Starting phenix.real_space_refine on Fri Feb 16 13:22:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ene_28271/02_2024/8ene_28271_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ene_28271/02_2024/8ene_28271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ene_28271/02_2024/8ene_28271.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ene_28271/02_2024/8ene_28271.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ene_28271/02_2024/8ene_28271_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ene_28271/02_2024/8ene_28271_updated.pdb" } resolution = 2.64 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= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 76 5.16 5 C 9805 2.51 5 N 2599 2.21 5 O 2916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 457": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15404 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3808 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 469} Chain: "B" Number of atoms: 3808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3808 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 469} Chain: "C" Number of atoms: 3804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3804 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 469} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3808 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 469} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.66, per 1000 atoms: 0.56 Number of scatterers: 15404 At special positions: 0 Unit cell: (109.08, 106.92, 100.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 P 8 15.00 O 2916 8.00 N 2599 7.00 C 9805 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: 6.11 Conformation dependent library (CDL) restraints added in 3.1 seconds 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3568 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 69 helices and 21 sheets defined 39.9% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.49 Creating SS restraints... Processing helix chain 'A' and resid 57 through 70 Processing helix chain 'A' and resid 76 through 79 No H-bonds generated for 'chain 'A' and resid 76 through 79' Processing helix chain 'A' and resid 82 through 98 Processing helix chain 'A' and resid 100 through 111 Processing helix chain 'A' and resid 115 through 120 Processing helix chain 'A' and resid 122 through 138 removed outlier: 4.654A pdb=" N ASP A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 185 Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 200 through 212 Processing helix chain 'A' and resid 229 through 235 Processing helix chain 'A' and resid 248 through 260 Processing helix chain 'A' and resid 284 through 300 removed outlier: 7.125A pdb=" N HIS A 298 " --> pdb=" O GLY A 294 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLN A 299 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY A 300 " --> pdb=" O PHE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 329 removed outlier: 5.760A pdb=" N ASP A 317 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU A 318 " --> pdb=" O ILE A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 364 Processing helix chain 'A' and resid 395 through 397 No H-bonds generated for 'chain 'A' and resid 395 through 397' Processing helix chain 'A' and resid 414 through 422 Processing helix chain 'A' and resid 437 through 446 Processing helix chain 'A' and resid 480 through 486 removed outlier: 3.697A pdb=" N GLU A 485 " --> pdb=" O TYR A 481 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N TYR A 486 " --> pdb=" O GLY A 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 70 Processing helix chain 'B' and resid 76 through 79 No H-bonds generated for 'chain 'B' and resid 76 through 79' Processing helix chain 'B' and resid 82 through 98 Processing helix chain 'B' and resid 100 through 111 Processing helix chain 'B' and resid 115 through 120 Processing helix chain 'B' and resid 122 through 138 removed outlier: 4.701A pdb=" N ASP B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 185 Proline residue: B 182 - end of helix Processing helix chain 'B' and resid 200 through 212 Processing helix chain 'B' and resid 229 through 235 Processing helix chain 'B' and resid 248 through 260 Processing helix chain 'B' and resid 284 through 300 removed outlier: 7.153A pdb=" N HIS B 298 " --> pdb=" O GLY B 294 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N GLN B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY B 300 " --> pdb=" O PHE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 329 removed outlier: 5.749A pdb=" N ASP B 317 " --> pdb=" O SER B 314 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU B 318 " --> pdb=" O ILE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 364 Processing helix chain 'B' and resid 395 through 397 No H-bonds generated for 'chain 'B' and resid 395 through 397' Processing helix chain 'B' and resid 414 through 422 Processing helix chain 'B' and resid 437 through 446 Processing helix chain 'B' and resid 470 through 472 No H-bonds generated for 'chain 'B' and resid 470 through 472' Processing helix chain 'B' and resid 480 through 486 removed outlier: 3.713A pdb=" N GLU B 485 " --> pdb=" O TYR B 481 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR B 486 " --> pdb=" O GLY B 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 70 Processing helix chain 'C' and resid 76 through 79 No H-bonds generated for 'chain 'C' and resid 76 through 79' Processing helix chain 'C' and resid 82 through 98 Processing helix chain 'C' and resid 100 through 111 Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'C' and resid 122 through 138 removed outlier: 4.666A pdb=" N ASP C 138 " --> pdb=" O ALA C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 185 Proline residue: C 182 - end of helix Processing helix chain 'C' and resid 200 through 212 Processing helix chain 'C' and resid 229 through 235 Processing helix chain 'C' and resid 248 through 259 Processing helix chain 'C' and resid 284 through 300 removed outlier: 7.124A pdb=" N HIS C 298 " --> pdb=" O GLY C 294 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLN C 299 " --> pdb=" O VAL C 295 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY C 300 " --> pdb=" O PHE C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 329 removed outlier: 5.584A pdb=" N ASP C 317 " --> pdb=" O SER C 314 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU C 318 " --> pdb=" O ILE C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 348 through 363 Processing helix chain 'C' and resid 395 through 397 No H-bonds generated for 'chain 'C' and resid 395 through 397' Processing helix chain 'C' and resid 414 through 