: 0.8990 (pp) REVERT: E 507 HIS cc_start: 0.8815 (t-90) cc_final: 0.8587 (t70) REVERT: E 509 TYR cc_start: 0.9122 (p90) cc_final: 0.8894 (p90) REVERT: F 25 ASN cc_start: 0.9044 (m-40) cc_final: 0.8720 (m110) REVERT: F 34 ASP cc_start: 0.8439 (m-30) cc_final: 0.8046 (m-30) REVERT: F 36 LEU cc_start: 0.9314 (tp) cc_final: 0.9050 (tp) REVERT: F 37 ILE cc_start: 0.9179 (mm) cc_final: 0.8774 (mm) REVERT: F 70 MET cc_start: 0.8133 (tpp) cc_final: 0.7599 (mmm) REVERT: F 103 GLU cc_start: 0.9548 (tp30) cc_final: 0.9128 (tp30) REVERT: F 106 LYS cc_start: 0.9395 (mtpt) cc_final: 0.9100 (mtpt) REVERT: F 108 LYS cc_start: 0.9196 (pttm) cc_final: 0.7887 (tppt) REVERT: F 131 PHE cc_start: 0.9517 (m-80) cc_final: 0.8906 (m-80) REVERT: F 132 GLU cc_start: 0.9503 (pt0) cc_final: 0.9195 (pt0) REVERT: F 179 MET cc_start: 0.6409 (ppp) cc_final: 0.6064 (ppp) REVERT: F 185 LEU cc_start: 0.8830 (mt) cc_final: 0.8327 (mt) REVERT: F 281 ILE cc_start: 0.9525 (tp) cc_final: 0.9197 (tp) REVERT: F 337 LEU cc_start: 0.9514 (mm) cc_final: 0.9293 (mm) REVERT: F 352 GLU cc_start: 0.8531 (pm20) cc_final: 0.8261 (pm20) REVERT: F 355 ARG cc_start: 0.8338 (ppt170) cc_final: 0.7911 (ttp-170) REVERT: F 372 HIS cc_start: 0.9141 (m170) cc_final: 0.8551 (m170) REVERT: F 404 ASP cc_start: 0.8801 (t0) cc_final: 0.8488 (t0) REVERT: G 47 ASP cc_start: 0.9679 (m-30) cc_final: 0.9126 (p0) REVERT: G 78 MET cc_start: 0.9605 (tpp) cc_final: 0.9157 (tpp) REVERT: G 82 MET cc_start: 0.9691 (tpp) cc_final: 0.9380 (tpp) REVERT: G 150 MET cc_start: 0.9004 (mmp) cc_final: 0.8534 (tpp) REVERT: G 216 ASP cc_start: 0.9319 (m-30) cc_final: 0.9090 (t70) REVERT: G 229 LYS cc_start: 0.9362 (ptpp) cc_final: 0.9100 (mmmt) REVERT: G 274 ASP cc_start: 0.8897 (t0) cc_final: 0.8463 (t70) REVERT: G 287 ILE cc_start: 0.9662 (mp) cc_final: 0.9226 (tt) REVERT: G 291 LYS cc_start: 0.9078 (ptpp) cc_final: 0.8735 (pttm) REVERT: G 333 THR cc_start: 0.9674 (p) cc_final: 0.9425 (p) REVERT: G 334 GLN cc_start: 0.9012 (mp10) cc_final: 0.8554 (mp10) REVERT: G 335 GLU cc_start: 0.8785 (tm-30) cc_final: 0.8111 (tm-30) REVERT: G 336 VAL cc_start: 0.9561 (m) cc_final: 0.8655 (m) REVERT: G 343 GLN cc_start: 0.9099 (pm20) cc_final: 0.8864 (pm20) REVERT: G 353 TYR cc_start: 0.8668 (t80) cc_final: 0.8362 (t80) REVERT: G 385 MET cc_start: 0.7150 (ttt) cc_final: 0.6577 (ttt) REVERT: G 386 MET cc_start: 0.9044 (tmm) cc_final: 0.8547 (tmm) REVERT: G 390 LEU cc_start: 0.9188 (pt) cc_final: 0.8963 (pt) REVERT: G 395 GLU cc_start: 0.8815 (mp0) cc_final: 0.8380 (mp0) REVERT: G 411 TYR cc_start: 0.9558 (t80) cc_final: 0.9297 (t80) REVERT: G 482 MET cc_start: 0.9316 (tpp) cc_final: 0.8913 (mmm) REVERT: G 504 HIS cc_start: 0.8504 (p90) cc_final: 0.8270 (p90) REVERT: H 21 GLN cc_start: 0.9158 (tp-100) cc_final: 0.8627 (tp40) REVERT: H 25 ASN cc_start: 0.8602 (m110) cc_final: 0.8085 (m110) REVERT: H 32 TYR cc_start: 0.9000 (m-80) cc_final: 0.8481 (m-10) REVERT: H 38 LEU cc_start: 0.9449 (mt) cc_final: 0.9233 (mt) REVERT: H 70 MET cc_start: 0.9489 (mpp) cc_final: 0.8865 (mpp) REVERT: H 91 ILE cc_start: 0.9336 (tp) cc_final: 0.8979 (tp) REVERT: H 93 HIS cc_start: 0.9051 (p-80) cc_final: 0.8835 (p-80) REVERT: H 112 GLN cc_start: 0.9277 (tm-30) cc_final: 0.8744 (tm-30) REVERT: H 158 ILE cc_start: 0.7154 (tp) cc_final: 0.6897 (tp) REVERT: H 179 MET cc_start: 0.7361 (ppp) cc_final: 0.6755 (ppp) REVERT: H 208 LYS cc_start: 0.8044 (tppp) cc_final: 0.7825 (tptp) REVERT: H 258 TYR cc_start: 0.9572 (t80) cc_final: 0.9353 (t80) REVERT: H 286 MET cc_start: 0.9597 (tpt) cc_final: 0.9350 (tpt) REVERT: H 311 LYS cc_start: 0.9212 (ttpt) cc_final: 0.8722 (ttpt) REVERT: H 315 ASP cc_start: 0.9528 (m-30) cc_final: 0.8940 (p0) REVERT: H 335 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8698 (tm-30) REVERT: H 352 GLU cc_start: 0.9228 (tm-30) cc_final: 0.8951 (tm-30) REVERT: H 385 MET cc_start: 0.8614 (tpt) cc_final: 0.7829 (tpt) REVERT: H 414 MET cc_start: 0.9040 (pmm) cc_final: 0.8708 (pmm) REVERT: H 418 ASP cc_start: 0.9402 (t70) cc_final: 0.9187 (t0) REVERT: H 465 GLN cc_start: 0.8589 (pp30) cc_final: 0.8241 (tt0) REVERT: H 478 GLN cc_start: 0.9442 (mt0) cc_final: 0.9053 (mt0) REVERT: H 482 MET cc_start: 0.9222 (tpp) cc_final: 0.8881 (tpt) REVERT: H 492 LYS cc_start: 0.9203 (pttt) cc_final: 0.8799 (pttp) REVERT: J 12 TYR cc_start: 0.8890 (t80) cc_final: 0.8110 (t80) REVERT: L 1 MET cc_start: 0.8305 (mpp) cc_final: 0.8070 (pmm) outliers start: 0 outliers final: 0 residues processed: 1359 average time/residue: 0.4207 time to fit residues: 929.1320 Evaluate side-chains 1180 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1180 time to evaluate : 3.