Starting phenix.real_space_refine on Fri Feb 16 23:34:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3i_35153/02_2024/8i3i_35153_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3i_35153/02_2024/8i3i_35153.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3i_35153/02_2024/8i3i_35153.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3i_35153/02_2024/8i3i_35153.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3i_35153/02_2024/8i3i_35153_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i3i_35153/02_2024/8i3i_35153_updated.pdb" } resolution = 2.68 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= 0.064 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 72 5.16 5 C 10736 2.51 5 N 2816 2.21 5 O 3168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A GLU 375": "OE1" <-> "OE2" Residue "A GLU 436": "OE1" <-> "OE2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 335": "OE1" <-> "OE2" Residue "D GLU 375": "OE1" <-> "OE2" Residue "D GLU 436": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "B GLU 335": "OE1" <-> "OE2" Residue "B GLU 375": "OE1" <-> "OE2" Residue "B GLU 436": "OE1" <-> "OE2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C GLU 335": "OE1" <-> "OE2" Residue "C GLU 375": "OE1" <-> "OE2" Residue "C GLU 436": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16808 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4170 Classifications: {'peptide': 522} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 498} Chain breaks: 1 Chain: "D" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4170 Classifications: {'peptide': 522} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 498} Chain breaks: 1 Chain: "B" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4170 Classifications: {'peptide': 522} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 498} Chain breaks: 1 Chain: "C" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4170 Classifications: {'peptide': 522} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 498} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.35, per 1000 atoms: 0.56 Number of scatterers: 16808 At special positions: 0 Unit cell: (94.302, 120.666, 120.666, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 72 16.00 P 12 15.00 Mg 4 11.99 O 3168 8.00 N 2816 7.00 C 10736 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=0, symmetry=0 Time building additional restraints: 6.84 Conformation dependent library (CDL) restraints added in 3.1 seconds 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3920 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 76 helices and 24 sheets defined 32.2% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.69 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 41 through 57 removed outlier: 3.968A pdb=" N ASP A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 86 Proline residue: A 84 - end of helix Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 121 through 126 Processing helix chain 'A' and resid 147 through 152 Processing helix chain 'A' and resid 189 through 204 Processing helix chain 'A' and resid 228 through 239 Proline residue: A 233 - end of helix removed outlier: 3.828A pdb=" N ALA A 236 " --> pdb=" O PRO A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 4.604A pdb=" N GLU A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 280 through 284 removed outlier: 3.862A pdb=" N ALA A 284 " --> pdb=" O LYS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 309 Processing helix chain 'A' and resid 341 through 349 Processing helix chain 'A' and resid 396 through 401 Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 427 through 429 No H-bonds generated for 'chain 'A' and resid 427 through 429' Processing helix chain 'A' and resid 440 through 449 Processing helix chain 'A' and resid 482 through 491 removed outlier: 3.563A pdb=" N GLU A 486 " --> pdb=" O VAL A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 531 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 41 through 57 removed outlier: 3.967A pdb=" N ASP D 46 " --> pdb=" O LYS D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 86 Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 99 through 109 Processing helix chain 'D' and resid 121 through 126 Processing helix chain 'D' and resid 147 through 152 Processing helix chain 'D' and resid 189 through 204 Processing helix chain 'D' and resid 228 through 239 Proline residue: D 233 - end of helix removed outlier: 3.828A pdb=" N ALA D 236 " --> pdb=" O PRO D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 removed outlier: 4.604A pdb=" N GLU D 259 " --> pdb=" O LEU D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 278 Processing helix chain 'D' and resid 280 through 284 removed outlier: 3.862A pdb=" N ALA D 284 " --> pdb=" O LYS D 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 309 Processing helix chain 'D' and resid 341 through 349 Processing helix chain 'D' and resid 396 through 401 Processing helix chain 'D' and resid 403 through 405 No H-bonds generated for 'chain 'D' and resid 403 through 405' Processing helix chain 'D' and