Starting phenix.real_space_refine on Sat Mar 16 22:57:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g8z_4362/03_2024/6g8z_4362.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g8z_4362/03_2024/6g8z_4362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g8z_4362/03_2024/6g8z_4362.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g8z_4362/03_2024/6g8z_4362.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g8z_4362/03_2024/6g8z_4362.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6g8z_4362/03_2024/6g8z_4362.pdb" } resolution = 3.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 10530 2.51 5 N 2562 2.21 5 O 2772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 148": "NH1" <-> "NH2" Residue "A ARG 262": "NH1" <-> "NH2" Residue "A ARG 306": "NH1" <-> "NH2" Residue "A ARG 345": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B ARG 148": "NH1" <-> "NH2" Residue "B ARG 262": "NH1" <-> "NH2" Residue "B ARG 306": "NH1" <-> "NH2" Residue "B ARG 345": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 389": "NH1" <-> "NH2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C ARG 148": "NH1" <-> "NH2" Residue "C ARG 262": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C ARG 345": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 389": "NH1" <-> "NH2" Residue "D ARG 18": "NH1" <-> "NH2" Residue "D ARG 148": "NH1" <-> "NH2" Residue "D ARG 262": "NH1" <-> "NH2" Residue "D ARG 306": "NH1" <-> "NH2" Residue "D ARG 345": "NH1" <-> "NH2" Residue "D ARG 357": "NH1" <-> "NH2" Residue "D ARG 389": "NH1" <-> "NH2" Residue "E ARG 18": "NH1" <-> "NH2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "E ARG 262": "NH1" <-> "NH2" Residue "E ARG 306": "NH1" <-> "NH2" Residue "E ARG 345": "NH1" <-> "NH2" Residue "E ARG 357": "NH1" <-> "NH2" Residue "E ARG 389": "NH1" <-> "NH2" Residue "F ARG 18": "NH1" <-> "NH2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "F ARG 262": "NH1" <-> "NH2" Residue "F ARG 306": "NH1" <-> "NH2" Residue "F ARG 345": "NH1" <-> "NH2" Residue "F ARG 357": "NH1" <-> "NH2" Residue "F ARG 389": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15966 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2661 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain breaks: 2 Chain: "B" Number of atoms: 2661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2661 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain breaks: 2 Chain: "C" Number of atoms: 2661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2661 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain breaks: 2 Chain: "D" Number of atoms: 2661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2661 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain breaks: 2 Chain: "E" Number of atoms: 2661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2661 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain breaks: 2 Chain: "F" Number of atoms: 2661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2661 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 9, 'TRANS': 308} Chain breaks: 2 Time building chain proxies: 8.49, per 1000 atoms: 0.53 Number of scatterers: 15966 At special positions: 0 Unit cell: (104.275, 104.275, 132.225, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 2772 8.00 N 2562 7.00 C 10530 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.55 Conformation dependent library (CDL) restraints added in 2.7 seconds 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3708 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 6 sheets defined 74.8% alpha, 5.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 22 through 50 Processing helix chain 'A' and resid 102 through 116 removed outlier: 3.627A pdb=" N TYR A 106 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 146 removed outlier: 3.631A pdb=" N LYS A 123 " --> pdb=" O HIS A 119 " (cutoff:3.500A) Proline residue: A 126 - end of helix removed outlier: 5.398A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 3.981A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 176 removed outlier: 4.027A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 3.559A pdb=" N GLU A 245 " --> pdb=" O LYS A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 286 removed outlier: 4.188A pdb=" N ARG A 262 " --> pdb=" O ASP A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 314 through 347 removed outlier: 3.736A pdb=" N SER A 347 " --> pdb=" O MET A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 removed outlier: 4.011A pdb=" N ARG A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 removed outlier: 3.685A pdb=" N LEU A 376 " --> pdb=" O PHE A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 395 removed outlier: 3.773A pdb=" N VAL A 392 " --> pdb=" O LYS A 388 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE A 393 " --> pdb=" O ARG A 389 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU A 394 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 408 removed outlier: 3.675A pdb=" N GLU A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN A 404 " --> pdb=" O ASN A 400 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 405 " --> pdb=" O LYS A 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 50 Processing helix chain 'B' and resid 102 through 116 removed outlier: 3.627A pdb=" N TYR B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN B 107 " --> pdb=" O ARG B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 146 removed outlier: 3.630A pdb=" N