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 3.9990 chunk 361 optimal weight: 5.9990 chunk 330 optimal weight: 9.9990 chunk 352 optimal weight: 9.9990 chunk 211 optimal weight: 8.9990 chunk 153 optimal weight: 4.9990 chunk 276 optimal weight: 0.8980 chunk 108 optimal weight: 9.9990 chunk 318 optimal weight: 2.9990 chunk 332 optimal weight: 2.9990 chunk 350 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 HIS ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 303 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 HIS ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 507 HIS ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 32212 Z= 0.358 Angle : 0.878 10.867 43712 Z= 0.442 Chirality : 0.053 0.364 4984 Planarity : 0.005 0.148 5452 Dihedral : 15.517 179.901 5344 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 31.68 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.71 % Favored : 89.26 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.97 (0.12), residues: 3968 helix: -1.76 (0.13), residues: 1194 sheet: -2.90 (0.21), residues: 436 loop : -1.91 (0.13), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.002 HIS H 92 PHE 0.021 0.002 PHE C 131 TYR 0.026 0.002 TYR H 32 ARG 0.015 0.001 ARG D 322 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1358 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1358 time to evaluate : 3.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8880 (t70) cc_final: 0.8522 (t70) REVERT: A 32 TYR cc_start: 0.8980 (m-10) cc_final: 0.8771 (m-10) REVERT: A 36 LEU cc_start: 0.9046 (tp) cc_final: 0.8839 (tp) REVERT: A 38 LEU cc_start: 0.9671 (mm) cc_final: 0.8892 (mm) REVERT: A 48 GLN cc_start: 0.9289 (mt0) cc_final: 0.8805 (mt0) REVERT: A 58 LYS cc_start: 0.9396 (mttm) cc_final: 0.8994 (mttm) REVERT: A 78 MET cc_start: 0.9230 (tpp) cc_final: 0.8816 (tpp) REVERT: A 179 MET cc_start: 0.7155 (pmm) cc_final: 0.6884 (pmm) REVERT: A 231 ARG cc_start: 0.9333 (ptm160) cc_final: 0.9075 (ptm-80) REVERT: A 246 CYS cc_start: 0.9471 (t) cc_final: 0.8568 (p) REVERT: A 254 GLU cc_start: 0.9415 (tp30) cc_final: 0.9173 (pm20) REVERT: A 258 TYR cc_start: 0.9606 (t80) cc_final: 0.9372 (t80) REVERT: A 273 LEU cc_start: 0.9435 (tt) cc_final: 0.9035 (tt) REVERT: A 294 TYR cc_start: 0.9239 (m-80) cc_final: 0.8969 (m-80) REVERT: A 332 ILE cc_start: 0.9384 (pt) cc_final: 0.9118 (pt) REVERT: A 335 GLU cc_start: 0.8475 (mp0) cc_final: 0.7936 (mp0) REVERT: A 343 GLN cc_start: 0.8405 (pp30) cc_final: 0.7951 (pp30) REVERT: A 352 GLU cc_start: 0.9195 (tm-30) cc_final: 0.8805 (tm-30) REVERT: A 356 ARG cc_start: 0.9052 (mtt180) cc_final: 0.8719 (mtt-85) REVERT: A 375 LYS cc_start: 0.9682 (pttt) cc_final: 0.9365 (pttt) REVERT: A 385 MET cc_start: 0.8875 (ttp) cc_final: 0.8393 (ttp) REVERT: A 386 MET cc_start: 0.8405 (ppp) cc_final: 0.7898 (ppp) REVERT: A 420 MET cc_start: 0.8439 (mtm) cc_final: 0.8025 (mtp) REVERT: A 469 GLN cc_start: 0.9059 (tp40) cc_final: 0.8740 (tt0) REVERT: A 482 MET cc_start: 0.9127 (ttt) cc_final: 0.8897 (ttt) REVERT: A 483 MET cc_start: 0.9566 (tmm) cc_final: 0.9057 (tmm) REVERT: A 488 LEU cc_start: 0.9222 (pt) cc_final: 0.8996 (pp) REVERT: A 509 TYR cc_start: 0.9097 (p90) cc_final: 0.8211 (p90) REVERT: B 18 LEU cc_start: 0.9528 (tp) cc_final: 0.9301 (tp) REVERT: B 32 TYR cc_start: 0.8665 (m-80) cc_final: 0.8324 (m-80) REVERT: B 34 ASP cc_start: 0.8482 (m-30) cc_final: 0.7964 (m-30) REVERT: B 36 LEU cc_start: 0.9359 (tp) cc_final: 0.8950 (tp) REVERT: B 37 ILE cc_start: 0.9373 (mm) cc_final: 0.8955 (mm) REVERT: B 41 TYR cc_start: 0.9177 (t80) cc_final: 0.8857 (t80) REVERT: B 103 GLU cc_start: 0.9448 (mm-30) cc_final: 0.9041 (mm-30) REVERT: B 108 LYS cc_start: 0.9412 (pttm) cc_final: 0.8625 (tppt) REVERT: B 131 PHE cc_start: 0.9328 (m-80) cc_final: 0.8758 (m-80) REVERT: B 132 GLU cc_start: 0.9603 (pt0) cc_final: 0.9287 (pt0) REVERT: B 134 LYS cc_start: 0.9688 (pttm) cc_final: 0.9483 (pmtt) REVERT: B 181 LYS cc_start: 0.9105 (tppt) cc_final: 0.8728 (tppt) REVERT: B 185 LEU cc_start: 0.8853 (mt) cc_final: 0.8466 (mt) REVERT: B 199 GLU cc_start: 0.9506 (pp20) cc_final: 0.9039 (pp20) REVERT: B 200 ILE cc_start: 0.9682 (mt) cc_final: 0.9430 (mm) REVERT: B 224 ARG cc_start: 0.8986 (ttt180) cc_final: 0.8655 (ttt180) REVERT: B 250 ILE cc_start: 0.9246 (mp) cc_final: 0.8630 (tp) REVERT: B 334 GLN cc_start: 0.9153 (mt0) cc_final: 0.8844 (mm-40) REVERT: B 335 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8228 (tm-30) REVERT: B 348 TYR cc_start: 0.9404 (t80) cc_final: 0.8931 (t80) REVERT: B 352 GLU cc_start: 0.8766 (pm20) cc_final: 