resid 427 through 429 No H-bonds generated for 'chain 'D' and resid 427 through 429' Processing helix chain 'D' and resid 440 through 449 Processing helix chain 'D' and resid 482 through 491 removed outlier: 3.563A pdb=" N GLU D 486 " --> pdb=" O VAL D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 525 through 531 Processing helix chain 'B' and resid 15 through 20 Processing helix chain 'B' and resid 41 through 57 removed outlier: 3.969A pdb=" N ASP B 46 " --> pdb=" O LYS B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 86 Proline residue: B 84 - end of helix Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 147 through 152 Processing helix chain 'B' and resid 189 through 204 Processing helix chain 'B' and resid 228 through 239 Proline residue: B 233 - end of helix removed outlier: 3.828A pdb=" N ALA B 236 " --> pdb=" O PRO B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 260 removed outlier: 4.604A pdb=" N GLU B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 280 through 284 removed outlier: 3.862A pdb=" N ALA B 284 " --> pdb=" O LYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 309 Processing helix chain 'B' and resid 341 through 349 Processing helix chain 'B' and resid 396 through 401 Processing helix chain 'B' and resid 403 through 405 No H-bonds generated for 'chain 'B' and resid 403 through 405' Processing helix chain 'B' and resid 427 through 429 No H-bonds generated for 'chain 'B' and resid 427 through 429' Processing helix chain 'B' and resid 440 through 449 Processing helix chain 'B' and resid 482 through 491 removed outlier: 3.563A pdb=" N GLU B 486 " --> pdb=" O VAL B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 531 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 41 through 57 removed outlier: 3.967A pdb=" N ASP C 46 " --> pdb=" O LYS C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 86 Proline residue: C 84 - end of helix Processing helix chain 'C' and resid 99 through 109 Processing helix chain 'C' and resid 121 through 126 Processing helix chain 'C' and resid 147 through 152 Processing helix chain 'C' and resid 189 through 204 Processing helix chain 'C' and resid 228 through 239 Proline residue: C 233 - end of helix removed outlier: 3.828A pdb=" N ALA C 236 " --> pdb=" O PRO C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 260 removed outlier: 4.604A pdb=" N GLU C 259 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 278 Processing helix chain 'C' and resid 280 through 284 removed outlier: 3.863A pdb=" N ALA C 284 " --> pdb=" O LYS C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 309 Processing helix chain 'C' and resid 341 through 349 Processing helix chain 'C' and resid 396 through 401 Processing helix chain 'C' and resid 403 through 405 No H-bonds generated for 'chain 'C' and resid 403 through 405' Processing helix chain 'C' and resid 427 through 429 No H-bonds generated for 'chain 'C' and resid 427 through 429' Processing helix chain 'C' and resid 440 through 449 Processing helix chain 'C' and resid 482 through 491 removed outlier: 3.563A pdb=" N GLU C 486 " --> pdb=" O VAL C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 531 Processing sheet with id= A, first strand: chain 'A' and resid 37 through 40 removed outlier: 6.357A pdb=" N GLN A 243 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE A 265 " --> pdb=" O MET A 219 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LYS A 291 " --> pdb=" O SER A 266 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N CYS A 268 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL A 293 " --> pdb=" O CYS A 268 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASP A 313 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE A 294 " --> pdb=" O ASP A 313 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE A 315 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 136 through 140 removed outlier: 6.242A pdb=" N LYS A 89 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL A 68 " --> pdb=" O LYS A 89 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N HIS A 91 " --> pdb=" O VAL A 68 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TYR A 174 " --> pdb=" O MET A 92 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N PHE A 187 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR A 172 " --> pdb=" O VAL A 185 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL A 185 " --> pdb=" O THR A 172 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 361 through 363 Processing sheet with id= D, first strand: chain 'A' and resid 508 through 511 Processing sheet with id= E, first strand: chain 'A' and resid 317 through 319 Processing sheet with id= F, first strand: chain 'A' and resid 411 through 415 removed outlier: 6.630A pdb=" N HIS A 414 " --> pdb=" O ILE A 423 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE A 423 " --> pdb=" O HIS A 414 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 37 through 40 removed outlier: 6.357A pdb=" N GLN D 243 " --> pdb=" O VAL D 32 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE D 265 " --> pdb=" O MET D 219 