LYS B 123 " --> pdb=" O HIS B 119 " (cutoff:3.500A) Proline residue: B 126 - end of helix removed outlier: 5.398A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 165 removed outlier: 3.981A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 176 removed outlier: 4.028A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 176 " --> pdb=" O ALA B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 removed outlier: 3.559A pdb=" N GLU B 245 " --> pdb=" O LYS B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 286 removed outlier: 4.189A pdb=" N ARG B 262 " --> pdb=" O ASP B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 314 through 347 removed outlier: 3.737A pdb=" N SER B 347 " --> pdb=" O MET B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 removed outlier: 4.011A pdb=" N ARG B 357 " --> pdb=" O PHE B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 removed outlier: 3.685A pdb=" N LEU B 376 " --> pdb=" O PHE B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 395 removed outlier: 3.772A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE B 393 " --> pdb=" O ARG B 389 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU B 394 " --> pdb=" O PHE B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 408 removed outlier: 3.675A pdb=" N GLU B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN B 404 " --> pdb=" O ASN B 400 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 405 " --> pdb=" O LYS B 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 50 Processing helix chain 'C' and resid 102 through 116 removed outlier: 3.627A pdb=" N TYR C 106 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN C 107 " --> pdb=" O ARG C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 146 removed outlier: 3.630A pdb=" N LYS C 123 " --> pdb=" O HIS C 119 " (cutoff:3.500A) Proline residue: C 126 - end of helix removed outlier: 5.399A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 165 removed outlier: 3.982A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 176 removed outlier: 4.028A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR C 176 " --> pdb=" O ALA C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 removed outlier: 3.559A pdb=" N GLU C 245 " --> pdb=" O LYS C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 286 removed outlier: 4.189A pdb=" N ARG C 262 " --> pdb=" O ASP C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 314 through 347 removed outlier: 3.737A pdb=" N SER C 347 " --> pdb=" O MET C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 removed outlier: 4.011A pdb=" N ARG C 357 " --> pdb=" O PHE C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 383 removed outlier: 3.686A pdb=" N LEU C 376 " --> pdb=" O PHE C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 395 removed outlier: 3.772A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU C 394 " --> pdb=" O PHE C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 408 removed outlier: 3.675A pdb=" N GLU C 399 " --> pdb=" O SER C 395 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN C 404 " --> pdb=" O ASN C 400 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU C 405 " --> pdb=" O LYS C 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 50 Processing helix chain 'D' and resid 102 through 116 removed outlier: 3.626A pdb=" N TYR D 106 " --> pdb=" O ASP D 102 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN D 107 " --> pdb=" O ARG D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 146 removed outlier: 3.631A pdb=" N LYS D 123 " --> pdb=" O HIS D 119 " (cutoff:3.500A) Proline residue: D 126 - end of helix removed outlier: 5.399A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 165 removed outlier: 3.982A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 176 removed outlier: 4.027A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR D 176 " --> pdb=" O ALA D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 removed outlier: 3.559A pdb=" N GLU D 245 " --> pdb=" O LYS D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 286 removed outlier: 4.188A pdb=" N ARG D 262 " --> pdb=" O ASP D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 314 through 347 removed outlier: 3.737A pdb=" N SER D 347 " --> pdb=" O MET D 343 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 361 removed outlier: 4.011A pdb=" N ARG D 357 " --> pdb=" O PHE D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 383 removed outlier: 3.685A pdb=" N LEU D 376 " --> pdb=" O PHE D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 395 removed outlier: 3.773A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE D 393 " --> pdb=" O ARG D 389 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU D 394 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 408 removed outlier: 3.675A pdb=" N GLU D 399 " --> pdb=" O SER D 395 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN D 404 " --> pdb=" O ASN D 400 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU D 405 " --> pdb=" O LYS D 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 50 Processing helix chain 'E' and resid 102 through 116 removed outlier: 3.628A pdb=" N TYR E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN E 107 " --> pdb=" O ARG E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 146 removed outlier: 3.632A pdb=" N LYS E 123 " --> pdb=" O HIS E 119 " (cutoff:3.500A) Proline residue: E 126 - end of helix removed outlier: 5.398A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 