0.8223 (pm20) REVERT: B 372 HIS cc_start: 0.9084 (m170) cc_final: 0.8538 (m170) REVERT: B 399 GLU cc_start: 0.8090 (mp0) cc_final: 0.7861 (pm20) REVERT: B 403 SER cc_start: 0.9377 (t) cc_final: 0.9176 (t) REVERT: B 404 ASP cc_start: 0.8826 (t0) cc_final: 0.8576 (t0) REVERT: B 482 MET cc_start: 0.8937 (ptp) cc_final: 0.8682 (ptp) REVERT: B 491 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8078 (tm-30) REVERT: C 47 ASP cc_start: 0.9688 (m-30) cc_final: 0.9143 (p0) REVERT: C 78 MET cc_start: 0.9284 (mmp) cc_final: 0.8873 (mmt) REVERT: C 82 MET cc_start: 0.9574 (tpp) cc_final: 0.9207 (tpp) REVERT: C 90 PHE cc_start: 0.9179 (m-80) cc_final: 0.8550 (m-80) REVERT: C 111 GLU cc_start: 0.9363 (tp30) cc_final: 0.9095 (mp0) REVERT: C 199 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8785 (tp30) REVERT: C 200 ILE cc_start: 0.9358 (mm) cc_final: 0.9145 (mm) REVERT: C 229 LYS cc_start: 0.9383 (ptpp) cc_final: 0.9022 (mmmt) REVERT: C 290 ILE cc_start: 0.9404 (pt) cc_final: 0.9112 (pt) REVERT: C 333 THR cc_start: 0.9680 (p) cc_final: 0.9448 (p) REVERT: C 334 GLN cc_start: 0.9054 (mp10) cc_final: 0.8657 (mp10) REVERT: C 335 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8294 (tm-30) REVERT: C 349 LYS cc_start: 0.9011 (mtpt) cc_final: 0.8462 (mtpt) REVERT: C 386 MET cc_start: 0.9059 (tmm) cc_final: 0.8532 (tmm) REVERT: C 390 LEU cc_start: 0.9370 (pt) cc_final: 0.9107 (pt) REVERT: C 482 MET cc_start: 0.9369 (tpp) cc_final: 0.8972 (tpp) REVERT: C 487 GLU cc_start: 0.8502 (pm20) cc_final: 0.8228 (pm20) REVERT: D 12 TYR cc_start: 0.8059 (t80) cc_final: 0.7292 (m-80) REVERT: D 16 ASP cc_start: 0.8392 (m-30) cc_final: 0.8173 (m-30) REVERT: D 21 GLN cc_start: 0.8840 (tm-30) cc_final: 0.7878 (tm-30) REVERT: D 25 ASN cc_start: 0.8603 (m110) cc_final: 0.8328 (m110) REVERT: D 32 TYR cc_start: 0.9088 (m-80) cc_final: 0.8763 (m-10) REVERT: D 36 LEU cc_start: 0.9237 (pt) cc_final: 0.9031 (pt) REVERT: D 38 LEU cc_start: 0.9462 (mt) cc_final: 0.9261 (mt) REVERT: D 71 ASP cc_start: 0.9583 (t0) cc_final: 0.9187 (t0) REVERT: D 91 ILE cc_start: 0.9286 (tp) cc_final: 0.9062 (tp) REVERT: D 164 ASP cc_start: 0.8995 (t0) cc_final: 0.8780 (p0) REVERT: D 175 LEU cc_start: 0.8003 (mt) cc_final: 0.7744 (mt) REVERT: D 242 LYS cc_start: 0.9417 (mmpt) cc_final: 0.9208 (mmmt) REVERT: D 258 TYR cc_start: 0.9512 (t80) cc_final: 0.9300 (t80) REVERT: D 289 TYR cc_start: 0.9388 (t80) cc_final: 0.9148 (t80) REVERT: D 290 ILE cc_start: 0.9772 (pt) cc_final: 0.9395 (pt) REVERT: D 335 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8719 (tm-30) REVERT: D 349 LYS cc_start: 0.9543 (mmmm) cc_final: 0.9328 (mmmm) REVERT: D 352 GLU cc_start: 0.9227 (tm-30) cc_final: 0.8948 (tm-30) REVERT: D 364 ASP cc_start: 0.6383 (m-30) cc_final: 0.6092 (m-30) REVERT: D 385 MET cc_start: 0.8783 (tpt) cc_final: 0.8045 (tpt) REVERT: D 386 MET cc_start: 0.8809 (ptm) cc_final: 0.8566 (ptm) REVERT: D 400 TYR cc_start: 0.7916 (m-80) cc_final: 0.7533 (m-80) REVERT: D 410 LYS cc_start: 0.9209 (mptt) cc_final: 0.8934 (mptt) REVERT: D 414 MET cc_start: 0.8800 (pmm) cc_final: 0.8586 (pmm) REVERT: D 441 GLN cc_start: 0.7516 (mp-120) cc_final: 0.7173 (mp-120) REVERT: D 465 GLN cc_start: 0.9081 (tt0) cc_final: 0.8713 (tt0) REVERT: D 478 GLN cc_start: 0.9439 (mt0) cc_final: 0.9034 (mt0) REVERT: D 482 MET cc_start: 0.9419 (tpp) cc_final: 0.8681 (tpt) REVERT: D 487 GLU cc_start: 0.9065 (pm20) cc_final: 0.8532 (pm20) REVERT: D 491 GLU cc_start: 0.8837 (tp30) cc_final: 0.8511 (tm-30) REVERT: D 492 LYS cc_start: 0.9292 (pttt) cc_final: 0.8988 (pttt) REVERT: N 12 TYR cc_start: 0.8787 (t80) cc_final: 0.8395 (t80) REVERT: P 1 MET cc_start: 0.8531 (mpp) cc_final: 0.8223 (pmm) REVERT: E 15 ASP cc_start: 0.8346 (p0) cc_final: 0.8090 (p0) REVERT: E 28 ASP cc_start: 0.9095 (t70) cc_final: 0.8643 (t70) REVERT: E 32 TYR cc_start: 0.9369 (m-80) cc_final: 0.8539 (m-80) REVERT: E 38 LEU cc_start: 0.9666 (mm) cc_final: 0.8939 (mm) REVERT: E 48 GLN cc_start: 0.9181 (mt0) cc_final: 0.8661 (mt0) REVERT: E 82 MET cc_start: 0.9523 (ttp) cc_final: 0.9169 (ttp) REVERT: E 105 ARG cc_start: 0.9117 (mmm160) cc_final: 0.8601 (tpm170) REVERT: E 108 LYS cc_start: 0.9541 (tppt) cc_final: 0.8943 (mmtt) REVERT: E 150 MET cc_start: 0.7807 (tpt) cc_final: 0.7294 (tpt) REVERT: E 158 ILE cc_start: 0.8922 (mm) cc_final: 0.8475 (tp) REVERT: E 165 PHE cc_start: 0.8646 (p90) cc_final: 0.8377 (p90) REVERT: E 179 MET cc_start: 0.7748 (pmm) cc_final: 0.7171 (pmm) REVERT: E 228 LYS cc_start: 0.9500 (ptpp) cc_final: 0.9285 (ptpp) REVERT: E 244 LEU cc_start: 0.9531 (pt) cc_final: 0.9281 (pt) REVERT: E 246 CYS cc_start: 0.9480 (t) cc_final: 0.9042 (t) REVERT: E 250 ILE cc_start: 0.9459 (pt) cc_final: 0.9166 (pt) REVERT: E 254 GLU cc_start: 0.9610 (tp30) cc_final: 0.9367 (tp30) REVERT: E 269 ASP cc_start: 0.8171 (m-30) cc_final: 0.7847 (m-30) REVERT: E 288 LYS cc_start: 0.9477 (mtmm) cc_final: 0.9224 (mttt) REVERT: E 294 TYR cc_start: 0.9305 (m-80) cc_final: 0.8949 (m-80) REVERT: E 306 THR cc_start: 0.9440 (p) cc_final: 0.8717 (p) REVERT: E 325 MET cc_start: 0.8976 (ptm) cc_final: 0.8562 (ptm) REVERT: E 332 ILE cc_start: 0.9463 (pt) cc_final: 0.9191 (pt) REVERT: E 335 GLU cc_start: 0.8644 (mp0) cc_final: 0.8103 (mp0) REVERT: E 352 GLU cc_start: 0.9140 (tm-30) cc_final: 0.8826 (tm-30) REVERT: E 355 ARG cc_start: 0.9005 (ptm160) cc_final: 0.8654 (ptt90) REVERT: E 356 ARG cc_start: 0.8984 (mtt180) cc_final: 0.8571 (mtt-85) REVERT: E 375 LYS cc_start: 0.9686 (pttt) cc_final: 0.9290 (pttt) REVERT: E 385 MET cc_start: 0.8546 (ttp) cc_final: 0.7865 (ttp) REVERT: E 386 MET cc_start: 0.8452 (ppp) cc_final: 0.8092 (tmm) REVERT: E 420 MET cc_start: 0.8392 (mtm) cc_final: 0.7919 (mtp) REVERT: E 454 HIS cc_start: 0.8799 (m90) cc_final: 0.8490 (m90) REVERT: E 482 MET cc_start: 0.9023 (ttt) cc_final: 0.8793 (ttt) REVERT: E 483 MET cc_start: 0.9508 (tmm) cc_final: 0.9001 (tmm) REVERT: E 488 LEU cc_start: 0.9212 (pt) cc_final: 0.8978 (pp) REVERT: E 507 HIS cc_start: 0.8875 (t-90) cc_final: 0.8651 (t70) REVERT: E 509 TYR cc_start: 0.9121 (p90) cc_final: 0.8882 (p90) REVERT: F 25 ASN cc_start: 0.9047 (m-40) cc_final: 0.8704 (m110) REVERT: F 31 THR cc_start: 0.8442 (m) cc_final: 0.8148 (m) REVERT: F 34 ASP cc_start: 0.8436 (m-30) cc_final: 0.8112 (m-30) REVERT: F 37 ILE cc_start: 0.9212 (mm) cc_final: 0.8759 (mm) REVERT: F 70 MET cc_start: 0.8173 (tpp) cc_final: 0.7792 (mmm) REVERT: F 103 GLU cc_start: 0.9605 (tp30) cc_final: 0.9137 (tp30) REVERT: F 108 LYS cc_start: 0.9297 (pttm) cc_final: 0.8021 (tppt) REVERT: F 131 PHE cc_start: 0.9504 (m-80) cc_final: 0.8372 (m-80) REVERT: F 132 GLU cc_start: 0.9508 (pt0) cc_final: 0.9141 (pt0) REVERT: F 134 LYS cc_start: 0.9441 (pttt) cc_final: 0.9048 (tttt) REVERT: F 179 MET cc_start: 0.6458 (ppp) cc_final: 0.6117 (ppp) REVERT: F 185 LEU cc_start: 0.8770 (mt) cc_final: 0.8211 (mt) REVERT: F 281 ILE cc_start: 0.9530 (tp) cc_final: 0.9231 (tp) REVERT: F 287 ILE cc_start: 0.9517 (pt) cc_final: 0.9293 (pt) REVERT: F 332 ILE cc_start: 0.9285 (pt) cc_final: 0.9068 (pt) REVERT: F 335 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8075 (tm-30) REVERT: F 352 GLU cc_start: 0.8567 (pm20) cc_final: 0.8301 (pm20) REVERT: F 355 ARG cc_start: 0.8368 (ppt170) cc_final: 0.7977 (ttp-170) REVERT: F 372 HIS cc_start: 0.9172 (m170) cc_final: 0.8591 (m170) REVERT: F 404 ASP cc_start: 0.8822 (t0) cc_final: 0.8509 (t0) REVERT: G 74 THR cc_start: 0.6602 (t) cc_final: 0.6184 (t) REVERT: G 78 MET cc_start: 0.9592 (tpp) cc_final: 0.9161 (tpp) REVERT: G 82 MET cc_start: 0.9690 (tpp) cc_final: 0.9392 (tpp) REVERT: G 150 MET cc_start: 0.8971 (mmp) cc_final: 0.8637 (tpp) REVERT: G 222 ILE cc_start: 0.7646 (mm) cc_final: 0.7388 (mm) REVERT: G 229 LYS cc_start: 0.9354 (ptpp) cc_final: 0.9110 (mmmt) REVERT: G 287 ILE cc_start: 0.9672 (mp) cc_final: 0.9183 (tt) REVERT: G 291 LYS cc_start: 0.9071 (ptpp) cc_final: 0.8630 (pttm) REVERT: G 333 THR cc_start: 0.9682 (p) cc_final: 0.9440 (p) REVERT: G 334 GLN cc_start: 0.9045 (mp10) cc_final: 0.8561 (mp10) REVERT: G 335 GLU cc_start: 0.8828 (tm-30) cc_final: 0.8206 (tm-30) REVERT: G 336 VAL cc_start: 0.9537 (m) cc_final: 0.8591 (m) REVERT: G 343 GLN cc_start: 0.9157 (pm20) cc_final: 0.8919 (pm20) REVERT: G 385 MET cc_start: 0.7077 (ttt) cc_final: 0.6487 (ttt) REVERT: G 386 MET cc_start: 0.9144 (tmm) cc_final: 0.8535 (tmm) REVERT: G 390 LEU cc_start: 0.9172 (pt) cc_final: 0.8962 (pt) REVERT: G 395 GLU cc_start: 0.8801 (mp0) cc_final: 0.8463 (mp0) REVERT: G 411 TYR cc_start: 0.9539 (t80) cc_final: 0.9279 (t80) REVERT: G 482 MET cc_start: 0.9303 (tpp) cc_final: 0.8868 (mmm) REVERT: H 21 GLN cc_start: 0.9148 (tp-100) cc_final: 0.8588 (tp40) REVERT: H 25 ASN cc_start: 0.8608 (m110) cc_final: 0.8066 (m110) REVERT: H 38 LEU cc_start: 0.9467 (mt) cc_final: 0.9256 (mt) REVERT: H 91 ILE cc_start: 0.9282 (tp) cc_final: 0.8900 (tp) REVERT: H 112 GLN cc_start: 0.9298 (tm-30) cc_final: 0.9025 (tm-30) REVERT: H 258 TYR cc_start: 0.9564 (t80) cc_final: 0.9318 (t80) REVERT: H 286 MET cc_start: 0.9590 (tpt) cc_final: 0.9326 (tpt) REVERT: H 289 TYR cc_start: 0.9477 (t80) cc_final: 0.9268 (t80) REVERT: H 311 LYS cc_start: 0.9231 (ttpt) cc_final: 0.8747 (ttpt) REVERT: H 315 ASP cc_start: 0.9532 (m-30) cc_final: 0.8947 (p0) REVERT: H 335 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8650 (tm-30) REVERT: H 352 GLU cc_start: 0.9253 (tm-30) cc_final: 0.8988 (tm-30) REVERT: H 379 LEU cc_start: 0.9671 (mm) cc_final: 0.9464 (mm) REVERT: H 385 MET cc_start: 0.8750 (tpt) cc_final: 0.8136 (tpt) REVERT: H 414 MET cc_start: 0.9017 (pmm) cc_final: 0.8537 (pmm) REVERT: H 418 ASP cc_start: 0.9442 (t70) cc_final: 0.9218 (t0) REVERT: H 465 GLN cc_start: 0.8595 (pp30) cc_final: 0.8275 (tt0) REVERT: H 478 GLN cc_start: 0.9450 (mt0) cc_final: 0.9010 (mt0) REVERT: H 482 MET cc_start: 0.9247 (tpp) cc_final: 0.8909 (tpt) REVERT: J 12 TYR cc_start: 0.8891 (t80) cc_final: 0.7998 (t80) REVERT: L 1 MET cc_start: 0.8392 (mpp) cc_final: 0.8114 (pmm) outliers start: 0 outliers final: 0 residues processed: 1358 average time/residue: 0.3958 time to fit residues: 869.6428 Evaluate side-chains 1147 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1147 time to evaluate : 3.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 0.0270 chunk 372 optimal weight: 0.6980 chunk 227 optimal weight: 2.9990 chunk 176 optimal weight: 3.9990 chunk 258 optimal weight: 0.0970 chunk 390 optimal weight: 9.9990 chunk 359 optimal weight: 0.0070 chunk 310 optimal weight: 0.2980 chunk 32 optimal weight: 2.9990 chunk 240 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 overall best weight: 0.2254 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 466 HIS B 507 HIS ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 454 HIS ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 HIS F 21 GLN F 171 HIS ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 507 HIS ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 ASN ** G 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 HIS ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 454 HIS ** H 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32212 Z= 0.203 Angle : 0.858 15.570 43712 Z= 0.416 Chirality : 0.052 0.339 4984 Planarity : 0.005 0.114 5452 Dihedral : 14.857 160.248 5344 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 22.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.13), residues: 3968 helix: -1.64 (0.13), residues: 1166 sheet: -2.38 (0.23), residues: 372 loop : -1.73 (0.13), residues: 2430 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 92 PHE 0.024 0.002 PHE F 456 TYR 0.029 0.002 TYR G 110 ARG 0.020 0.001 ARG D 322 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7936 Ramachandran restraints generated. 3968 Oldfield, 0 Emsley, 3968 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1417 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1417 time to evaluate : 3.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8933 (t70) cc_final: 0.8673 (t70) REVERT: A 32 TYR cc_start: 0.8892 (m-10) cc_final: 0.8413 (m-10) REVERT: A 36 LEU cc_start: 0.8879 (tp) cc_final: 0.8306 (tp) REVERT: A 38 LEU cc_start: 0.9523 (mm) cc_final: 0.8767 (mm) REVERT: A 48 GLN cc_start: 0.9239 (mt0) cc_final: 0.8826 (mt0) REVERT: A 108 LYS cc_start: 0.9610 (tppt) cc_final: 0.9218 (mmtt) REVERT: A 150 MET cc_start: 0.8026 (tpt) cc_final: 0.7349 (tpt) REVERT: A 179 MET cc_start: 0.7138 (pmm) cc_final: 0.6907 (pmm) REVERT: A 231 ARG cc_start: 0.9331 (ptm160) cc_final: 0.9021 (ptm-80) REVERT: A 254 GLU cc_start: 0.9444 (tp30) cc_final: 0.9223 (pm20) REVERT: A 273 LEU cc_start: 0.9388 (tt) cc_final: 0.9037 (tt) REVERT: A 284 ILE cc_start: 0.9428 (pt) cc_final: 0.9184 (pt) REVERT: A 288 LYS cc_start: 0.9547 (mtmm) cc_final: 0.9317 (ptpt) REVERT: A 294 TYR cc_start: 0.9174 (m-80) cc_final: 0.8834 (m-80) REVERT: A 332 ILE cc_start: 0.9197 (pt) cc_final: 0.8929 (pt) REVERT: A 335 GLU cc_start: 0.8473 (mp0) cc_final: 0.7927 (mp0) REVERT: A 343 GLN cc_start: 0.8504 (pp30) cc_final: 0.7695 (pp30) REVERT: A 356 ARG cc_start: 0.8813 (mtt180) cc_final: 0.8388 (mtp85) REVERT: A 372 HIS cc_start: 0.9184 (m170) cc_final: 0.8466 (m90) REVERT: A 386 MET cc_start: 0.8482 (ppp) cc_final: 0.8218 (ppp) REVERT: A 420 MET cc_start: 0.8371 (mtm) cc_final: 0.7932 (mtp) REVERT: A 449 ASP cc_start: 0.8224 (t0) cc_final: 0.6726 (t0) REVERT: A 469 GLN cc_start: 0.8938 (tp40) cc_final: 0.8735 (tt0) REVERT: A 482 MET cc_start: 0.9065 (ttt) cc_final: 0.8829 (ttt) REVERT: A 483 MET cc_start: 0.9482 (tmm) cc_final: 0.8947 (tmm) REVERT: A 509 TYR cc_start: 0.9025 (p90) cc_final: 0.8750 (p90) REVERT: B 16 ASP cc_start: 0.7574 (t0) cc_final: 0.6571 (t0) REVERT: B 18 LEU cc_start: 0.9370 (tp) cc_final: 0.9132 (tp) REVERT: B 34 ASP cc_start: 0.8307 (m-30) cc_final: 0.7848 (m-30) REVERT: B 36 LEU cc_start: 0.9469 (tp) cc_final: 0.9190 (tp) REVERT: B 37 ILE cc_start: 0.9252 (mm) cc_final: 0.8865 (mm) REVERT: B 41 TYR cc_start: 0.9146 (t80) cc_final: 0.8719 (t80) REVERT: B 103 GLU cc_start: 0.9423 (mm-30) cc_final: 0.9065 (mm-30) REVERT: B 108 LYS cc_start: 0.9283 (pttm) cc_final: 0.8507 (tptt) REVERT: B 131 PHE cc_start: 0.9318 (m-80) cc_final: 0.8754 (m-80) REVERT: B 132 GLU cc_start: 0.9547 (pt0) cc_final: 0.9262 (pp20) REVERT: B 134 LYS cc_start: 0.9697 (pttm) cc_final: 0.9479 (pttt) REVERT: B 185 LEU cc_start: 0.8819 (mt) cc_final: 0.8459 (mt) REVERT: B 229 LYS cc_start: 0.9531 (mtpt) cc_final: 0.9310 (mtmt) REVERT: B 238 LYS cc_start: 0.8913 (mmmt) cc_final: 0.8668 (tppt) REVERT: B 250 ILE cc_start: 0.9232 (mp) cc_final: 0.8969 (tp) REVERT: B 281 ILE cc_start: 0.9515 (tp) cc_final: 0.9175 (tp) REVERT: B 334 GLN cc_start: 0.9129 (mt0) cc_final: 0.8718 (mm-40) REVERT: B 335 GLU cc_start: 0.8617 (tm-30) cc_final: 0.8292 (tm-30) REVERT: B 337 LEU cc_start: 0.9374 (mm) cc_final: 0.9152 (mm) REVERT: B 352 GLU cc_start: 0.8841 (pm20) cc_final: 0.8428 (pm20) REVERT: B 355 ARG cc_start: 0.8434 (ppt170) cc_final: 0.7945 (ttp-170) REVERT: B 372 HIS cc_start: 0.8861 (m170) cc_final: 0.8658 (m90) REVERT: B 399 GLU cc_start: 0.7737 (mp0) cc_final: 0.7496 (mp0) REVERT: B 404 ASP cc_start: 0.8700 (t0) cc_final: 0.8427 (t0) REVERT: B 438 LYS cc_start: 0.8509 (mmtt) cc_final: 0.7842 (mtpt) REVERT: B 441 GLN cc_start: 0.8987 (mt0) cc_final: 0.8478 (mt0) REVERT: B 449 ASP cc_start: 0.8615 (t70) cc_final: 0.8238 (t70) REVERT: C 32 TYR cc_start: 0.8873 (m-10) cc_final: 0.8410 (m-10) REVERT: C 47 ASP cc_start: 0.9678 (m-30) cc_final: 0.9035 (p0) REVERT: C 50 ASP cc_start: 0.8626 (t70) cc_final: 0.8416 (t0) REVERT: C 66 VAL cc_start: 0.9554 (p) cc_final: 0.8941 (p) REVERT: C 78 MET cc_start: 0.9389 (mmp) cc_final: 0.9030 (mmt) REVERT: C 82 MET cc_start: 0.9579 (tpp) cc_final: 0.9282 (tpp) REVERT: C 90 PHE cc_start: 0.9203 (m-80) cc_final: 0.8449 (m-80) REVERT: C 199 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8600 (tp30) REVERT: C 200 ILE cc_start: 0.9348 (mm) cc_final: 0.8917 (mm) REVERT: C 203 ARG cc_start: 0.8865 (mtm-85) cc_final: 0.8337 (mtm110) REVERT: C 229 LYS cc_start: 0.9405 (ptpp) cc_final: 0.9091 (mmmt) REVERT: C 274 ASP cc_start: 0.8998 (t0) cc_final: 0.8419 (t70) REVERT: C 306 THR cc_start: 0.9114 (t) cc_final: 0.8811 (t) REVERT: C 331 CYS cc_start: 0.8944 (t) cc_final: 0.8700 (t) REVERT: C 333 THR cc_start: 0.9672 (p) cc_final: 0.9225 (p) REVERT: C 334 GLN cc_start: 0.8966 (mp10) cc_final: 0.8377 (mp10) REVERT: C 335 GLU cc_start: 0.8682 (tm-30) cc_final: 0.8023 (tm-30) REVERT: C 343 GLN cc_start: 0.8841 (pm20) cc_final: 0.8581 (pm20) REVERT: C 349 LYS cc_start: 0.9007 (mtpt) cc_final: 0.8563 (mtmt) REVERT: C 386 MET cc_start: 0.8982 (tmm) cc_final: 0.8431 (tmm) REVERT: C 390 LEU cc_start: 0.9054 (pt) cc_final: 0.8819 (pt) REVERT: C 441 GLN cc_start: 0.8365 (mp-120) cc_final: 0.8075 (mp10) REVERT: C 482 MET cc_start: 0.9352 (tpp) cc_final: 0.8839 (tpp) REVERT: D 12 TYR cc_start: 0.7978 (t80) cc_final: 0.7250 (m-80) REVERT: D 21 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8003 (tm-30) REVERT: D 25 ASN cc_start: 0.8658 (m110) cc_final: 0.8253 (m110) REVERT: D 32 TYR cc_start: 0.9057 (m-80) cc_final: 0.8800 (m-10) REVERT: D 71 ASP cc_start: 0.9619 (t0) cc_final: 0.8791 (t0) REVERT: D 91 ILE cc_start: 0.9160 (tp) cc_final: 0.8885 (tp) REVERT: D 215 ASP cc_start: 0.9507 (m-30) cc_final: 0.9044 (p0) REVERT: D 242 LYS cc_start: 0.9353 (mmpt) cc_final: 0.9116 (mmmt) REVERT: D 283 GLN cc_start: 0.8730 (mt0) cc_final: 0.8468 (mt0) REVERT: D 286 MET cc_start: 0.9586 (tpt) cc_final: 0.9367 (tpt) REVERT: D 289 TYR cc_start: 0.9385 (t80) cc_final: 0.9128 (t80) REVERT: D 290 ILE cc_start: 0.9770 (pt) cc_final: 0.9367 (pt) REVERT: D 332 ILE cc_start: 0.8963 (tp) cc_final: 0.8255 (tp) REVERT: D 335 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8456 (tm-30) REVERT: D 352 GLU cc_start: 0.9220 (tm-30) cc_final: 0.8944 (tm-30) REVERT: D 385 MET cc_start: 0.8732 (tpt) cc_final: 0.7833 (tpt) REVERT: D 386 MET cc_start: 0.8290 (ptm) cc_final: 0.7900 (ptm) REVERT: D 400 TYR cc_start: 0.7831 (m-80) cc_final: 0.7600 (m-80) REVERT: D 410 LYS cc_start: 0.9146 (mptt) cc_final: 0.8795 (mptt) REVERT: D 414 MET cc_start: 0.8534 (pmm) cc_final: 0.8251 (pmm) REVERT: D 453 ILE cc_start: 0.9718 (pt) cc_final: 0.9281 (pt) REVERT: D 465 GLN cc_start: 0.9083 (tt0) cc_final: 0.8820 (mm-40) REVERT: D 478 GLN cc_start: 0.9469 (mt0) cc_final: 0.8995 (mt0) REVERT: D 482 MET cc_start: 0.9207 (tpp) cc_final: 0.8768 (tpt) REVERT: O 1 MET cc_start: 0.8369 (mmp) cc_final: 