421 Processing helix chain 'C' and resid 438 through 446 Processing helix chain 'C' and resid 480 through 486 removed outlier: 3.670A pdb=" N GLU C 485 " --> pdb=" O TYR C 481 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N TYR C 486 " --> pdb=" O GLY C 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 70 Processing helix chain 'D' and resid 76 through 79 No H-bonds generated for 'chain 'D' and resid 76 through 79' Processing helix chain 'D' and resid 82 through 98 Processing helix chain 'D' and resid 100 through 111 Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 122 through 138 removed outlier: 4.624A pdb=" N ASP D 138 " --> pdb=" O ALA D 134 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 185 Proline residue: D 182 - end of helix Processing helix chain 'D' and resid 200 through 212 Processing helix chain 'D' and resid 229 through 235 Processing helix chain 'D' and resid 248 through 260 Processing helix chain 'D' and resid 284 through 300 removed outlier: 7.060A pdb=" N HIS D 298 " --> pdb=" O GLY D 294 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLN D 299 " --> pdb=" O VAL D 295 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY D 300 " --> pdb=" O PHE D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 329 removed outlier: 5.740A pdb=" N ASP D 317 " --> pdb=" O SER D 314 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU D 318 " --> pdb=" O ILE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 348 through 364 Processing helix chain 'D' and resid 395 through 397 No H-bonds generated for 'chain 'D' and resid 395 through 397' Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 438 through 446 Processing helix chain 'D' and resid 480 through 486 removed outlier: 3.683A pdb=" N GLU D 485 " --> pdb=" O TYR D 481 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N TYR D 486 " --> pdb=" O GLY D 482 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 23 through 25 Processing sheet with id= B, first strand: chain 'A' and resid 143 through 145 removed outlier: 4.238A pdb=" N THR A 153 " --> pdb=" O ILE A 145 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 265 through 269 removed outlier: 6.349A pdb=" N THR A 189 " --> pdb=" O CYS A 163 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N GLN A 165 " --> pdb=" O THR A 189 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL A 191 " --> pdb=" O GLN A 165 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 452 through 454 removed outlier: 6.644A pdb=" N ALA A 430 " --> pdb=" O TRP A 453 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N PHE A 433 " --> pdb=" O PRO A 275 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE A 277 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N CYS A 276 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE A 309 " --> pdb=" O CYS A 276 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 278 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL A 311 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N VAL A 405 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ILE A 309 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLN A 407 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N VAL A 311 " --> pdb=" O GLN A 407 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N MET A 409 " --> pdb=" O VAL A 311 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR A 385 " --> pdb=" O GLN A 406 " (cutoff:3.500A) removed outlier: 8.155A pdb=" N ILE A 408 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N PHE A 387 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N LYS A 410 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS A 370 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N SER A 388 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 5.545A pdb=" N LEU A 368 " --> pdb=" O SER A 388 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 37 through 42 removed outlier: 3.787A pdb=" N CYS A 50 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N ASN A 42 " --> pdb=" O GLU A 48 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLU A 48 " --> pdb=" O ASN A 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 23 through 25 Processing sheet with id= G, first strand: chain 'B' and resid 143 through 145 removed outlier: 4.225A pdb=" N THR B 153 " --> pdb=" O ILE B 145 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 265 through 269 removed outlier: 6.393A pdb=" N THR B 189 " --> pdb=" O CYS B 163 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N GLN B 165 " --> pdb=" O THR B 189 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL B 191 " --> pdb=" O GLN B 165 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 367 through 370 removed outlier: 6.468A pdb=" N VAL B 386 " --> pdb=" O GLU B 369 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER B 307 " --> pdb=" O VAL B 405 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN B 407 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N SER B 274 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ILE B 309 " --> pdb=" O SER B 274 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N CYS B 276 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N VAL B 311 " --> pdb=" O CYS B 276 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL B 278 " --> pdb=" O VAL B 311 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 429 through 432 removed outlier: 6.671A pdb=" N THR B 451 " --> pdb=" O ALA B 430 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL B 432 " --> pdb=" O THR B 451 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TRP B 453 " --> pdb=" O VAL B 432 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 37 through 42 removed outlier: 3.789A pdb=" N CYS B 50 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ASN B 42 " --> pdb=" O GLU B 48 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU B 48 " --> pdb=" O ASN B 42 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 23 through 25 Processing sheet with id= M, first strand: chain 'C' and resid 143 through 145 removed outlier: 4.261A pdb=" N THR C 153 " --> pdb=" O ILE C 145 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 265 through 269 removed outlier: 6.372A pdb=" N THR C 189 " --> pdb=" O CYS C 163 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N GLN C 165 " --> pdb=" O THR C 189 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL C 191 " --> pdb=" O GLN C 165 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 451 through 454 removed outlier: 8.496A pdb=" N PHE C 433 " --> pdb=" O PRO C 275 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N ILE C 277 " --> pdb=" O PHE C 433 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N CYS