165 removed outlier: 3.981A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 176 removed outlier: 4.027A pdb=" N ARG E 171 " --> pdb=" O PRO E 167 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR E 176 " --> pdb=" O ALA E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 3.560A pdb=" N GLU E 245 " --> pdb=" O LYS E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 286 removed outlier: 4.189A pdb=" N ARG E 262 " --> pdb=" O ASP E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 314 through 347 removed outlier: 3.737A pdb=" N SER E 347 " --> pdb=" O MET E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 353 through 361 removed outlier: 4.011A pdb=" N ARG E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 383 removed outlier: 3.685A pdb=" N LEU E 376 " --> pdb=" O PHE E 372 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 395 removed outlier: 3.772A pdb=" N VAL E 392 " --> pdb=" O LYS E 388 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE E 393 " --> pdb=" O ARG E 389 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU E 394 " --> pdb=" O PHE E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 408 removed outlier: 3.675A pdb=" N GLU E 399 " --> pdb=" O SER E 395 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN E 404 " --> pdb=" O ASN E 400 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU E 405 " --> pdb=" O LYS E 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 50 Processing helix chain 'F' and resid 102 through 116 removed outlier: 3.626A pdb=" N TYR F 106 " --> pdb=" O ASP F 102 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASN F 107 " --> pdb=" O ARG F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 146 removed outlier: 3.631A pdb=" N LYS F 123 " --> pdb=" O HIS F 119 " (cutoff:3.500A) Proline residue: F 126 - end of helix removed outlier: 5.398A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 165 removed outlier: 3.981A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 176 removed outlier: 4.027A pdb=" N ARG F 171 " --> pdb=" O PRO F 167 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR F 176 " --> pdb=" O ALA F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 255 removed outlier: 3.560A pdb=" N GLU F 245 " --> pdb=" O LYS F 241 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 286 removed outlier: 4.190A pdb=" N ARG F 262 " --> pdb=" O ASP F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 289 No H-bonds generated for 'chain 'F' and resid 287 through 289' Processing helix chain 'F' and resid 314 through 347 removed outlier: 3.738A pdb=" N SER F 347 " --> pdb=" O MET F 343 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 361 removed outlier: 4.011A pdb=" N ARG F 357 " --> pdb=" O PHE F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 383 removed outlier: 3.685A pdb=" N LEU F 376 " --> pdb=" O PHE F 372 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 395 removed outlier: 3.772A pdb=" N VAL F 392 " --> pdb=" O LYS F 388 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N PHE F 393 " --> pdb=" O ARG F 389 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU F 394 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 408 removed outlier: 3.676A pdb=" N GLU F 399 " --> pdb=" O SER F 395 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN F 404 " --> pdb=" O ASN F 400 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU F 405 " --> pdb=" O LYS F 401 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 56 removed outlier: 8.829A pdb=" N ARG A 306 " --> pdb=" O VAL A 297 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL A 297 " --> pdb=" O ARG A 306 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 56 removed outlier: 8.828A pdb=" N ARG B 306 " --> pdb=" O VAL B 297 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL B 297 " --> pdb=" O ARG B 306 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 56 removed outlier: 8.828A pdb=" N ARG C 306 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL C 297 " --> pdb=" O ARG C 306 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 56 removed outlier: 8.827A pdb=" N ARG D 306 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL D 297 " --> pdb=" O ARG D 306 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 56 removed outlier: 8.828A pdb=" N ARG E 306 " --> pdb=" O VAL E 297 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N VAL E 297 " --> pdb=" O ARG E 306 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 56 removed outlier: 8.829A pdb=" N ARG F 306 " --> pdb=" O VAL F 297 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL F 297 " --> pdb=" O ARG F 306 " (cutoff:3.500A) 1038 hydrogen bonds defined for protein. 3096 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: 4.27 Time building geometry restraints manager: 6.