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N LYS D 291 " --> pdb=" O SER D 266 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N CYS D 268 " --> pdb=" O LYS D 291 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL D 293 " --> pdb=" O CYS D 268 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASP D 313 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE D 294 " --> pdb=" O ASP D 313 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE D 315 " --> pdb=" O ILE D 294 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 136 through 140 removed outlier: 6.242A pdb=" N LYS D 89 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL D 68 " --> pdb=" O LYS D 89 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N HIS D 91 " --> pdb=" O VAL D 68 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TYR D 174 " --> pdb=" O MET D 92 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N PHE D 187 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR D 172 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL D 185 " --> pdb=" O THR D 172 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 361 through 363 Processing sheet with id= J, first strand: chain 'D' and resid 508 through 511 Processing sheet with id= K, first strand: chain 'D' and resid 317 through 319 Processing sheet with id= L, first strand: chain 'D' and resid 411 through 415 removed outlier: 6.630A pdb=" N HIS D 414 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ILE D 423 " --> pdb=" O HIS D 414 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 37 through 40 removed outlier: 6.357A pdb=" N GLN B 243 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE B 265 " --> pdb=" O MET B 219 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LYS B 291 " --> pdb=" O SER B 266 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N CYS B 268 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N VAL B 293 " --> pdb=" O CYS B 268 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP B 313 " --> pdb=" O VAL B 292 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE B 294 " --> pdb=" O ASP B 313 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE B 315 " --> pdb=" O ILE B 294 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 136 through 140 removed outlier: 6.242A pdb=" N LYS B 89 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL B 68 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N HIS B 91 " --> pdb=" O VAL B 68 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TYR B 174 " --> pdb=" O MET B 92 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N PHE B 187 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR B 172 " --> pdb=" O VAL B 185 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 185 " --> pdb=" O THR B 172 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 361 through 363 Processing sheet with id= P, first strand: chain 'B' and resid 508 through 511 Processing sheet with id= Q, first strand: chain 'B' and resid 317 through 319 Processing sheet with id= R, first strand: chain 'B' and resid 411 through 415 removed outlier: 6.630A pdb=" N HIS B 414 " --> pdb=" O ILE B 423 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE B 423 " --> pdb=" O HIS B 414 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 37 through 40 removed outlier: 6.357A pdb=" N GLN C 243 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N PHE C 265 " --> pdb=" O MET C 219 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N LYS C 291 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N CYS C 268 " --> pdb=" O LYS C 291 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL C 293 " --> pdb=" O CYS C 268 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ASP C 313 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE C 294 " --> pdb=" O ASP C 313 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N PHE C 315 " --> pdb=" O ILE C 294 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 136 through 140 removed outlier: 6.242A pdb=" N LYS C 89 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N VAL C 68 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N HIS C 91 " --> pdb=" O VAL C 68 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N TYR C 174 " --> pdb=" O MET C 92 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N PHE C 187 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR C 172 " --> pdb=" O VAL C 185 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL C 185 " --> pdb=" O THR C 172 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'C' and resid 361 through 363 Processing sheet with id= V, first strand: chain 'C' and resid 508 through 511 Processing sheet with id= W, first strand: chain 'C' and resid 317 through 319 Processing sheet with id= X, first strand: chain 'C' and resid 411 through 415 removed outlier: 6.630A pdb=" N HIS C 414 " --> pdb=" O ILE C 423 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N ILE C 423 " --> pdb=" O HIS C 414 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1308 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: 5.42 Time building geometry restraints manager: 7.