C 276 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ILE C 309 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N VAL C 278 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL C 311 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N VAL C 405 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N ILE C 309 " --> pdb=" O VAL C 405 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLN C 407 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N VAL C 311 " --> pdb=" O GLN C 407 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N MET C 409 " --> pdb=" O VAL C 311 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N THR C 385 " --> pdb=" O GLN C 406 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ILE C 408 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N PHE C 387 " --> pdb=" O ILE C 408 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N LYS C 410 " --> pdb=" O PHE C 387 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N CYS C 370 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N SER C 388 " --> pdb=" O LEU C 368 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N LEU C 368 " --> pdb=" O SER C 388 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 37 through 42 removed outlier: 3.744A pdb=" N CYS C 50 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ASN C 42 " --> pdb=" O GLU C 48 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N GLU C 48 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 23 through 25 Processing sheet with id= R, first strand: chain 'D' and resid 143 through 145 removed outlier: 4.207A pdb=" N THR D 153 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 265 through 269 removed outlier: 6.374A pdb=" N THR D 189 " --> pdb=" O CYS D 163 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLN D 165 " --> pdb=" O THR D 189 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL D 191 " --> pdb=" O GLN D 165 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 452 through 454 removed outlier: 6.628A pdb=" N ALA D 430 " --> pdb=" O TRP D 453 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N PHE D 433 " --> pdb=" O PRO D 275 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE D 277 " --> pdb=" O PHE D 433 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N CYS D 276 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ILE D 309 " --> pdb=" O CYS D 276 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL D 278 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VAL D 311 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 8.031A pdb=" N VAL D 405 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N ILE D 309 " --> pdb=" O VAL D 405 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N GLN D 407 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL D 311 " --> pdb=" O GLN D 407 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N MET D 409 " --> pdb=" O VAL D 311 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR D 385 " --> pdb=" O GLN D 406 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE D 408 " --> pdb=" O THR D 385 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N PHE D 387 " --> pdb=" O ILE D 408 " (cutoff:3.500A) removed outlier: 8.609A pdb=" N LYS D 410 " --> pdb=" O PHE D 387 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N CYS D 370 " --> pdb=" O VAL D 386 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N SER D 388 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LEU D 368 " --> pdb=" O SER D 388 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 37 through 42 removed outlier: 3.812A pdb=" N CYS D 50 " --> pdb=" O VAL D 40 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASN D 42 " --> pdb=" O GLU D 48 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N GLU D 48 " --> pdb=" O ASN D 42 " (cutoff:3.500A) 610 hydrogen bonds defined for protein. 1635 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: 5.02 Time building geometry restraints manager: 6.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5004 1.34 - 1.46: 3410 1.46 - 1.58: 7214 1.58 - 1.69: 12 1.69 - 1.81: 108 Bond restraints: 15748 Sorted by residual: bond pdb=" C3N NAD C 601 " pdb=" C4N NAD C 601 " ideal model delta sigma weight residual 1.390 1.499 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C3N NAD A 601 " pdb=" C4N NAD A 601 " ideal model delta sigma weight residual 1.390 1.499 -0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C3N NAD D 601 " pdb=" C4N NAD D 601 " ideal model delta sigma weight residual 1.390 1.499 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C3N NAD B 601 " pdb=" C4N NAD B 601 " ideal model delta sigma weight residual 1.390 1.498 -0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C4N NAD B 601 " pdb=" C5N NAD B 601 " ideal model delta sigma weight residual 1.384 1.485 -0.101 2.00e-02 2.50e+03 2.54e+01 ... (remaining 15743 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.70: 663 107.70 - 114.97: 9375 114.97 - 122.24: 8721 122.24 - 129.51: 2497 129.51 - 136.78: 96 Bond angle restraints: 21352 Sorted by residual: angle pdb=" PA NAD A 601 " pdb=" O3 NAD A 601 " pdb=" PN NAD A 601 " ideal model delta sigma weight residual 126.50 136.78 -10.28 3.00e+00 1.11e-01 1.17e+01 angle pdb=" PA NAD D 601 " pdb=" O3 NAD D 601 " pdb=" PN NAD D 601 " ideal model delta sigma weight residual 126.50 136.74 -10.24 3.00e+00 1.11e-01 1.17e+01 angle pdb=" PA NAD B 601 " pdb=" O3 NAD B 601 " pdb=" PN NAD B 601 " ideal model delta sigma weight residual 126.50 136.70 -10.20 3.00e+00 1.11e-01 1.16e+01 angle pdb=" PA NAD C 601 " pdb=" O3 NAD C 601 " pdb=" PN NAD C 601 " ideal model delta sigma weight residual 126.50 136.68 -10.18 3.00e+00 1.11e-01 1.15e+01 angle pdb=" C3N NAD C 601 " pdb=" C4N NAD C 601 " pdb=" C5N NAD C 601 " ideal model delta sigma weight residual 119.68 110.28 9.40 3.00e+00 1.11e-01 9.81e+00 ... (remaining 21347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.87: 8304 11.87 - 23.74: 792 23.74 - 35.61: 231 35.61 - 47.48: 98 47.48 - 59.35: 83 Dihedral angle restraints: 9508 sinusoidal: 3908 harmonic: 5600 Sorted by residual: dihedral pdb=" CA THR D 144 " pdb=" C THR D 144 " pdb=" N ILE D 145 " pdb=" CA ILE D 145 " ideal model delta harmonic sigma weight residual 180.00 -160.40 -19.60 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA THR C 144 " pdb=" C THR C 144 " pdb=" N ILE C 145 " pdb=" CA ILE C 145 " ideal model delta harmonic sigma weight residual -180.00 -160.98 -19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA THR A 144 " pdb=" C THR A 144 " pdb=" N ILE A 145 " pdb=" CA ILE A 145 " ideal model delta harmonic sigma weight residual 180.00 -161.82 -18.18 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 