0.8136 (tpp) REVERT: P 1 MET cc_start: 0.8400 (mpp) cc_final: 0.8189 (pmm) REVERT: E 28 ASP cc_start: 0.9047 (t70) cc_final: 0.8549 (t70) REVERT: E 32 TYR cc_start: 0.9238 (m-80) cc_final: 0.8555 (m-80) REVERT: E 36 LEU cc_start: 0.8657 (tp) cc_final: 0.8442 (tp) REVERT: E 38 LEU cc_start: 0.9547 (mm) cc_final: 0.8749 (mm) REVERT: E 45 THR cc_start: 0.8954 (p) cc_final: 0.8556 (t) REVERT: E 48 GLN cc_start: 0.9159 (mt0) cc_final: 0.8786 (mt0) REVERT: E 82 MET cc_start: 0.9535 (ttp) cc_final: 0.9169 (ttp) REVERT: E 105 ARG cc_start: 0.9016 (mmm160) cc_final: 0.8518 (tpm170) REVERT: E 106 LYS cc_start: 0.8880 (ptpp) cc_final: 0.8348 (ptpt) REVERT: E 108 LYS cc_start: 0.9494 (tppt) cc_final: 0.8911 (mmtt) REVERT: E 150 MET cc_start: 0.7720 (tpt) cc_final: 0.7508 (tpt) REVERT: E 158 ILE cc_start: 0.8976 (mm) cc_final: 0.8562 (tp) REVERT: E 165 PHE cc_start: 0.8437 (p90) cc_final: 0.8159 (p90) REVERT: E 179 MET cc_start: 0.7681 (pmm) cc_final: 0.7204 (pmm) REVERT: E 228 LYS cc_start: 0.9503 (ptpp) cc_final: 0.9273 (ptpp) REVERT: E 244 LEU cc_start: 0.9463 (pt) cc_final: 0.9171 (pt) REVERT: E 246 CYS cc_start: 0.9487 (t) cc_final: 0.9257 (t) REVERT: E 254 GLU cc_start: 0.9354 (tp30) cc_final: 0.8994 (pm20) REVERT: E 288 LYS cc_start: 0.9527 (mtmm) cc_final: 0.9296 (mttt) REVERT: E 294 TYR cc_start: 0.9224 (m-80) cc_final: 0.8823 (m-80) REVERT: E 306 THR cc_start: 0.9463 (p) cc_final: 0.8857 (p) REVERT: E 319 ASP cc_start: 0.7666 (t70) cc_final: 0.7011 (t70) REVERT: E 332 ILE cc_start: 0.9303 (pt) cc_final: 0.9051 (pt) REVERT: E 335 GLU cc_start: 0.8662 (mp0) cc_final: 0.8079 (mp0) REVERT: E 341 ARG cc_start: 0.9522 (ptm160) cc_final: 0.8803 (ptm160) REVERT: E 345 THR cc_start: 0.9434 (p) cc_final: 0.9054 (p) REVERT: E 353 TYR cc_start: 0.8814 (t80) cc_final: 0.8480 (t80) REVERT: E 355 ARG cc_start: 0.8879 (ptm160) cc_final: 0.8635 (ptt90) REVERT: E 356 ARG cc_start: 0.8875 (mtt180) cc_final: 0.8455 (mtp85) REVERT: E 357 PHE cc_start: 0.9172 (m-80) cc_final: 0.8952 (m-10) REVERT: E 364 ASP cc_start: 0.8501 (m-30) cc_final: 0.8120 (m-30) REVERT: E 368 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8080 (mm-40) REVERT: E 375 LYS cc_start: 0.9571 (pttt) cc_final: 0.9293 (pttt) REVERT: E 386 MET cc_start: 0.8557 (ppp) cc_final: 0.8297 (tmm) REVERT: E 420 MET cc_start: 0.8381 (mtm) cc_final: 0.7881 (mtp) REVERT: E 454 HIS cc_start: 0.8787 (m90) cc_final: 0.8493 (m90) REVERT: E 482 MET cc_start: 0.8935 (ttt) cc_final: 0.8709 (ttt) REVERT: E 483 MET cc_start: 0.9318 (tmm) cc_final: 0.8946 (tmm) REVERT: E 507 HIS cc_start: 0.8751 (t-90) cc_final: 0.8545 (t70) REVERT: F 18 LEU cc_start: 0.9215 (tp) cc_final: 0.8995 (tp) REVERT: F 34 ASP cc_start: 0.8250 (m-30) cc_final: 0.7936 (m-30) REVERT: F 37 ILE cc_start: 0.8940 (mm) cc_final: 0.8595 (mm) REVERT: F 70 MET cc_start: 0.7943 (tpp) cc_final: 0.6972 (tpt) REVERT: F 82 MET cc_start: 0.9444 (ttt) cc_final: 0.9201 (ttt) REVERT: F 103 GLU cc_start: 0.9532 (tp30) cc_final: 0.9084 (tp30) REVERT: F 131 PHE cc_start: 0.9485 (m-80) cc_final: 0.8350 (m-80) REVERT: F 132 GLU cc_start: 0.9431 (pt0) cc_final: 0.9094 (pt0) REVERT: F 134 LYS cc_start: 0.9368 (pttt) cc_final: 0.9022 (tttt) REVERT: F 179 MET cc_start: 0.6438 (ppp) cc_final: 0.6158 (ppp) REVERT: F 185 LEU cc_start: 0.8778 (mt) cc_final: 0.8209 (mt) REVERT: F 199 GLU cc_start: 0.9552 (mt-10) cc_final: 0.9351 (mt-10) REVERT: F 238 LYS cc_start: 0.9039 (mmmm) cc_final: 0.8774 (tppt) REVERT: F 274 ASP cc_start: 0.9040 (t0) cc_final: 0.8765 (t0) REVERT: F 281 ILE cc_start: 0.9523 (tp) cc_final: 0.9199 (tp) REVERT: F 322 ARG cc_start: 0.8382 (ttt-90) cc_final: 0.8120 (ttt180) REVERT: F 334 GLN cc_start: 0.9210 (mt0) cc_final: 0.8904 (mm-40) REVERT: F 355 ARG cc_start: 0.8286 (ppt170) cc_final: 0.7902 (ttt180) REVERT: F 372 HIS cc_start: 0.8909 (m170) cc_final: 0.8574 (m90) REVERT: F 388 SER cc_start: 0.8516 (p) cc_final: 0.8246 (p) REVERT: F 404 ASP cc_start: 0.8590 (t0) cc_final: 0.8331 (t0) REVERT: F 449 ASP cc_start: 0.8564 (t70) cc_final: 0.8236 (t70) REVERT: F 493 ARG cc_start: 0.8603 (ptt-90) cc_final: 0.8291 (ptt-90) REVERT: F 508 SER cc_start: 0.9367 (p) cc_final: 0.8894 (m) REVERT: G 47 ASP cc_start: 0.9676 (m-30) cc_final: 0.9105 (p0) REVERT: G 78 MET cc_start: 0.9568 (tpp) cc_final: 0.9164 (tpp) REVERT: G 82 MET cc_start: 0.9657 (tpp) cc_final: 0.9431 (tpp) REVERT: G 150 MET cc_start: 0.8984 (mmp) cc_final: 0.8451 (tpp) REVERT: G 216 ASP cc_start: 0.9253 (m-30) cc_final: 0.8979 (t70) REVERT: G 222 ILE cc_start: 0.7430 (mm) cc_final: 0.7108 (mm) REVERT: G 229 LYS cc_start: 0.9381 (ptpp) cc_final: 0.9080 (mmmt) REVERT: G 274 ASP cc_start: 0.9014 (t0) cc_final: 0.8589 (t70) REVERT: G 291 LYS cc_start: 0.8996 (ptpp) cc_final: 0.8776 (pttm) REVERT: G 333 THR cc_start: 0.9640 (p) cc_final: 0.9333 (p) REVERT: G 334 GLN cc_start: 0.8879 (mp10) cc_final: 0.8372 (mp10) REVERT: G 335 GLU cc_start: 0.8628 (tm-30) cc_final: 0.7903 (tm-30) REVERT: G 336 VAL cc_start: 0.9341 (m) cc_final: 0.8281 (m) REVERT: G 343 GLN cc_start: 0.9028 (pm20) cc_final: 0.8754 (pm20) REVERT: G 385 MET cc_start: 0.6482 (ttt) cc_final: 0.5912 (ttt) REVERT: G 386 MET cc_start: 0.9027 (tmm) cc_final: 0.8439 (tmm) REVERT: G 395 GLU cc_start: 0.8835 (mp0) cc_final: 0.8631 (mp0) REVERT: G 441 GLN cc_start: 0.8384 (mp-120) cc_final: 0.8009 (mp10) REVERT: G 482 MET cc_start: 0.9313 (tpp) cc_final: 0.8887 (mmm) REVERT: G 504 HIS cc_start: 0.8648 (p90) cc_final: 0.8359 (p90) REVERT: H 21 GLN cc_start: 0.9091 (tp-100) cc_final: 0.8498 (tp40) REVERT: H 25 ASN cc_start: 0.8458 (m110) cc_final: 0.7939 (m110) REVERT: H 26 CYS cc_start: 0.8701 (m) cc_final: 0.8464 (m) REVERT: H 62 LYS cc_start: 0.9332 (mmtt) cc_final: 0.8887 (mtpp) REVERT: H 91 ILE cc_start: 0.9309 (tp) cc_final: 0.8958 (tp) REVERT: H 112 GLN cc_start: 0.9171 (tm-30) cc_final: 0.8924 (tm-30) REVERT: H 158 ILE cc_start: 0.6624 (tp) cc_final: 0.5865 (tp) REVERT: H 179 MET cc_start: 0.7154 (ptm) cc_final: 0.4709 (tmm) REVERT: H 229 LYS cc_start: 0.8883 (pttt) cc_final: 0.8669 (mmtt) REVERT: H 286 MET cc_start: 0.9590 (tpt) cc_final: 0.9311 (tpt) REVERT: H 289 TYR cc_start: 0.9469 (t80) cc_final: 0.9259 (t80) REVERT: H 315 ASP cc_start: 0.9473 (m-30) cc_final: 0.8860 (p0) REVERT: H 352 GLU cc_start: 0.9224 (tm-30) cc_final: 0.8954 (tm-30) REVERT: H 385 MET cc_start: 0.8107 (tpt) cc_final: 0.7194 (tpt) REVERT: H 386 MET cc_start: 0.7109 (ptm) cc_final: 0.6554 (ppp) REVERT: H 400 TYR cc_start: 0.6584 (m-80) cc_final: 0.6373 (m-80) REVERT: H 410 LYS cc_start: 0.9186 (mptt) cc_final: 0.8937 (mmtm) REVERT: H 414 MET cc_start: 0.8566 (pmm) cc_final: 0.8176 (pmm) REVERT: H 453 ILE cc_start: 0.9633 (pt) cc_final: 0.9176 (pt) REVERT: H 465 GLN cc_start: 0.8535 (pp30) cc_final: 0.8178 (tt0) REVERT: H 478 GLN cc_start: 0.9475 (mt0) cc_final: 0.9037 (mt0) REVERT: H 482 MET cc_start: 0.9143 (tpp) cc_final: 0.8792 (tpt) REVERT: I 1 MET cc_start: 0.7274 (mtp) cc_final: 0.6696 (ttm) REVERT: K 1 MET cc_start: 0.8423 (mmp) cc_final: 0.8188 (tpp) outliers start: 0 outliers final: 0 residues processed: 1417 average time/residue: 0.4117 time to fit residues: 944.7783 Evaluate side-chains 1210 residues out of total 3272 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1210 time to evaluate : 3.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 2.9990 chunk 331 optimal weight: 0.1980 chunk 95 optimal weight: 0.9990 chunk 286 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 311 optimal weight: 0.3980 chunk 130 optimal weight: 2.9990 chunk 319 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 57 optimal weight: 0.2980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 343 GLN B 466 HIS B 507 HIS ** C 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 279 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 HIS ** D 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 21 GLN ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 466 HIS F 507 HIS ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN ** G 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 HIS ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.127515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.091036 restraints weight = 73744.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.094887 restraints weight = 41811.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.097574 restraints weight = 27733.349| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.4697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 32212 Z= 0.208 Angle : 0.855 13.940 43712 Z= 0.414 Chirality : 0.051 0.324 4984 Planarity : 0.005 0.142 5452 Dihedral : 14.493 159.404 5344 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 23.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.25 % Favored : 90.73 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.12), residues: 3968 helix: -1.66 (0.13), residues: 1188 sheet: -2.54 (0.22), residues: 424 loop : -1.75 (0.13), residues: 2356 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS G 92 PHE 0.037 0.002 PHE B 456 TYR 0.042 0.002 TYR E 110 ARG 0.021 0.001 ARG D 322 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12626.00 seconds wall clock time: 224 minutes 53.31 seconds (13493.31 seconds total)