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2848 1.31 - 1.44: 4428 1.44 - 1.56: 9756 1.56 - 1.68: 24 1.68 - 1.80: 132 Bond restraints: 17188 Sorted by residual: bond pdb=" O3A ANP C1002 " pdb=" PB ANP C1002 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.28e+01 bond pdb=" O3A ANP D1002 " pdb=" PB ANP D1002 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" O3A ANP B1002 " pdb=" PB ANP B1002 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" O3A ANP A1002 " pdb=" PB ANP A1002 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" N3B ANP D1002 " pdb=" PG ANP D1002 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.84e+01 ... (remaining 17183 not shown) Histogram of bond angle deviations from ideal: 99.54 - 106.72: 576 106.72 - 113.91: 9846 113.91 - 121.10: 8159 121.10 - 128.28: 4579 128.28 - 135.47: 176 Bond angle restraints: 23336 Sorted by residual: angle pdb=" N MET B 367 " pdb=" CA MET B 367 " pdb=" C MET B 367 " ideal model delta sigma weight residual 111.28 122.70 -11.42 1.35e+00 5.49e-01 7.16e+01 angle pdb=" N MET D 367 " pdb=" CA MET D 367 " pdb=" C MET D 367 " ideal model delta sigma weight residual 111.28 122.69 -11.41 1.35e+00 5.49e-01 7.14e+01 angle pdb=" N MET C 367 " pdb=" CA MET C 367 " pdb=" C MET C 367 " ideal model delta sigma weight residual 111.28 122.68 -11.40 1.35e+00 5.49e-01 7.14e+01 angle pdb=" N MET A 367 " pdb=" CA MET A 367 " pdb=" C MET A 367 " ideal model delta sigma weight residual 111.28 122.68 -11.40 1.35e+00 5.49e-01 7.13e+01 angle pdb=" N PHE D 181 " pdb=" CA PHE D 181 " pdb=" C PHE D 181 " ideal model delta sigma weight residual 110.40 99.63 10.77 1.31e+00 5.83e-01 6.76e+01 ... (remaining 23331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.95: 9466 20.95 - 41.90: 723 41.90 - 62.85: 143 62.85 - 83.80: 24 83.80 - 104.75: 12 Dihedral angle restraints: 10368 sinusoidal: 4280 harmonic: 6088 Sorted by residual: dihedral pdb=" C MET D 367 " pdb=" N MET D 367 " pdb=" CA MET D 367 " pdb=" CB MET D 367 " ideal model delta harmonic sigma weight residual -122.60 -134.86 12.26 0 2.50e+00 1.60e-01 2.41e+01 dihedral pdb=" C MET B 367 " pdb=" N MET B 367 " pdb=" CA MET B 367 " pdb=" CB MET B 367 " ideal model delta harmonic sigma weight residual -122.60 -134.85 12.25 0 2.50e+00 1.60e-01 2.40e+01 dihedral pdb=" C MET A 367 " pdb=" N MET A 367 " pdb=" CA MET A 367 " pdb=" CB MET A 367 " ideal model delta harmonic sigma weight residual -122.60 -134.82 12.22 0 2.50e+00 1.60e-01 2.39e+01 ... (remaining 10365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 2509 0.121 - 0.242: 96 0.242 - 0.363: 19 0.363 - 0.483: 4 0.483 - 0.604: 4 Chirality restraints: 2632 Sorted by residual: chirality pdb=" CA MET B 367 " pdb=" N MET B 367 " pdb=" C MET B 367 " pdb=" CB MET B 367 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.13e+00 chirality pdb=" CA MET D 367 " pdb=" N MET D 367 " pdb=" C MET D 367 " pdb=" CB MET D 367 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.07e+00 chirality pdb=" CA MET A 367 " pdb=" N MET A 367 " pdb=" C MET A 367 " pdb=" CB MET A 367 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 9.04e+00 ... (remaining 2629 not shown) Planarity restraints: 2948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D 222 " -0.065 5.00e-02 4.00e+02 9.76e-02 1.52e+01 pdb=" N PRO D 223 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO D 223 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO D 223 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 222 " -0.065 5.00e-02 4.00e+02 9.75e-02 1.52e+01 pdb=" N PRO A 223 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 223 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 223 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 222 " 0.065 5.00e-02 4.00e+02 9.75e-02 1.52e+01 pdb=" N PRO C 223 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO C 223 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 223 " 0.052 5.00e-02 4.00e+02 ... (remaining 2945 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 723 2.72 - 3.26: 16337 3.26 - 3.81: 27115 3.81 - 4.35: 35445 4.35 - 4.90: 60625 Nonbonded interactions: 140245 Sorted by model distance: nonbonded pdb="MG MG B1001 " pdb=" O2G ANP B1002 " model vdw 2.175 2.170 nonbonded pdb="MG MG A1001 " pdb=" O2G ANP A1002 " model vdw 2.176 2.170 nonbonded pdb="MG MG D1001 " pdb=" O2G ANP D1002 " model vdw 2.176 2.170 nonbonded pdb="MG MG C1001 " pdb=" O2G ANP C1002 " model vdw 2.176 2.170 nonbonded pdb=" ND2 ASN A 206 " pdb=" O GLN A 209 " model vdw 2.283 2.520 ... (remaining 140240 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 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: 7.900 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 47.510 Find NCS groups from input model: 1.100 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:13.