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4752 1.34 - 1.46: 4260 1.46 - 1.58: 7260 1.58 - 1.70: 0 1.70 - 1.82: 144 Bond restraints: 16416 Sorted by residual: bond pdb=" N ASP B 50 " pdb=" CA ASP B 50 " ideal model delta sigma weight residual 1.457 1.480 -0.022 1.29e-02 6.01e+03 3.00e+00 bond pdb=" N ASP E 50 " pdb=" CA ASP E 50 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.29e-02 6.01e+03 2.91e+00 bond pdb=" N ASP F 50 " pdb=" CA ASP F 50 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.29e-02 6.01e+03 2.88e+00 bond pdb=" N ASP D 50 " pdb=" CA ASP D 50 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.29e-02 6.01e+03 2.82e+00 bond pdb=" N ASP C 50 " pdb=" CA ASP C 50 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.29e-02 6.01e+03 2.81e+00 ... (remaining 16411 not shown) Histogram of bond angle deviations from ideal: 100.35 - 107.10: 390 107.10 - 113.86: 8984 113.86 - 120.61: 7309 120.61 - 127.36: 5349 127.36 - 134.12: 198 Bond angle restraints: 22230 Sorted by residual: angle pdb=" N ASP E 371 " pdb=" CA ASP E 371 " pdb=" CB ASP E 371 " ideal model delta sigma weight residual 114.17 110.18 3.99 1.14e+00 7.69e-01 1.22e+01 angle pdb=" N ASP C 371 " pdb=" CA ASP C 371 " pdb=" CB ASP C 371 " ideal model delta sigma weight residual 114.17 110.20 3.97 1.14e+00 7.69e-01 1.21e+01 angle pdb=" N ASP D 371 " pdb=" CA ASP D 371 " pdb=" CB ASP D 371 " ideal model delta sigma weight residual 114.17 110.22 3.95 1.14e+00 7.69e-01 1.20e+01 angle pdb=" N ASP B 371 " pdb=" CA ASP B 371 " pdb=" CB ASP B 371 " ideal model delta sigma weight residual 114.17 110.23 3.94 1.14e+00 7.69e-01 1.19e+01 angle pdb=" N ASP F 371 " pdb=" CA ASP F 371 " pdb=" CB ASP F 371 " ideal model delta sigma weight residual 114.17 110.24 3.93 1.14e+00 7.69e-01 1.19e+01 ... (remaining 22225 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 9252 16.16 - 32.31: 342 32.31 - 48.47: 78 48.47 - 64.63: 0 64.63 - 80.79: 6 Dihedral angle restraints: 9678 sinusoidal: 3948 harmonic: 5730 Sorted by residual: dihedral pdb=" CB CYS D 57 " pdb=" SG CYS D 57 " pdb=" SG CYS D 65 " pdb=" CB CYS D 65 " ideal model delta sinusoidal sigma weight residual 93.00 173.79 -80.79 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS B 57 " pdb=" SG CYS B 57 " pdb=" SG CYS B 65 " pdb=" CB CYS B 65 " ideal model delta sinusoidal sigma weight residual 93.00 173.78 -80.78 1 1.00e+01 1.00e-02 8.06e+01 dihedral pdb=" CB CYS A 57 " pdb=" SG CYS A 57 " pdb=" SG CYS A 65 " pdb=" CB CYS A 65 " ideal model delta sinusoidal sigma weight residual 93.00 173.76 -80.76 1 1.00e+01 1.00e-02 8.06e+01 ... (remaining 9675 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2078 0.061 - 0.123: 340 0.123 - 0.184: 24 0.184 - 0.245: 0 0.245 - 0.307: 6 Chirality restraints: 2448 Sorted by residual: chirality pdb=" CB THR D 92 " pdb=" CA THR D 92 " pdb=" OG1 THR D 92 " pdb=" CG2 THR D 92 " both_signs ideal model delta sigma weight residual False 2.55 2.24 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CB THR F 92 " pdb=" CA THR F 92 " pdb=" OG1 THR F 92 " pdb=" CG2 THR F 92 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CB THR B 92 " pdb=" CA THR B 92 " pdb=" OG1 THR B 92 " pdb=" CG2 THR B 92 " both_signs ideal model delta sigma weight residual False 2.55 2.25 0.31 2.00e-01 2.50e+01 2.34e+00 ... (remaining 2445 not shown) Planarity restraints: 2688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 21 " -0.041 5.00e-02 4.00e+02 6.04e-02 5.84e+00 pdb=" N PRO E 22 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO E 22 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 22 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS D 21 " -0.041 5.00e-02 4.00e+02 6.04e-02 5.83e+00 pdb=" N PRO D 22 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO D 22 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO D 22 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 21 " -0.041 5.00e-02 4.00e+02 6.04e-02 5.83e+00 pdb=" N PRO F 22 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO F 22 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO F 22 " -0.033 5.00e-02 4.00e+02 ... (remaining 2685 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 5319 2.87 - 3.38: 16657 3.38 - 3.88: 24681 3.88 - 4.39: 26984 4.39 - 4.90: 47089 Nonbonded interactions: 120730 Sorted by model distance: nonbonded pdb=" OE2 GLU A 115 " pdb=" OG1 THR B 316 " model vdw 2.362 2.440 nonbonded pdb=" O PHE B 324 " pdb=" OG SER B 327 " model vdw 2.403 2.440 nonbonded pdb=" O PHE D 324 " pdb=" OG SER D 327 " model vdw 2.404 2.440 nonbonded pdb=" O PHE A 324 " pdb=" OG SER A 327 " model vdw 2.404 2.440 nonbonded pdb=" O PHE E 324 " pdb=" OG SER E 327 " model vdw 2.404 2.440 ... (remaining 120725 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 1.130 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: 0.010 Extract box with map and model: 6.680 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 41.040 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.070 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:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 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 : 0.005 0.039 16416 Z= 0.331 Angle : 0.774 8.118 22230 Z= 0.431 Chirality : 0.045 0.307 2448 Planarity : 0.005 0.060 2688 Dihedral : 8.701 44.834 5916 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 0.