Starting phenix.real_space_refine (version: 1.21rc1) on Mon Aug 14 05:20:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ene_28271/08_2023/8ene_28271_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ene_28271/08_2023/8ene_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_28271/08_2023/8ene_28271.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ene_28271/08_2023/8ene_28271.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ene_28271/08_2023/8ene_28271_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ene_28271/08_2023/8ene_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: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: 7.37, per 1000 atoms: 0.48 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: 6.02 Conformation dependent library (CDL) restraints added in 2.3 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: 2.62 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: 4.89 Time building geometry restraints manager: 6.48 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: 8218 11.87 - 23.74: 774 23.74 - 35.61: 200 35.61 - 47.48: 67 47.48 - 59.35: 49 Dihedral angle restraints: 9308 sinusoidal: 3708 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 9305 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: 1.100 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: 7.250 Check model and map are aligned: 0.220 Set scattering table: 0.120 Process input model: 40.360 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.100 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:12.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.340 ------------------------------------------------------------------------------- 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 : 11.369 59.347 5740 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 % 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 *********************** 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 : 1.780 Fit side-chains revert: symmetry clash outliers start: 35 outliers final: 12 residues processed: 369 average time/residue: 1.2464 time to fit residues: 508.8981 Evaluate side-chains 244 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 232 time to evaluate : 1.695 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 4 average time/residue: 0.1923 time to fit residues: 3.5880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 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: 0.5980 chunk 93 optimal weight: 2.9990 chunk 114 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 474 ASN B 157 HIS B 220 ASN B 262 ASN B 299 GLN B 301 GLN B 342 GLN C 157 HIS C 262 ASN C 299 GLN C 342 GLN D 299 GLN D 301 GLN D 342 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 15748 Z= 0.298 Angle : 0.554 7.908 21352 Z= 0.292 Chirality : 0.044 0.169 2364 Planarity : 0.005 0.045 2736 Dihedral : 5.517 49.333 2124 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 5.21 % 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: 0.25 (0.19), residues: 1964 helix: 0.88 (0.18), residues: 832 sheet: -0.06 (0.26), residues: 420 loop : -0.39 (0.24), residues: 712 *********************** 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 325 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 240 time to evaluate : 1.757 Fit side-chains revert: symmetry clash outliers start: 85 outliers final: 42 residues processed: 284 average time/residue: 1.2546 time to fit residues: 394.4391 Evaluate side-chains 276 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 234 time to evaluate : 1.656 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 23 residues processed: 22 average time/residue: 0.2734 time to fit residues: 11.0675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 148 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 178 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 158 optimal weight: 3.9990 chunk 176 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN B 69 GLN B 262 ASN B 389 ASN C 69 GLN C 262 ASN D 69 GLN D 157 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 15748 Z= 0.243 Angle : 0.510 6.111 21352 Z= 0.269 Chirality : 0.042 0.162 2364 Planarity : 0.004 0.034 2736 Dihedral : 5.397 49.946 2124 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 4.97 % 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: 0.28 (0.19), residues: 1964 helix: 0.89 (0.18), residues: 828 sheet: -0.04 (0.26), residues: 420 loop : -0.35 (0.24), residues: 716 *********************** 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 311 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 230 time to evaluate : 1.742 Fit side-chains revert: symmetry clash outliers start: 81 outliers final: 48 residues processed: 282 average time/residue: 1.2760 time to fit residues: 398.1487 Evaluate side-chains 266 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 218 time to evaluate : 1.716 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 32 residues processed: 17 average time/residue: 0.2641 time to fit residues: 8.9286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 3.9990 chunk 134 optimal weight: 0.9980 chunk 92 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 85 optimal weight: 0.5980 chunk 119 optimal weight: 0.7980 chunk 178 optimal weight: 0.9990 chunk 189 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 51 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1782 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= 0.176 Angle : 0.477 5.379 21352 Z= 0.251 Chirality : 0.041 0.157 2364 Planarity : 0.004 0.033 2736 Dihedral : 5.158 48.617 2124 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer Outliers : 4.84 % 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: 0.45 (0.19), residues: 1964 helix: 1.03 (0.18), residues: 824 sheet: 0.03 (0.26), residues: 420 loop : -0.22 (0.24), residues: 720 *********************** 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 310 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 231 time to evaluate : 1.875 Fit side-chains outliers start: 79 outliers final: 50 residues processed: 287 average time/residue: 1.2745 time to fit residues: 405.7861 Evaluate side-chains 269 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 219 time to evaluate : 1.801 