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 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 : 0.007 0.145 17188 Z= 0.472 Angle : 0.936 18.020 23336 Z= 0.541 Chirality : 0.065 0.604 2632 Planarity : 0.007 0.098 2948 Dihedral : 15.822 104.751 6448 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.14 % Favored : 92.66 % Rotamer: Outliers : 0.44 % Allowed : 13.07 % Favored : 86.49 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 4.35 % 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: -1.00 (0.18), residues: 2072 helix: 0.45 (0.20), residues: 684 sheet: -0.82 (0.26), residues: 424 loop : -1.37 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 230 HIS 0.010 0.002 HIS B 228 PHE 0.011 0.002 PHE D 20 TYR 0.015 0.002 TYR D 76 ARG 0.003 0.000 ARG C 310 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 168 time to evaluate : 2.022 Fit side-chains REVERT: A 42 LYS cc_start: 0.8225 (tmtm) cc_final: 0.7885 (tppt) REVERT: A 461 MET cc_start: 0.6405 (OUTLIER) cc_final: 0.5899 (ttm) REVERT: D 461 MET cc_start: 0.6281 (OUTLIER) cc_final: 0.5888 (ptp) REVERT: D 508 LYS cc_start: 0.6621 (mttt) cc_final: 0.6317 (mttm) REVERT: C 42 LYS cc_start: 0.8205 (tmtm) cc_final: 0.7907 (tppt) REVERT: C 461 MET cc_start: 0.6272 (OUTLIER) cc_final: 0.5825 (ttm) REVERT: C 508 LYS cc_start: 0.6543 (mttt) cc_final: 0.6159 (mttm) outliers start: 8 outliers final: 3 residues processed: 172 average time/residue: 1.3853 time to fit residues: 264.5245 Evaluate side-chains 156 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 150 time to evaluate : 2.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 461 MET Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 461 MET Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 461 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 2.9990 chunk 157 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 163 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.0766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17188 Z= 0.237 Angle : 0.568 6.417 23336 Z= 0.304 Chirality : 0.048 0.160 2632 Planarity : 0.005 0.073 2948 Dihedral : 9.407 103.584 2387 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 2.29 % Allowed : 12.69 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.77 (0.18), residues: 2072 helix: 0.61 (0.20), residues: 684 sheet: -0.66 (0.26), residues: 424 loop : -1.22 (0.18), residues: 964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 230 HIS 0.005 0.001 HIS A 408 PHE 0.010 0.002 PHE A 81 TYR 0.016 0.002 TYR D 249 ARG 0.003 0.000 ARG B 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 149 time to evaluate : 2.177 Fit side-chains REVERT: A 18 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8921 (mp) REVERT: D 18 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8925 (mp) REVERT: D 70 ASP cc_start: 0.8657 (p0) cc_final: 0.8409 (p0) REVERT: D 508 LYS cc_start: 0.6349 (mttt) cc_final: 0.6022 (mttm) REVERT: B 18 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8932 (mp) REVERT: B 70 ASP cc_start: 0.8641 (p0) cc_final: 0.8329 (p0) REVERT: C 18 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8928 (mp) REVERT: C 42 LYS cc_start: 0.8390 (tmtm) cc_final: 0.8046 (tppt) REVERT: C 70 ASP cc_start: 0.8654 (p0) cc_final: 0.8394 (p0) REVERT: C 508 LYS cc_start: 0.6277 (mttt) cc_final: 0.5963 (mttm) outliers start: 42 outliers final: 12 residues processed: 174 average time/residue: 1.3508 time to fit residues: 261.9897 Evaluate side-chains 163 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 147 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 189 optimal weight: 0.9980 chunk 204 optimal weight: 0.0870 chunk 168 optimal weight: 2.9990 chunk 187 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 chunk 151 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 ASN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17188 Z= 0.154 Angle : 0.510 6.490 23336 Z= 0.272 Chirality : 0.046 0.150 2632 Planarity : 0.004 0.061 2948 Dihedral : 8.537 99.599 2372 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 2.72 % Allowed : 12.64 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.57 (0.18), residues: 2072 helix: 0.79 (0.20), residues: 684 sheet: -0.59 (0.28), residues: 372 loop : -1.07 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 230 HIS 0.004 0.001 HIS D 39 PHE 0.009 0.001 PHE A 225 TYR 0.011 0.001 TYR D 148 ARG 0.002 0.000 ARG D 130 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 173 time to evaluate : 2.048 Fit side-chains REVERT: A 70 ASP cc_start: 0.8678 (p0) cc_final: 0.8438 (p0) REVERT: D 70 ASP cc_start: 0.8655 (p0) cc_final: 0.8360 (p0) REVERT: D 260 GLN cc_start: 0.7969 (OUTLIER) cc_final: 0.7627 (tt0) REVERT: D 508 LYS cc_start: 0.6315 (mttt) cc_final: 0.6038 (mttm) REVERT: B 70 ASP cc_start: 0.8637 (p0) cc_final: 0.8353 (p0) REVERT: B 96 ARG cc_start: 0.8183 (mtm-85) cc_final: 0.7861 (mtt90) REVERT: C 70 ASP cc_start: 0.8636 (p0) cc_final: 0.8334 (p0) REVERT: C 96 ARG cc_start: 0.8151 (mtm-85) cc_final: 0.7837 (mtt90) REVERT: C 461 MET cc_start: 0.5134 (ttp) cc_final: 0.4711 (ttm) REVERT: C 508 LYS cc_start: 0.6280 (mttt) cc_final: 0.5999 (mttm) outliers start: 50 outliers final: 25 residues processed: 211 average time/residue: 1.1279 time to fit residues: 269.4047 Evaluate side-chains 177 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 2.9990 