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.18), residues: 1872 helix: -0.18 (0.12), residues: 1266 sheet: 1.28 (0.47), residues: 96 loop : -1.02 (0.31), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 24 HIS 0.011 0.002 HIS E 132 PHE 0.040 0.003 PHE E 136 TYR 0.010 0.002 TYR C 106 ARG 0.008 0.001 ARG F 262 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 371 ASP cc_start: 0.7993 (t70) cc_final: 0.7793 (t0) REVERT: B 383 ASP cc_start: 0.7829 (t0) cc_final: 0.7401 (p0) REVERT: C 154 GLU cc_start: 0.7389 (pp20) cc_final: 0.7173 (pp20) REVERT: C 383 ASP cc_start: 0.8136 (t0) cc_final: 0.7300 (p0) REVERT: D 154 GLU cc_start: 0.7433 (pp20) cc_final: 0.7123 (pp20) REVERT: D 383 ASP cc_start: 0.8050 (t0) cc_final: 0.7288 (p0) REVERT: E 33 ILE cc_start: 0.8471 (mm) cc_final: 0.8181 (mm) REVERT: E 102 ASP cc_start: 0.7869 (m-30) cc_final: 0.7588 (p0) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 0.2249 time to fit residues: 88.6971 Evaluate side-chains 128 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.8980 chunk 140 optimal weight: 0.9980 chunk 78 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 145 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 88 optimal weight: 9.9990 chunk 108 optimal weight: 4.9990 chunk 168 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 267 GLN ** A 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 GLN B 404 GLN C 267 GLN C 404 GLN D 267 GLN ** D 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 267 GLN ** E 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 GLN F 267 GLN F 404 GLN ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16416 Z= 0.171 Angle : 0.510 5.296 22230 Z= 0.288 Chirality : 0.039 0.151 2448 Planarity : 0.004 0.054 2688 Dihedral : 4.269 19.907 2112 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.19 % Allowed : 4.58 % Favored : 94.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.19), residues: 1872 helix: 1.53 (0.14), residues: 1290 sheet: 2.16 (0.53), residues: 96 loop : -0.94 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 143 HIS 0.006 0.001 HIS B 253 PHE 0.022 0.002 PHE A 136 TYR 0.021 0.001 TYR E 281 ARG 0.002 0.000 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 MET cc_start: 0.8000 (mtp) cc_final: 0.7776 (ttm) REVERT: A 239 GLN cc_start: 0.7696 (mm-40) cc_final: 0.7359 (mm110) REVERT: A 353 PHE cc_start: 0.7021 (OUTLIER) cc_final: 0.6370 (t80) REVERT: A 404 GLN cc_start: 0.8586 (mm-40) cc_final: 0.8304 (mm110) REVERT: B 353 PHE cc_start: 0.7322 (OUTLIER) cc_final: 0.6713 (t80) REVERT: B 371 ASP cc_start: 0.7815 (t70) cc_final: 0.7527 (t0) REVERT: B 404 GLN cc_start: 0.8437 (mm-40) cc_final: 0.8179 (mm110) REVERT: C 110 ASP cc_start: 0.8065 (t0) cc_final: 0.7830 (t0) REVERT: C 154 GLU cc_start: 0.7495 (pp20) cc_final: 0.7216 (pp20) REVERT: C 353 PHE cc_start: 0.7068 (OUTLIER) cc_final: 0.6464 (t80) REVERT: D 154 GLU cc_start: 0.7522 (pp20) cc_final: 0.7220 (pp20) REVERT: F 110 ASP cc_start: 0.8161 (t0) cc_final: 0.7932 (t0) REVERT: F 404 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8637 (mm110) outliers start: 21 outliers final: 9 residues processed: 182 average time/residue: 0.2295 time to fit residues: 67.3749 Evaluate side-chains 130 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 118 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 353 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 182 optimal weight: 0.7980 chunk 150 optimal weight: 9.9990 chunk 167 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 135 optimal weight: 0.4980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 267 GLN C 267 GLN C 404 GLN D 267 GLN E 267 GLN E 404 GLN F 267 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 16416 Z= 0.308 Angle : 0.567 5.514 22230 Z= 0.316 Chirality : 0.041 0.157 2448 Planarity : 0.004 0.053 2688 Dihedral : 4.404 20.332 2112 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.03 % Allowed : 8.31 % Favored : 89.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.20), residues: 1872 helix: 1.80 (0.14), residues: 1302 sheet: 1.80 (0.55), residues: 102 loop : -0.94 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP F 143 HIS 0.005 0.002 HIS B 253 PHE 0.020 0.002 PHE F 353 TYR 0.018 0.002 TYR E 281 ARG 0.006 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 133 time to evaluate : 1.707 Fit side-chains REVERT: A 265 MET cc_start: 0.8141 (mmm) cc_final: 0.7813 (mmm) REVERT: A 353 PHE cc_start: 0.7754 (OUTLIER) cc_final: 0.7159 (t80) REVERT: B 104 HIS cc_start: 0.8781 (OUTLIER) cc_final: 0.7997 (t-90) REVERT: B 353 PHE cc_start: 0.7939 (OUTLIER) cc_final: 0.7327 (t80) REVERT: C 239 GLN cc_start: 0.8215 (mm-40) cc_final: 0.8013 (mm-40) REVERT: C 353 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.6914 (t80) REVERT: D 353 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.6727 (t80) REVERT: E 104 HIS cc_start: 0.8216 (OUTLIER) cc_final: 0.7694 (t-90) REVERT: E 239 GLN cc_start: 0.8011 (mm110) cc_final: 0.7722 (mm-40) REVERT: E 353 PHE cc_start: 0.7245 (OUTLIER) cc_final: 0.6867 (t80) REVERT: F 52 MET cc_start: 0.8352 (mtp) cc_final: 0.8101 (ttt) REVERT: F 239 GLN cc_start: 0.8362 (mm-40) cc_final: 0.8129 (mm-40) REVERT: F 353 PHE cc_start: 0.7616 (OUTLIER) cc_final: 0.7041 (t80) outliers start: 36 outliers final: 20 residues processed: 167 average time/residue: 0.2396 time to fit residues: 63.0864 Evaluate side-chains 139 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 111 time to evaluate : 1.