9505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1504 0.031 - 0.061: 550 0.061 - 0.092: 159 0.092 - 0.123: 144 0.123 - 0.154: 7 Chirality restraints: 2364 Sorted by residual: chirality pdb=" C2B NAD D 601 " pdb=" C1B NAD D 601 " pdb=" C3B NAD D 601 " pdb=" O2B NAD D 601 " both_signs ideal model delta sigma weight residual False -2.53 -2.69 0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" C2B NAD B 601 " pdb=" C1B NAD B 601 " pdb=" C3B NAD B 601 " pdb=" O2B NAD B 601 " both_signs ideal model delta sigma weight residual False -2.53 -2.68 0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" C2B NAD C 601 " pdb=" C1B NAD C 601 " pdb=" C3B NAD C 601 " pdb=" O2B NAD C 601 " both_signs ideal model delta sigma weight residual False -2.53 -2.68 0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 2361 not shown) Planarity restraints: 2736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD B 601 " -0.025 2.00e-02 2.50e+03 6.53e-02 8.52e+01 pdb=" C2N NAD B 601 " -0.057 2.00e-02 2.50e+03 pdb=" C3N NAD B 601 " -0.059 2.00e-02 2.50e+03 pdb=" C4N NAD B 601 " -0.068 2.00e-02 2.50e+03 pdb=" C5N NAD B 601 " -0.010 2.00e-02 2.50e+03 pdb=" C6N NAD B 601 " 0.109 2.00e-02 2.50e+03 pdb=" C7N NAD B 601 " 0.100 2.00e-02 2.50e+03 pdb=" N1N NAD B 601 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD D 601 " 0.024 2.00e-02 2.50e+03 5.70e-02 6.49e+01 pdb=" C2N NAD D 601 " 0.047 2.00e-02 2.50e+03 pdb=" C3N NAD D 601 " 0.054 2.00e-02 2.50e+03 pdb=" C4N NAD D 601 " 0.051 2.00e-02 2.50e+03 pdb=" C5N NAD D 601 " 0.020 2.00e-02 2.50e+03 pdb=" C6N NAD D 601 " -0.101 2.00e-02 2.50e+03 pdb=" C7N NAD D 601 " -0.084 2.00e-02 2.50e+03 pdb=" N1N NAD D 601 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD A 601 " -0.009 2.00e-02 2.50e+03 4.55e-02 4.14e+01 pdb=" C2N NAD A 601 " 0.056 2.00e-02 2.50e+03 pdb=" C3N NAD A 601 " 0.057 2.00e-02 2.50e+03 pdb=" C4N NAD A 601 " 0.034 2.00e-02 2.50e+03 pdb=" C5N NAD A 601 " -0.009 2.00e-02 2.50e+03 pdb=" C6N NAD A 601 " -0.049 2.00e-02 2.50e+03 pdb=" C7N NAD A 601 " -0.080 2.00e-02 2.50e+03 pdb=" N1N NAD A 601 " -0.000 2.00e-02 2.50e+03 ... (remaining 2733 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3514 2.79 - 3.32: 14679 3.32 - 3.84: 26441 3.84 - 4.37: 32763 4.37 - 4.90: 54722 Nonbonded interactions: 132119 Sorted by model distance: nonbonded pdb=" O SER B 307 " pdb=" NE2 GLN B 407 " model vdw 2.262 2.520 nonbonded pdb=" OD1 ASP C 281 " pdb=" OG1 THR C 434 " model vdw 2.269 2.440 nonbonded pdb=" OD1 ASP A 281 " pdb=" OG1 THR A 434 " model vdw 2.273 2.440 nonbonded pdb=" OG SER B 461 " pdb=" OE1 GLN B 463 " model vdw 2.274 2.440 nonbonded pdb=" O SER A 307 " pdb=" NE2 GLN A 407 " model vdw 2.290 2.520 ... (remaining 132114 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 501 or resid 601)) selection = (chain 'B' and (resid 9 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 501 or resid 601)) selection = chain 'C' selection = (chain 'D' and (resid 9 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 501 or resid 601)) } 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.500 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 43.960 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.090 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:12.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 65.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 15748 Z= 0.293 Angle : 0.598 10.283 21352 Z= 0.308 Chirality : 0.041 0.154 2364 Planarity : 0.005 0.065 2736 Dihedral : 12.542 59.347 5940 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.15 % Allowed : 6.01 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.20), residues: 1964 helix: 1.11 (0.19), residues: 828 sheet: 0.10 (0.26), residues: 420 loop : -0.39 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 453 HIS 0.002 0.001 HIS D 204 PHE 0.009 0.001 PHE D 290 TYR 0.016 0.001 TYR D 351 ARG 0.004 0.000 ARG D 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 346 time to evaluate : 1.896 Fit side-chains revert: symmetry clash REVERT: A 13 LEU cc_start: 0.5007 (OUTLIER) cc_final: 0.4634 (pp) REVERT: A 409 MET cc_start: 0.7342 (mtp) cc_final: 0.7068 (mtm) REVERT: A 441 ILE cc_start: 0.7706 (mm) cc_final: 0.7497 (mm) REVERT: B 13 LEU cc_start: 0.4899 (OUTLIER) cc_final: 0.4532 (pp) REVERT: B 341 THR cc_start: 0.7504 (p) cc_final: 0.7219 (p) REVERT: B 441 ILE cc_start: 0.7592 (mm) cc_final: 0.7357 (mm) REVERT: C 13 LEU cc_start: 0.4919 (OUTLIER) cc_final: 0.4543 (pp) REVERT: C 330 TYR cc_start: 0.6776 (OUTLIER) cc_final: 0.5236 (t80) REVERT: C 409 MET cc_start: 0.7381 (mtp) cc_final: 0.7121 (mtm) REVERT: C 441 ILE cc_start: 0.7596 (mm) cc_final: 0.7348 (mm) REVERT: D 330 TYR cc_start: 0.6799 (OUTLIER) cc_final: 0.5385 (t80) REVERT: D 409 MET cc_start: 0.7305 (mtp) cc_final: 0.7051 (mtm) outliers start: 35 outliers final: 12 residues processed: 369 average time/residue: 1.2489 time to fit residues: 509.5687 Evaluate side-chains 249 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 232 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 469 PHE Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 469 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 0.0870 chunk 50 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 59 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 299 GLN ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 ASN B 157 HIS B 220 ASN B 262 ASN B 299 GLN B 301 GLN B 342 GLN ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 157 HIS ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 GLN C 342 GLN D 299 GLN D 301 GLN D 342 GLN ** D 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15748 Z= 0.275 Angle : 0.527 6.530 21352 Z= 0.279 Chirality : 0.043 0.169 2364 Planarity : 0.005 0.040 2736 Dihedral : 9.896 57.977 2353 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.15 % Allowed : 14.16 % Favored : 80.