chunk 142 optimal weight: 0.2980 chunk 98 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 189 optimal weight: 0.9980 chunk 201 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 HIS A 260 GLN A 368 ASN ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 HIS B 260 GLN ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 228 HIS C 260 GLN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17188 Z= 0.246 Angle : 0.576 10.075 23336 Z= 0.303 Chirality : 0.048 0.153 2632 Planarity : 0.005 0.063 2948 Dihedral : 8.846 108.328 2372 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 3.32 % Allowed : 13.45 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.65 (0.18), residues: 2072 helix: 0.70 (0.20), residues: 676 sheet: -0.75 (0.26), residues: 424 loop : -1.02 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 290 HIS 0.006 0.001 HIS B 228 PHE 0.013 0.001 PHE A 225 TYR 0.011 0.001 TYR D 245 ARG 0.002 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 143 time to evaluate : 2.013 Fit side-chains REVERT: A 18 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8925 (mp) REVERT: A 28 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: A 260 GLN cc_start: 0.8035 (tt0) cc_final: 0.7676 (tt0) REVERT: D 18 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8905 (mp) REVERT: D 260 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7556 (tt0) REVERT: B 18 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8912 (mp) REVERT: B 28 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7751 (mp0) REVERT: C 18 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8901 (mp) REVERT: C 96 ARG cc_start: 0.8156 (mmm-85) cc_final: 0.7839 (mtt90) outliers start: 61 outliers final: 37 residues processed: 187 average time/residue: 1.2431 time to fit residues: 260.7232 Evaluate side-chains 174 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 130 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 2 optimal weight: 0.0030 chunk 149 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 171 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 180 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 17188 Z= 0.304 Angle : 0.608 10.145 23336 Z= 0.319 Chirality : 0.049 0.155 2632 Planarity : 0.005 0.064 2948 Dihedral : 9.088 111.700 2372 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.24 % Favored : 92.57 % Rotamer: Outliers : 4.41 % Allowed : 13.07 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.72 (0.18), residues: 2072 helix: 0.66 (0.20), residues: 672 sheet: -0.76 (0.25), residues: 420 loop : -1.11 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 230 HIS 0.006 0.001 HIS C 228 PHE 0.012 0.002 PHE A 225 TYR 0.011 0.001 TYR B 148 ARG 0.003 0.000 ARG B 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 133 time to evaluate : 1.976 Fit side-chains REVERT: A 18 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8947 (mp) REVERT: A 28 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7724 (mp0) REVERT: D 18 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8951 (mp) REVERT: D 28 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7766 (mp0) REVERT: B 18 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8941 (mp) REVERT: B 28 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: C 18 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8931 (mp) REVERT: C 461 MET cc_start: 0.5402 (ttp) cc_final: 0.5060 (ttm) outliers start: 81 outliers final: 42 residues processed: 196 average time/residue: 1.1991 time to fit residues: 264.3529 Evaluate side-chains 176 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 127 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 362 ILE Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 362 ILE Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 0.0020 chunk 181 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 118 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 201 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 105 optimal weight: 0.7980 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17188 Z= 0.189 Angle : 0.547 9.973 23336 Z= 0.288 Chirality : 0.046 0.164 2632 Planarity : 0.004 0.059 2948 Dihedral : 8.767 108.932 2372 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.38 % Favored : 92.47 % Rotamer: Outliers : 3.65 % Allowed : 13.51 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.64 (0.18), residues: 2072 helix: 0.76 (0.20), residues: 672 sheet: -0.70 (0.27), residues: 380 loop : -1.09 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 466 HIS 0.004 0.001 HIS D 39 PHE 0.009 0.001 PHE B 225 TYR 0.011 0.001 TYR A 148 ARG 0.002 0.000 ARG D 130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 154 time to evaluate : 1.991 Fit side-chains REVERT: A 28 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: A 70 ASP cc_start: 0.8657 (p0) cc_final: 0.8386 (p0) REVERT: A 260 GLN cc_start: 0.7861 (tp40) cc_final: 0.7120 (tt0) REVERT: D 28 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7747 (mp0) REVERT: D 70 ASP cc_start: 0.8660 (p0) cc_final: 0.8402 (p0) REVERT: B 18 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8932 (mp) REVERT: B 28 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7761 (mp0) REVERT: B 70 ASP cc_start: 0.8651 (p0) cc_final: 0.8337 (p0) REVERT: C 70 ASP cc_start: 0.8662 (p0) cc_final: 0.8424 (p0) REVERT: C 260 GLN cc_start: 0.7827 (tp40) cc_final: 0.7289 (tt0) REVERT: C 461 MET cc_start: 0.5272 (ttp) cc_final: 0.4935 (ttm) outliers start: 67 outliers final: 39 residues processed: 204 average time/residue: 1.1473 time to fit residues: 265.6077 Evaluate side-chains 189 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 146 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 0.0000 chunk 22 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 chunk 169 optimal weight: 0.0970 chunk 112 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 125 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17188 Z= 0.145 Angle : 0.520 9.522 23336 Z= 0.272 Chirality : 0.046 0.187 2632 Planarity : 0.004 0.056 2948 Dihedral : 8.360 103.784 2372 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 2.89 % Allowed : 14.38 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.49 (0.18), residues: 2072 helix: 0.91 (0.20), residues: 672 sheet: -0.64 (0.27), residues: 372 loop : -1.00 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 466 HIS 0.003 0.001 HIS B 463 PHE 0.008 0.001 PHE A 225 TYR 0.011 0.001 TYR A 148 ARG 0.002 0.000 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 164 time to evaluate : 1.984 Fit side-chains REVERT: A 28 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: A 70 ASP cc_start: 0.8630 (p0) cc_final: 0.8354 (p0) REVERT: A 224 MET cc_start: 0.8644 (ttt) cc_final: 0.8279 (ttt) REVERT: A 260 GLN cc_start: 0.7702 (tp40) cc_final: 0.7119 (tt0) REVERT: D 70 ASP cc_start: 0.8629 (p0) cc_final: 0.8317 (p0) REVERT: B 70 ASP cc_start: 0.8625 (p0) cc_final: 0.8319 (p0) REVERT: B 260 GLN cc_start: 0.7807 (tp40) cc_final: 0.7139 (tt0) REVERT: C 70 ASP cc_start: 0.8656 (p0) cc_final: 0.8420 (p0) REVERT: C 260 GLN cc_start: 0.7761 (tp40) cc_final: 0.7232 (tt0) outliers start: 53 outliers final: 30 residues processed: 207 average time/residue: 1.1671 time to fit residues: 273.5831 Evaluate side-chains 186 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 155 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 136 optimal weight: 0.4980 chunk 99 optimal weight: 0.0270 chunk 18 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 overall best weight: 1.1042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17188 Z= 0.229 Angle : 0.573 10.786 23336 Z= 0.299 Chirality : 0.048 0.200 2632 Planarity : 0.004 0.058 2948 Dihedral : 8.717 109.932 2372 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 2.83 % Allowed : 14.92 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.69 (0.18), residues: 2072 helix: 0.74 (0.20), residues: 692 sheet: -0.66 (0.27), residues: 380 loop : -1.20 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 466 HIS 0.004 0.001 HIS B 228 PHE 0.011 0.001 PHE A 225 TYR 0.011 0.001 TYR D 148 ARG 0.002 0.000 ARG B 130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 139 time to evaluate : 2.014 Fit side-chains REVERT: A 28 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: A 260 GLN cc_start: 0.7925 (tp40) cc_final: 0.7342 (tt0) REVERT: D 28 GLU cc_start: 0.8009 (OUTLIER) cc_final: 0.7777 (mp0) REVERT: B 28 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: B 260 GLN cc_start: 0.7991 (tp40) cc_final: 0.7341 (tt0) REVERT: C 260 GLN cc_start: 0.7900 (tp40) cc_final: 0.7345 (tt0) REVERT: C 461 MET cc_start: 0.5407 (ttp) cc_final: 0.5017 (ttm) outliers start: 52 outliers final: 44 residues processed: 178 average time/residue: 1.2253 time to fit residues: 245.3832 Evaluate side-chains 185 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 138 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 182 optimal weight: 1.9990 chunk 192 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 186 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 168 optimal weight: 1.9990 chunk 176 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17188 Z= 0.230 Angle : 0.574 10.802 23336 Z= 0.299 Chirality : 0.048 0.178 2632 Planarity : 0.004 0.058 2948 Dihedral : 8.834 111.301 2372 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.72 % Favored : 92.08 % Rotamer: Outliers : 3.32 % Allowed : 14.49 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.72 (0.18), residues: 2072 helix: 0.69 (0.20), residues: 692 sheet: -0.68 (0.27), residues: 380 loop : -1.21 (0.19), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 466 HIS 0.005 0.001 HIS C 228 PHE 0.010 0.001 PHE A 225 TYR 0.011 0.001 TYR A 148 ARG 0.002 0.000 ARG C 130 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 143 time to evaluate : 2.724 Fit side-chains REVERT: A 28 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7671 (mp0) REVERT: A 70 ASP cc_start: 0.8638 (p0) cc_final: 0.8342 (p0) REVERT: A 260 GLN cc_start: 0.7936 (tp40) cc_final: 0.7340 (tt0) REVERT: D 28 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: B 18 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8908 (mp) REVERT: B 28 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7734 (mp0) REVERT: B 260 GLN cc_start: 0.7995 (tp40) cc_final: 0.7345 (tt0) REVERT: C 18 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8912 (mp) REVERT: C 70 ASP cc_start: 0.8693 (p0) cc_final: 0.8418 (p0) REVERT: C 260 GLN cc_start: 0.7960 (tp40) cc_final: 0.7408 (tt0) REVERT: C 461 MET cc_start: 0.5296 (ttp) cc_final: 0.4950 (ttm) outliers start: 61 outliers final: 47 residues processed: 192 average time/residue: 1.2555 time to fit residues: 272.4382 Evaluate side-chains 193 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 141 time to evaluate : 2.