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 353 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 87 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 169 optimal weight: 9.9990 chunk 179 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 160 optimal weight: 0.4980 chunk 48 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 GLN B 267 GLN B 404 GLN C 267 GLN D 267 GLN E 267 GLN E 404 GLN F 267 GLN F 404 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16416 Z= 0.157 Angle : 0.472 9.327 22230 Z= 0.261 Chirality : 0.038 0.156 2448 Planarity : 0.003 0.050 2688 Dihedral : 4.053 18.676 2112 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.69 % Allowed : 12.32 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.20), residues: 1872 helix: 2.11 (0.14), residues: 1302 sheet: 2.43 (0.52), residues: 96 loop : -0.99 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 341 HIS 0.006 0.001 HIS B 253 PHE 0.015 0.001 PHE E 393 TYR 0.015 0.001 TYR E 281 ARG 0.001 0.000 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 142 time to evaluate : 1.988 Fit side-chains REVERT: A 353 PHE cc_start: 0.7708 (OUTLIER) cc_final: 0.6900 (t80) REVERT: B 104 HIS cc_start: 0.8591 (OUTLIER) cc_final: 0.7070 (t-90) REVERT: B 353 PHE cc_start: 0.7866 (OUTLIER) cc_final: 0.7286 (t80) REVERT: C 353 PHE cc_start: 0.7622 (OUTLIER) cc_final: 0.6767 (t80) REVERT: D 353 PHE cc_start: 0.7949 (OUTLIER) cc_final: 0.6796 (t80) REVERT: E 104 HIS cc_start: 0.8031 (OUTLIER) cc_final: 0.6619 (t-90) REVERT: E 353 PHE cc_start: 0.7174 (OUTLIER) cc_final: 0.6901 (t80) REVERT: F 353 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.7003 (t80) outliers start: 30 outliers final: 11 residues processed: 170 average time/residue: 0.2155 time to fit residues: 60.8935 Evaluate side-chains 135 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain F residue 353 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 153 optimal weight: 2.9990 chunk 124 optimal weight: 0.0270 chunk 0 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 161 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 GLN B 404 GLN C 404 GLN E 404 GLN F 404 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16416 Z= 0.178 Angle : 0.488 9.138 22230 Z= 0.263 Chirality : 0.038 0.149 2448 Planarity : 0.003 0.048 2688 Dihedral : 3.939 16.993 2112 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.81 % Allowed : 14.18 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.20), residues: 1872 helix: 2.19 (0.14), residues: 1302 sheet: 2.59 (0.53), residues: 96 loop : -0.91 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 341 HIS 0.006 0.001 HIS E 253 PHE 0.014 0.001 PHE E 393 TYR 0.014 0.001 TYR A 281 ARG 0.002 0.000 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 123 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 353 PHE cc_start: 0.7947 (OUTLIER) cc_final: 0.6755 (t80) REVERT: B 104 HIS cc_start: 0.8617 (OUTLIER) cc_final: 0.7058 (t-90) REVERT: B 353 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.7464 (t80) REVERT: C 353 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.6859 (t80) REVERT: D 353 PHE cc_start: 0.8067 (OUTLIER) cc_final: 0.6838 (t80) REVERT: E 46 GLN cc_start: 0.7727 (tm-30) cc_final: 0.7377 (tm-30) REVERT: E 104 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.6545 (t-90) REVERT: E 353 PHE cc_start: 0.7306 (OUTLIER) cc_final: 0.6983 (t80) REVERT: F 37 MET cc_start: 0.8499 (mtp) cc_final: 0.8076 (ttm) REVERT: F 353 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.7025 (t80) outliers start: 32 outliers final: 20 residues processed: 150 average time/residue: 0.2193 time to fit residues: 54.2014 Evaluate side-chains 142 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 114 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain B residue 37 MET Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 353 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 0.8980 chunk 161 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 179 optimal weight: 3.9990 chunk 149 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 94 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 GLN C 404 GLN E 404 GLN F 404 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16416 Z= 0.176 Angle : 0.476 8.002 22230 Z= 0.259 Chirality : 0.037 0.145 2448 Planarity : 0.003 0.047 2688 Dihedral : 3.867 16.910 2112 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.26 % Allowed : 14.07 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.19), residues: 1872 helix: 2.24 (0.14), residues: 1302 sheet: 2.63 (0.53), residues: 96 loop : -0.77 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 341 HIS 0.006 0.001 HIS B 253 PHE 0.014 0.001 PHE E 393 TYR 0.012 0.001 TYR B 281 ARG 0.002 0.000 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 132 time to evaluate : 1.910 Fit side-chains revert: symmetry clash REVERT: A 239 GLN cc_start: 0.7894 (mm110) cc_final: 0.7515 (mm110) REVERT: A 353 PHE cc_start: 0.8023 (OUTLIER) cc_final: 0.6549 (t80) REVERT: B 104 HIS cc_start: 0.8636 (OUTLIER) cc_final: 0.7166 (t-90) REVERT: B 353 PHE cc_start: 0.8078 (OUTLIER) cc_final: 0.7535 (t80) REVERT: C 37 MET cc_start: 0.8460 (OUTLIER) cc_final: 0.8091 (ttm) REVERT: C 353 PHE cc_start: 0.7805 (OUTLIER) cc_final: 0.6884 (t80) REVERT: D 353 PHE cc_start: 0.8112 (OUTLIER) cc_final: 0.6831 (t80) REVERT: E 104 HIS cc_start: 0.8032 (OUTLIER) cc_final: 0.6585 (t-90) REVERT: E 239 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7808 (mm110) REVERT: E 353 PHE cc_start: 0.7290 (OUTLIER) cc_final: 0.6958 (t80) REVERT: F 37 MET cc_start: 0.8502 (mtp) cc_final: 0.8243 (ttm) REVERT: F 353 PHE cc_start: 0.7922 (OUTLIER) cc_final: 0.7102 (t80) outliers start: 40 outliers final: 24 residues processed: 167 average time/residue: 0.2302 time to fit residues: 61.9347 Evaluate side-chains 148 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 115 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 353 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 131 optimal weight: 0.8980 chunk 101 optimal weight: 0.2980 chunk 151 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 GLN C 404 GLN E 404 GLN F 404 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16416 