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.19), residues: 1964 helix: 0.94 (0.18), residues: 832 sheet: 0.00 (0.26), residues: 420 loop : -0.38 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 178 HIS 0.009 0.001 HIS C 484 PHE 0.011 0.002 PHE C 24 TYR 0.019 0.002 TYR D 351 ARG 0.004 0.001 ARG B 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 245 time to evaluate : 1.793 Fit side-chains revert: symmetry clash REVERT: A 13 LEU cc_start: 0.5052 (OUTLIER) cc_final: 0.4715 (pp) REVERT: A 19 GLN cc_start: 0.6971 (OUTLIER) cc_final: 0.6210 (mm-40) REVERT: A 156 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7684 (mtp85) REVERT: A 399 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7243 (mt-10) REVERT: A 409 MET cc_start: 0.7454 (mtp) cc_final: 0.7194 (mtm) REVERT: A 481 TYR cc_start: 0.6762 (t80) cc_final: 0.6428 (t80) REVERT: A 485 GLU cc_start: 0.6789 (OUTLIER) cc_final: 0.6256 (mp0) REVERT: B 13 LEU cc_start: 0.5005 (OUTLIER) cc_final: 0.4675 (pp) REVERT: B 19 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6398 (mm-40) REVERT: B 341 THR cc_start: 0.7326 (p) cc_final: 0.7033 (p) REVERT: B 399 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7400 (mt-10) REVERT: B 485 GLU cc_start: 0.6950 (OUTLIER) cc_final: 0.6727 (mm-30) REVERT: C 13 LEU cc_start: 0.4919 (OUTLIER) cc_final: 0.4585 (pp) REVERT: C 19 GLN cc_start: 0.6951 (OUTLIER) cc_final: 0.5914 (mm-40) REVERT: C 156 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7662 (mtp85) REVERT: C 409 MET cc_start: 0.7477 (mtp) cc_final: 0.7250 (mtm) REVERT: C 481 TYR cc_start: 0.6685 (t80) cc_final: 0.6400 (t80) REVERT: C 485 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6261 (mp0) REVERT: D 19 GLN cc_start: 0.6975 (OUTLIER) cc_final: 0.6309 (mm-40) REVERT: D 102 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7307 (tt) REVERT: D 156 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7644 (mtp85) REVERT: D 329 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7442 (mttp) REVERT: D 399 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.7241 (mt-10) REVERT: D 409 MET cc_start: 0.7498 (mtp) cc_final: 0.7146 (mtm) REVERT: D 481 TYR cc_start: 0.6702 (t80) cc_final: 0.6414 (t80) REVERT: D 485 GLU cc_start: 0.6708 (OUTLIER) cc_final: 0.6167 (mp0) outliers start: 84 outliers final: 37 residues processed: 286 average time/residue: 1.2324 time to fit residues: 390.5468 Evaluate side-chains 290 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 234 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 389 ASN Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 389 ASN Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 389 ASN Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 485 GLU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 469 PHE Chi-restraints excluded: chain D residue 485 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 178 optimal weight: 0.9980 chunk 192 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 389 ASN B 69 GLN B 262 ASN ** B 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 262 ASN C 350 GLN D 69 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15748 Z= 0.339 Angle : 0.557 7.454 21352 Z= 0.294 Chirality : 0.044 0.166 2364 Planarity : 0.005 0.045 2736 Dihedral : 9.233 59.908 2346 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 5.52 % Allowed : 15.88 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.19), residues: 1964 helix: 0.78 (0.18), residues: 824 sheet: -0.15 (0.25), residues: 420 loop : -0.36 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 178 HIS 0.007 0.001 HIS C 484 PHE 0.013 0.002 PHE D 290 TYR 0.022 0.002 TYR D 351 ARG 0.004 0.001 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 223 time to evaluate : 1.899 Fit side-chains REVERT: A 19 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6130 (mm-40) REVERT: A 156 ARG cc_start: 0.8197 (OUTLIER) cc_final: 0.7655 (mtp85) REVERT: A 399 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7296 (mt-10) REVERT: A 409 MET cc_start: 0.7464 (mtp) cc_final: 0.7189 (mtm) REVERT: B 19 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.6327 (mm-40) REVERT: B 58 GLU cc_start: 0.6736 (mp0) cc_final: 0.6354 (mp0) REVERT: B 341 THR cc_start: 0.7377 (p) cc_final: 0.7099 (p) REVERT: B 399 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7386 (mt-10) REVERT: C 19 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.6044 (mm-40) REVERT: C 156 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7616 (mtp85) REVERT: C 399 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7267 (mt-10) REVERT: C 409 MET cc_start: 0.7495 (mtp) cc_final: 0.7180 (mtm) REVERT: D 19 GLN cc_start: 0.7057 (OUTLIER) cc_final: 0.6317 (mm-40) REVERT: D 102 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7326 (tt) REVERT: D 156 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7625 (mtp85) REVERT: D 329 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7539 (mttp) REVERT: D 409 MET cc_start: 0.7563 (mtp) cc_final: 0.7248 (mtm) outliers start: 90 outliers final: 45 residues processed: 276 average time/residue: 1.2631 time to fit residues: 385.7638 Evaluate side-chains 276 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 219 time to evaluate : 1.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 389 ASN Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 402 PHE Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 389 ASN Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 389 ASN Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 469 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 119 optimal weight: 0.7980 chunk 178 optimal weight: 0.8980 chunk 189 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN B 69 GLN B 262 ASN B 389 ASN C 69 GLN C 262 ASN D 69 GLN D 157 HIS D 389 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15748 Z= 0.250 Angle : 0.512 6.103 21352 Z= 0.271 Chirality : 0.042 0.160 2364 Planarity : 0.004 0.035 2736 Dihedral : 8.689 59.875 2346 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.82 % Allowed : 17.04 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.19), residues: 1964 helix: 0.81 (0.18), residues: 824 sheet: -0.13 (0.25), residues: 420 loop : -0.34 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 178 HIS 0.007 0.001 HIS C 484 PHE 0.012 0.001 PHE D 290 TYR 0.020 0.002 TYR D 351 ARG 0.003 0.000 ARG C 395 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 224 time to evaluate : 1.597 Fit side-chains REVERT: A 19 GLN cc_start: 0.7004 (OUTLIER) cc_final: 0.6081 (mm-40) REVERT: A 156 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7632 (mtp85) REVERT: A 399 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7304 (mt-10) REVERT: A 409 MET cc_start: 0.7420 (mtp) cc_final: 0.7155 (mtm) REVERT: A 485 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6683 (mm-30) REVERT: B 19 GLN cc_start: 0.6970 (OUTLIER) cc_final: 0.6193 (mm-40) REVERT: B 58 GLU cc_start: 0.6697 (mp0) cc_final: 0.6378 (mp0) REVERT: B 341 THR cc_start: 0.7388 (p) cc_final: 0.7083 (p) REVERT: B 485 GLU cc_start: 0.6951 (OUTLIER) cc_final: 0.6698 (mm-30) REVERT: C 19 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6071 (mm-40) REVERT: C 156 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7596 (mtp85) REVERT: C 399 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7293 (mt-10) REVERT: D 19 GLN cc_start: 0.7018 (OUTLIER) cc_final: 0.6125 (mm-40) REVERT: D 102 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.7268 (tt) REVERT: D 156 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7610 (mtp85) REVERT: D 329 LYS cc_start: 0.7764 (OUTLIER) cc_final: 0.7513 (mttp) REVERT: D 399 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7296 (mt-10) REVERT: D 409 MET cc_start: 0.7461 (mtp) cc_final: 0.7169 (mtm) REVERT: D 485 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.6675 (mm-30) outliers start: 95 outliers final: 49 residues processed: 286 average time/residue: 1.3169 time to fit residues: 414.8412 Evaluate side-chains 277 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 213 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 389 ASN Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 329 LYS Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 469 PHE Chi-restraints excluded: chain D residue 485 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 157 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 2 optimal weight: 0.0970 chunk 141 optimal weight: 0.0670 chunk 78 optimal weight: 6.9990 chunk 161 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 170 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.0318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN B 69 GLN B 262 ASN C 69 GLN C 262 ASN D 69 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15748 Z= 0.219 Angle : 0.496 5.679 21352 Z= 0.263 Chirality : 0.041 0.166 2364 Planarity : 0.004 0.034 2736 Dihedral : 8.281 59.918 2346 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.76 % Allowed : 17.66 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.19), residues: 1964 helix: 0.87 (0.18), residues: 824 sheet: -0.11 (0.25), residues: 420 loop : -0.30 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 178 HIS 0.008 0.001 HIS C 484 PHE 0.011 0.001 PHE D 290 TYR 0.019 0.001 TYR D 351 ARG 0.003 0.000 ARG B 321 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 216 time to evaluate : 1.638 Fit side-chains REVERT: A 19 GLN cc_start: 0.7014 (OUTLIER) cc_final: 0.6045 (mm-40) REVERT: A 58 GLU cc_start: 0.6527 (mp0) cc_final: 0.6319 (mp0) REVERT: A 156 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7653 (mtp85) REVERT: A 399 GLU cc_start: 0.7626 (OUTLIER) cc_final: 0.7303 (mt-10) REVERT: A 409 MET cc_start: 0.7402 (mtp) cc_final: 0.7156 (mtm) REVERT: A 485 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.6656 (mm-30) REVERT: B 19 GLN cc_start: 0.6920 (OUTLIER) cc_final: 0.6205 (mm-40) REVERT: B 58 GLU cc_start: 0.6683 (mp0) cc_final: 0.6391 (mp0) REVERT: B 341 THR cc_start: 0.7417 (p) cc_final: 0.7060 (p) REVERT: B 485 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6698 (mm-30) REVERT: C 19 GLN cc_start: 0.7009 (OUTLIER) cc_final: 0.6054 (mm-40) REVERT: C 156 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7580 (mtp85) REVERT: C 399 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7296 (mt-10) REVERT: D 19 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.6086 (mm-40) REVERT: D 102 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7290 (tt) REVERT: D 156 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7602 (mtp85) REVERT: D 399 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7309 (mt-10) REVERT: D 409 MET cc_start: 0.7418 (mtp) cc_final: 0.7122 (mtm) REVERT: D 485 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6624 (mm-30) outliers start: 94 outliers final: 54 residues processed: 283 average time/residue: 1.2657 time to fit residues: 395.1856 Evaluate side-chains 281 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 213 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 412 LYS Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 389 ASN Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 412 LYS Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 469 PHE Chi-restraints excluded: chain D residue 485 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 63 optimal weight: 0.5980 chunk 170 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 46 optimal weight: 0.5980 chunk 189 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN B 69 GLN B 262 ASN C 69 GLN C 262 ASN D 69 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15748 Z= 0.184 Angle : 0.476 5.802 21352 Z= 0.253 Chirality : 0.041 0.162 2364 Planarity : 0.004 0.034 2736 Dihedral : 7.979 59.331 2346 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.58 % Allowed : 18.33 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.19), residues: 1964 helix: 0.97 (0.18), residues: 824 sheet: -0.08 (0.25), residues: 420 loop : -0.25 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 453 HIS 0.008 0.001 HIS A 484 PHE 0.010 0.001 PHE D 290 TYR 0.018 0.001 TYR D 351 ARG 0.004 0.000 ARG B 321 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 218 time to evaluate : 1.782 Fit side-chains REVERT: A 19 GLN cc_start: 0.7022 (OUTLIER) cc_final: 0.5999 (mm-40) REVERT: A 156 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7785 (mtp85) REVERT: A 367 LYS cc_start: 0.7303 (mtpp) cc_final: 0.6907 (ttpt) REVERT: A 399 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7297 (mt-10) REVERT: A 409 MET cc_start: 0.7394 (mtp) cc_final: 0.7180 (mtm) REVERT: A 485 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6673 (mm-30) REVERT: B 19 GLN cc_start: 0.6892 (OUTLIER) cc_final: 0.6119 (mm-40) REVERT: B 341 THR cc_start: 0.7399 (p) cc_final: 0.7037 (p) REVERT: B 485 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.6687 (mm-30) REVERT: C 19 GLN cc_start: 0.6981 (OUTLIER) cc_final: 0.6066 (mm-40) REVERT: C 156 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7677 (mtp85) REVERT: C 349 GLU cc_start: 0.6401 (OUTLIER) cc_final: 0.6102 (mp0) REVERT: C 367 LYS cc_start: 0.7301 (mtpp) cc_final: 0.6994 (ttpt) REVERT: C 399 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7295 (mt-10) REVERT: D 19 GLN cc_start: 0.6997 (OUTLIER) cc_final: 0.6006 (mm-40) REVERT: D 102 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7269 (tt) REVERT: D 156 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7578 (mtp85) REVERT: D 349 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.6202 (mp0) REVERT: D 409 MET cc_start: 0.7399 (mtp) cc_final: 0.7111 (mtm) REVERT: D 485 GLU cc_start: 0.6851 (OUTLIER) cc_final: 0.6615 (mm-30) outliers start: 91 outliers final: 53 residues processed: 283 average time/residue: 1.2791 time to fit residues: 400.2989 Evaluate side-chains 274 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 206 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 412 LYS Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 389 ASN Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 412 LYS Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 469 PHE Chi-restraints excluded: chain D residue 485 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 188 optimal weight: 0.1980 chunk 118 optimal weight: 0.6980 chunk 115 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN B 69 GLN B 262 ASN C 69 GLN C 262 ASN D 69 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15748 Z= 0.211 Angle : 0.490 6.151 21352 Z= 0.260 Chirality : 0.041 0.161 2364 Planarity : 0.004 0.034 2736 Dihedral : 7.859 59.946 2346 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 5.52 % Allowed : 18.82 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.19), residues: 1964 helix: 0.96 (0.18), residues: 824 sheet: -0.08 (0.25), residues: 420 loop : -0.27 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 178 HIS 0.010 0.001 HIS C 484 PHE 0.010 0.001 PHE C 290 TYR 0.019 0.001 TYR D 351 ARG 0.005 0.000 ARG D 321 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 208 time to evaluate : 1.909 Fit side-chains REVERT: A 19 GLN cc_start: 0.7030 (OUTLIER) cc_final: 0.6004 (mm-40) REVERT: A 156 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7763 (mtp85) REVERT: A 399 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7296 (mt-10) REVERT: A 409 MET cc_start: 0.7383 (mtp) cc_final: 0.7156 (mtm) REVERT: A 485 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6687 (mm-30) REVERT: B 19 GLN cc_start: 0.6900 (OUTLIER) cc_final: 0.6073 (mm-40) REVERT: B 58 GLU cc_start: 0.6656 (mp0) cc_final: 0.6399 (mp0) REVERT: B 341 THR cc_start: 0.7408 (p) cc_final: 0.7040 (p) REVERT: B 367 LYS cc_start: 0.7259 (mtpp) cc_final: 0.7032 (mtpm) REVERT: B 485 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6694 (mm-30) REVERT: C 19 GLN cc_start: 0.6983 (OUTLIER) cc_final: 0.6026 (mm-40) REVERT: C 156 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7716 (mtp85) REVERT: C 349 GLU cc_start: 0.6411 (OUTLIER) cc_final: 0.6127 (mp0) REVERT: C 367 LYS cc_start: 0.7330 (mtpp) cc_final: 0.7009 (ttpt) REVERT: C 399 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7272 (mt-10) REVERT: C 485 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6651 (mm-30) REVERT: D 19 GLN cc_start: 0.7041 (OUTLIER) cc_final: 0.6018 (mm-40) REVERT: D 102 LEU cc_start: 0.7542 (OUTLIER) cc_final: 0.7263 (tt) REVERT: D 156 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7583 (mtp85) REVERT: D 349 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.6238 (mp0) REVERT: D 399 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7350 (mt-10) REVERT: D 409 MET cc_start: 0.7413 (mtp) cc_final: 0.7127 (mtm) REVERT: D 485 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.6672 (mm-30) outliers start: 90 outliers final: 59 residues processed: 270 average time/residue: 1.3172 time to fit residues: 397.1485 Evaluate side-chains 280 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 204 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 412 LYS Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 220 ASN Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 389 ASN Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 412 LYS Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 485 GLU Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 469 PHE Chi-restraints excluded: chain D residue 485 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 116 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 120 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN B 69 GLN B 262 ASN C 69 GLN C 262 ASN D 69 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15748 Z= 0.216 Angle : 0.491 5.960 21352 Z= 0.260 Chirality : 0.041 0.160 2364 Planarity : 0.004 0.033 2736 Dihedral : 7.789 59.483 2346 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 5.52 % Allowed : 18.76 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.19), residues: 1964 helix: 0.95 (0.18), residues: 824 sheet: -0.08 (0.25), residues: 420 loop : -0.28 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 178 HIS 0.010 0.001 HIS C 484 PHE 0.010 0.001 PHE C 290 TYR 0.019 0.001 TYR D 351 ARG 0.006 0.000 ARG C 321 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 209 time to evaluate : 1.921 Fit side-chains REVERT: A 19 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.5964 (mm-40) REVERT: A 156 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7765 (mtp85) REVERT: A 367 LYS cc_start: 0.7335 (mtpp) cc_final: 0.6951 (ttpp) REVERT: A 399 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7298 (mt-10) REVERT: A 409 MET cc_start: 0.7389 (mtp) cc_final: 0.7159 (mtm) REVERT: A 485 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6695 (mm-30) REVERT: B 19 GLN cc_start: 0.6856 (OUTLIER) cc_final: 0.6014 (mm-40) REVERT: B 58 GLU cc_start: 0.6589 (mp0) cc_final: 0.6343 (mp0) REVERT: B 341 THR cc_start: 0.7416 (p) cc_final: 0.7048 (p) REVERT: B 485 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6700 (mm-30) REVERT: C 19 GLN cc_start: 0.6989 (OUTLIER) cc_final: 0.6036 (mm-40) REVERT: C 102 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7280 (tt) REVERT: C 156 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7715 (mtp85) REVERT: C 349 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.6129 (mp0) REVERT: C 367 LYS cc_start: 0.7305 (mtpp) cc_final: 0.6974 (ttpt) REVERT: C 399 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7274 (mt-10) REVERT: C 409 MET cc_start: 0.7670 (mtm) cc_final: 0.7460 (mtp) REVERT: C 485 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6705 (mm-30) REVERT: D 19 GLN cc_start: 0.7048 (OUTLIER) cc_final: 0.6027 (mm-40) REVERT: D 102 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7267 (tt) REVERT: D 156 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7585 (mtp85) REVERT: D 349 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.6241 (mp0) REVERT: D 399 GLU cc_start: 0.7662 (OUTLIER) cc_final: 0.7347 (mt-10) REVERT: D 409 MET cc_start: 0.7424 (mtp) cc_final: 0.7134 (mtm) REVERT: D 485 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.6684 (mm-30) outliers start: 90 outliers final: 58 residues processed: 271 average time/residue: 1.3305 time to fit residues: 398.4108 Evaluate side-chains 283 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 207 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 220 ASN Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 412 LYS Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 389 ASN Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 412 LYS Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 485 GLU Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 469 PHE Chi-restraints excluded: chain D residue 485 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 171 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 176 