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 292 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 chunk 207 optimal weight: 5.9990 chunk 190 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 127 optimal weight: 0.6980 chunk 101 optimal weight: 0.0970 chunk 131 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17188 Z= 0.193 Angle : 0.551 10.212 23336 Z= 0.287 Chirality : 0.047 0.185 2632 Planarity : 0.004 0.057 2948 Dihedral : 8.689 110.022 2372 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.16 % Favored : 91.80 % Rotamer: Outliers : 3.05 % Allowed : 14.81 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.54 (0.18), residues: 2072 helix: 0.84 (0.20), residues: 672 sheet: -0.64 (0.27), residues: 372 loop : -1.03 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 466 HIS 0.004 0.001 HIS B 39 PHE 0.010 0.001 PHE A 225 TYR 0.011 0.001 TYR C 148 ARG 0.002 0.000 ARG C 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4144 Ramachandran restraints generated. 2072 Oldfield, 0 Emsley, 2072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 149 time to evaluate : 2.192 Fit side-chains REVERT: A 28 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7699 (mp0) REVERT: A 70 ASP cc_start: 0.8642 (p0) cc_final: 0.8359 (p0) REVERT: A 260 GLN cc_start: 0.7891 (tp40) cc_final: 0.7206 (tt0) REVERT: D 28 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: B 28 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7726 (mp0) REVERT: B 260 GLN cc_start: 0.7975 (tp40) cc_final: 0.7350 (tt0) REVERT: C 70 ASP cc_start: 0.8669 (p0) cc_final: 0.8397 (p0) REVERT: C 260 GLN cc_start: 0.7926 (tp40) cc_final: 0.7398 (tt0) REVERT: C 461 MET cc_start: 0.5304 (ttp) cc_final: 0.4919 (ttm) outliers start: 56 outliers final: 48 residues processed: 193 average time/residue: 1.1034 time to fit residues: 241.5409 Evaluate side-chains 197 residues out of total 1836 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 146 time to evaluate : 1.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 76 TYR Chi-restraints excluded: chain A residue 132 ASP Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 514 GLU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 28 GLU Chi-restraints excluded: chain D residue 76 TYR Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain D residue 132 ASP Chi-restraints excluded: chain D residue 221 ILE Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 469 VAL Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 514 GLU Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 76 TYR Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain B residue 132 ASP Chi-restraints excluded: chain B residue 221 ILE Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 292 VAL Chi-restraints excluded: chain B residue 363 VAL Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 488 LEU Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 514 GLU Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 76 TYR Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 221 ILE Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 292 VAL Chi-restraints excluded: chain C residue 363 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 488 LEU Chi-restraints excluded: chain C residue 514 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 3.9990 chunk 50 optimal weight: 0.4980 chunk 152 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 165 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 169 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.112945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.096557 restraints weight = 24060.323| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.65 r_work: 0.3088 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 17188 Z= 0.271 Angle : 0.598 10.882 23336 Z= 0.312 Chirality : 0.049 0.187 2632 Planarity : 0.005 0.057 2948 Dihedral : 9.076 114.263 2372 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.96 % Favored : 91.84 % Rotamer: Outliers : 2.94 % Allowed : 15.20 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: -0.77 (0.18), residues: 2072 helix: 0.63 (0.20), residues: 692 sheet: -0.68 (0.26), residues: 420 loop : -1.23 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 466 HIS 0.005 0.001 HIS C 228 PHE 0.012 0.002 PHE A 225 TYR 0.011 0.001 TYR C 148 ARG 0.003 0.000 ARG C 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5089.73 seconds wall clock time: 91 minutes 56.87 seconds (5516.87 seconds total)