Z= 0.171 Angle : 0.483 8.296 22230 Z= 0.263 Chirality : 0.037 0.145 2448 Planarity : 0.003 0.046 2688 Dihedral : 3.803 16.846 2112 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.15 % Allowed : 14.75 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.19), residues: 1872 helix: 2.30 (0.14), residues: 1302 sheet: 2.66 (0.53), residues: 96 loop : -0.67 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 24 HIS 0.006 0.001 HIS B 253 PHE 0.013 0.001 PHE F 353 TYR 0.012 0.001 TYR B 281 ARG 0.001 0.000 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 130 time to evaluate : 1.515 Fit side-chains revert: symmetry clash REVERT: A 239 GLN cc_start: 0.7967 (mm110) cc_final: 0.7605 (mm110) REVERT: A 274 LYS cc_start: 0.8388 (ttpt) cc_final: 0.8142 (ttpp) REVERT: A 353 PHE cc_start: 0.8105 (OUTLIER) cc_final: 0.6564 (t80) REVERT: B 104 HIS cc_start: 0.8631 (OUTLIER) cc_final: 0.7087 (t-90) REVERT: B 353 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7580 (t80) REVERT: C 37 MET cc_start: 0.8463 (OUTLIER) cc_final: 0.8087 (ttm) REVERT: C 353 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7017 (t80) REVERT: D 353 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.6910 (t80) REVERT: E 104 HIS cc_start: 0.8020 (OUTLIER) cc_final: 0.6494 (t-90) REVERT: E 239 GLN cc_start: 0.8144 (mm-40) cc_final: 0.7834 (mm110) REVERT: E 353 PHE cc_start: 0.7363 (OUTLIER) cc_final: 0.6973 (t80) REVERT: F 37 MET cc_start: 0.8483 (mtp) cc_final: 0.8095 (ttm) REVERT: F 239 GLN cc_start: 0.8217 (mm-40) cc_final: 0.7952 (mm-40) REVERT: F 353 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7115 (t80) outliers start: 38 outliers final: 25 residues processed: 163 average time/residue: 0.2374 time to fit residues: 61.8907 Evaluate side-chains 148 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 114 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 353 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 0.0870 chunk 34 optimal weight: 0.9980 chunk 113 optimal weight: 0.2980 chunk 122 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 GLN C 404 GLN E 404 GLN F 404 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 16416 Z= 0.156 Angle : 0.471 7.259 22230 Z= 0.257 Chirality : 0.037 0.144 2448 Planarity : 0.003 0.046 2688 Dihedral : 3.751 16.679 2112 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.20 % Allowed : 15.14 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.19), residues: 1872 helix: 2.35 (0.14), residues: 1302 sheet: 2.69 (0.54), residues: 96 loop : -0.61 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 24 HIS 0.006 0.001 HIS B 253 PHE 0.020 0.001 PHE D 136 TYR 0.011 0.001 TYR B 281 ARG 0.001 0.000 ARG C 306 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 125 time to evaluate : 1.830 Fit side-chains revert: symmetry clash REVERT: A 239 GLN cc_start: 0.7916 (mm110) cc_final: 0.7618 (mm110) REVERT: A 353 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.6579 (t80) REVERT: B 104 HIS cc_start: 0.8565 (OUTLIER) cc_final: 0.7070 (t-90) REVERT: B 353 PHE cc_start: 0.8097 (OUTLIER) cc_final: 0.7542 (t80) REVERT: C 37 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8105 (ttm) REVERT: C 353 PHE cc_start: 0.7819 (OUTLIER) cc_final: 0.6960 (t80) REVERT: D 353 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.6854 (t80) REVERT: E 104 HIS cc_start: 0.7944 (OUTLIER) cc_final: 0.6480 (t-90) REVERT: E 239 GLN cc_start: 0.8139 (mm-40) cc_final: 0.7835 (mm110) REVERT: E 353 PHE cc_start: 0.7434 (OUTLIER) cc_final: 0.7103 (t80) REVERT: F 37 MET cc_start: 0.8473 (mtp) cc_final: 0.8106 (ttm) REVERT: F 239 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7944 (mm110) REVERT: F 353 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7189 (t80) outliers start: 39 outliers final: 26 residues processed: 159 average time/residue: 0.2167 time to fit residues: 56.8015 Evaluate side-chains 152 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 117 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 395 SER Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 379 ILE Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 395 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 chunk 156 optimal weight: 0.7980 chunk 167 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 131 optimal weight: 0.5980 chunk 51 optimal weight: 0.1980 chunk 150 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 166 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 GLN C 404 GLN E 404 GLN F 404 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16416 Z= 0.144 Angle : 0.469 7.286 22230 Z= 0.254 Chirality : 0.037 0.214 2448 Planarity : 0.003 0.046 2688 Dihedral : 3.697 19.591 2112 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.20 % Allowed : 15.93 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.57 (0.19), residues: 1872 helix: 2.37 (0.14), residues: 1308 sheet: 2.67 (0.53), residues: 96 loop : -0.51 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 24 HIS 0.007 0.001 HIS B 253 PHE 0.018 0.001 PHE D 136 TYR 0.010 0.001 TYR B 281 ARG 0.001 0.000 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 128 time to evaluate : 1.796 Fit side-chains revert: symmetry clash REVERT: A 239 GLN cc_start: 0.7956 (mm110) cc_final: 0.7645 (mm110) REVERT: A 353 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.6624 (t80) REVERT: B 104 HIS cc_start: 0.8548 (OUTLIER) cc_final: 0.6978 (t-90) REVERT: B 353 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.7530 (t80) REVERT: C 37 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8178 (ttm) REVERT: C 353 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.6977 (t80) REVERT: D 353 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.6882 (t80) REVERT: E 104 HIS cc_start: 0.7949 (OUTLIER) cc_final: 0.6426 (t-90) REVERT: E 239 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7856 (mm110) REVERT: E 353 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.7146 (t80) REVERT: F 37 MET cc_start: 0.8431 (mtp) cc_final: 0.8107 (ttm) REVERT: F 239 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7940 (mm110) REVERT: F 279 ILE cc_start: 0.9093 (OUTLIER) cc_final: 0.8884 (tp) REVERT: F 353 PHE cc_start: 0.7992 (OUTLIER) cc_final: 0.7128 (t80) outliers start: 39 outliers final: 23 residues processed: 164 average time/residue: 0.2244 time to fit residues: 60.0852 Evaluate side-chains 154 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 121 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 395 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.7980 chunk 176 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 185 optimal weight: 1.9990 chunk 170 optimal weight: 0.8980 chunk 147 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 GLN C 404 GLN D 239 GLN F 404 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16416 Z= 0.174 Angle : 0.485 7.797 22230 Z= 0.264 Chirality : 0.037 0.143 2448 Planarity : 0.003 0.046 2688 Dihedral : 3.726 18.286 2112 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.09 % Allowed : 16.21 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.19), residues: 1872 helix: 2.35 (0.14), residues: 1308 sheet: 2.58 (0.53), residues: 96 loop : -0.54 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 24 HIS 0.007 0.001 HIS B 253 PHE 0.020 0.001 PHE A 136 TYR 0.014 0.001 TYR F 281 ARG 0.001 0.000 ARG C 306 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3744 Ramachandran restraints generated. 1872 Oldfield, 0 Emsley, 1872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 118 time to evaluate : 1.941 Fit side-chains revert: symmetry clash REVERT: A 353 PHE cc_start: 0.8143 (OUTLIER) cc_final: 0.6757 (t80) REVERT: B 104 HIS cc_start: 0.8588 (OUTLIER) cc_final: 0.7140 (t-90) REVERT: B 353 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7602 (t80) REVERT: C 37 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8126 (ttm) REVERT: C 353 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.6977 (t80) REVERT: D 52 MET cc_start: 0.8502 (mtp) cc_final: 0.8209 (mtm) REVERT: D 327 SER cc_start: 0.9218 (OUTLIER) cc_final: 0.8781 (t) REVERT: D 353 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.6857 (t80) REVERT: E 104 HIS cc_start: 0.7971 (OUTLIER) cc_final: 0.6568 (t-90) REVERT: E 239 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7840 (mm110) REVERT: E 353 PHE cc_start: 0.7555 (OUTLIER) cc_final: 0.7208 (t80) REVERT: F 37 MET cc_start: 0.8434 (mtp) cc_final: 0.8129 (ttm) REVERT: F 239 GLN cc_start: 0.8276 (mm-40) cc_final: 0.8002 (mm110) REVERT: F 353 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7237 (t80) outliers start: 37 outliers final: 24 residues processed: 152 average time/residue: 0.2244 time to fit residues: 55.9944 Evaluate side-chains 149 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 115 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 353 PHE Chi-restraints excluded: chain A residue 395 SER Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 234 LYS Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 234 LYS Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 353 PHE Chi-restraints excluded: chain C residue 395 SER Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 243 LEU Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 353 PHE Chi-restraints excluded: chain D residue 395 SER Chi-restraints excluded: chain E residue 100 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 234 LYS Chi-restraints excluded: chain E residue 353 PHE Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 234 LYS Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 353 PHE Chi-restraints excluded: chain F residue 395 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 136 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 147 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 chunk 151 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 GLN C 404 GLN F 404 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.108470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.086343 restraints weight = 30845.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.089183 restraints weight = 14010.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.090947 restraints weight = 8418.034| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 16416 Z= 0.144 Angle : 0.470 7.451 22230 Z= 0.255 Chirality : 0.037 0.142 2448 Planarity : 0.003 0.046 2688 Dihedral : 3.649 17.780 2112 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.03 % Allowed : 16.33 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.60 (0.19), residues: 1872 helix: 2.42 (0.14), residues: 1308 sheet: 2.53 (0.53), residues: 96 loop : -0.52 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 24 HIS 0.006 0.001 HIS E 253 PHE 0.016 0.001 PHE D 136 TYR 0.013 0.001 TYR F 281 ARG 0.001 0.000 ARG C 306 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2430.48 seconds wall clock time: 45 minutes 22.42 seconds (2722.42 seconds total)