optimal weight: 0.2980 chunk 105 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 54 optimal weight: 0.3980 chunk 159 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN B 69 GLN B 262 ASN C 69 GLN C 262 ASN D 69 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15748 Z= 0.166 Angle : 0.470 6.295 21352 Z= 0.249 Chirality : 0.040 0.157 2364 Planarity : 0.004 0.033 2736 Dihedral : 7.556 59.708 2346 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.23 % Allowed : 20.17 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.20), residues: 1964 helix: 1.05 (0.18), residues: 824 sheet: 0.01 (0.26), residues: 420 loop : -0.25 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 178 HIS 0.011 0.001 HIS C 484 PHE 0.009 0.001 PHE C 290 TYR 0.017 0.001 TYR D 351 ARG 0.005 0.000 ARG A 321 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 214 time to evaluate : 1.992 Fit side-chains REVERT: A 19 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.5938 (mm-40) REVERT: A 156 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7740 (mtp85) REVERT: A 367 LYS cc_start: 0.7263 (mtpp) cc_final: 0.6903 (ttpp) REVERT: A 399 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7254 (mt-10) REVERT: B 19 GLN cc_start: 0.6817 (OUTLIER) cc_final: 0.5874 (mm-40) REVERT: B 58 GLU cc_start: 0.6564 (mp0) cc_final: 0.6310 (mp0) REVERT: B 341 THR cc_start: 0.7394 (p) cc_final: 0.7024 (p) REVERT: C 19 GLN cc_start: 0.6952 (OUTLIER) cc_final: 0.5991 (mm-40) REVERT: C 102 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7227 (tt) REVERT: C 156 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7689 (mtp85) REVERT: C 349 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.6010 (mp0) REVERT: C 367 LYS cc_start: 0.7247 (mtpp) cc_final: 0.6960 (ttpt) REVERT: C 399 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7261 (mt-10) REVERT: D 19 GLN cc_start: 0.7026 (OUTLIER) cc_final: 0.5957 (mm-40) REVERT: D 102 LEU cc_start: 0.7603 (OUTLIER) cc_final: 0.7327 (tt) REVERT: D 156 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7670 (mtp85) REVERT: D 399 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7335 (mt-10) REVERT: D 409 MET cc_start: 0.7386 (mtp) cc_final: 0.7100 (mtm) outliers start: 69 outliers final: 45 residues processed: 261 average time/residue: 1.2875 time to fit residues: 371.0992 Evaluate side-chains 267 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 209 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 412 LYS Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 389 ASN Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 469 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.8980 chunk 186 optimal weight: 0.0980 chunk 113 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 120 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 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 69 GLN B 69 GLN B 262 ASN C 69 GLN C 262 ASN D 69 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15748 Z= 0.232 Angle : 0.496 6.250 21352 Z= 0.263 Chirality : 0.041 0.159 2364 Planarity : 0.004 0.033 2736 Dihedral : 7.599 59.832 2346 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.23 % Allowed : 20.29 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.19), residues: 1964 helix: 0.96 (0.18), residues: 824 sheet: -0.03 (0.26), residues: 420 loop : -0.27 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP C 178 HIS 0.012 0.001 HIS C 484 PHE 0.010 0.001 PHE B 290 TYR 0.018 0.001 TYR D 351 ARG 0.005 0.001 ARG C 321 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 206 time to evaluate : 1.641 Fit side-chains REVERT: A 19 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.6016 (mm-40) REVERT: A 156 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7766 (mtp85) REVERT: A 367 LYS cc_start: 0.7275 (mtpp) cc_final: 0.6926 (ttpp) REVERT: A 399 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7291 (mt-10) REVERT: B 19 GLN cc_start: 0.6854 (OUTLIER) cc_final: 0.5909 (mm-40) REVERT: B 58 GLU cc_start: 0.6616 (mp0) cc_final: 0.6390 (mp0) REVERT: B 341 THR cc_start: 0.7376 (p) cc_final: 0.7002 (p) REVERT: C 19 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.6021 (mm-40) REVERT: C 102 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7236 (tt) REVERT: C 156 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7704 (mtp85) REVERT: C 349 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.6119 (mp0) REVERT: C 367 LYS cc_start: 0.7243 (mtpp) cc_final: 0.6942 (ttpt) REVERT: C 399 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7271 (mt-10) REVERT: D 19 GLN cc_start: 0.7053 (OUTLIER) cc_final: 0.5983 (mm-40) REVERT: D 102 LEU cc_start: 0.7545 (OUTLIER) cc_final: 0.7257 (tt) REVERT: D 156 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7718 (mtp85) REVERT: D 399 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7351 (mt-10) REVERT: D 409 MET cc_start: 0.7479 (mtp) cc_final: 0.7171 (mtm) outliers start: 69 outliers final: 46 residues processed: 253 average time/residue: 1.3644 time to fit residues: 381.6829 Evaluate side-chains 263 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 204 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 417 VAL Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 412 LYS Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 417 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 389 ASN Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 417 VAL Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 469 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 47 optimal weight: 0.3980 chunk 143 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 155 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN B 69 GLN B 262 ASN C 69 GLN C 262 ASN C 389 ASN D 69 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.154016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.134165 restraints weight = 17724.157| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.09 r_work: 0.3563 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15748 Z= 0.296 Angle : 0.571 12.895 21352 Z= 0.302 Chirality : 0.043 0.161 2364 Planarity : 0.005 0.086 2736 Dihedral : 7.835 58.916 2346 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 4.54 % Allowed : 20.11 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.19), residues: 1964 helix: 0.78 (0.18), residues: 824 sheet: -0.17 (0.25), residues: 420 loop : -0.34 (0.24), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 178 HIS 0.012 0.002 HIS C 484 PHE 0.012 0.002 PHE A 290 TYR 0.020 0.002 TYR D 351 ARG 0.005 0.001 ARG D 131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6390.82 seconds wall clock time: 114 minutes 10.48 seconds (6850.48 seconds total)