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 35 residues processed: 16 average time/residue: 0.1932 time to fit residues: 7.5394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 2 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 161 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 47 optimal weight: 0.0050 overall best weight: 2.3600 ------------------------------------------------------------------------------- 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 C 69 GLN C 262 ASN D 69 GLN D 389 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.050 15748 Z= 0.438 Angle : 0.618 9.035 21352 Z= 0.323 Chirality : 0.046 0.173 2364 Planarity : 0.005 0.044 2736 Dihedral : 5.718 48.574 2124 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 5.58 % 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: -0.03 (0.19), residues: 1964 helix: 0.60 (0.18), residues: 824 sheet: -0.32 (0.25), residues: 420 loop : -0.37 (0.24), residues: 720 *********************** 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 309 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 218 time to evaluate : 1.741 Fit side-chains outliers start: 91 outliers final: 48 residues processed: 283 average time/residue: 1.3036 time to fit residues: 407.7952 Evaluate side-chains 253 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 205 time to evaluate : 1.839 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 33 residues processed: 15 average time/residue: 0.1775 time to fit residues: 6.9523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 37 optimal weight: 0.9990 chunk 111 optimal weight: 0.1980 chunk 46 optimal weight: 7.9990 chunk 189 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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: 0.7428 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 15748 Z= 0.176 Angle : 0.481 5.729 21352 Z= 0.255 Chirality : 0.041 0.159 2364 Planarity : 0.004 0.035 2736 Dihedral : 5.301 50.825 2124 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer Outliers : 3.92 % 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: 0.30 (0.19), residues: 1964 helix: 0.90 (0.18), residues: 824 sheet: -0.08 (0.26), residues: 420 loop : -0.28 (0.24), residues: 720 *********************** 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 272 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 208 time to evaluate : 1.739 Fit side-chains revert: symmetry clash outliers start: 64 outliers final: 45 residues processed: 258 average time/residue: 1.2362 time to fit residues: 354.6583 Evaluate side-chains 241 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 196 time to evaluate : 1.696 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 37 residues processed: 8 average time/residue: 0.1550 time to fit residues: 4.5473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 182 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 188 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 484 HIS B 69 GLN B 262 ASN C 69 GLN C 262 ASN C 389 ASN C 484 HIS D 69 GLN D 389 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.039 15748 Z= 0.340 Angle : 0.567 7.829 21352 Z= 0.297 Chirality : 0.044 0.165 2364 Planarity : 0.005 0.038 2736 Dihedral : 5.578 51.561 2124 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer Outliers : 4.97 % 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: 0.07 (0.19), residues: 1964 helix: 0.71 (0.18), residues: 824 sheet: -0.25 (0.25), residues: 420 loop : -0.35 (0.24), residues: 720 *********************** 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 279 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 198 time to evaluate : 1.901 Fit side-chains outliers start: 81 outliers final: 50 residues processed: 258 average time/residue: 1.2204 time to fit residues: 351.2783 Evaluate side-chains 245 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 195 time to evaluate : 1.909 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 40 residues processed: 10 average time/residue: 0.1493 time to fit residues: 5.3948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 112 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 148 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 484 HIS B 69 GLN B 262 ASN B 484 HIS C 69 GLN C 262 ASN C 389 ASN C 484 HIS D 69 GLN D 484 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.2105 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= 0.200 Angle : 0.495 5.608 21352 Z= 0.262 Chirality : 0.041 0.157 2364 Planarity : 0.004 0.035 2736 Dihedral : 5.342 53.301 2124 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 3.74 % 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: 0.25 (0.19), residues: 1964 helix: 0.88 (0.18), residues: 824 sheet: -0.13 (0.26), residues: 420 loop : -0.30 (0.24), residues: 720 *********************** 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 255 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 194 time to evaluate : 1.921 Fit side-chains outliers start: 61 outliers final: 46 residues processed: 244 average time/residue: 1.1773 time to fit residues: 320.5027 Evaluate side-chains 238 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 192 time to evaluate : 1.713 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 40 residues processed: 6 average time/residue: 0.1452 time to fit residues: 4.2561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 165 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 138 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 484 HIS B 69 GLN B 262 ASN C 69 GLN C 262 ASN C 389 ASN C 484 HIS D 69 GLN D 389 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.2125 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 : 0.502 5.758 21352 Z= 0.265 Chirality : 0.041 0.158 2364 Planarity : 0.004 0.035 2736 Dihedral : 5.297 53.827 2124 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 3.74 % 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: 0.29 (0.19), residues: 1964 helix: 0.90 (0.18), residues: 824 sheet: -0.13 (0.26), residues: 420 loop : -0.27 (0.24), residues: 720 *********************** 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 258 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 197 time to evaluate : 1.680 Fit side-chains outliers start: 61 outliers final: 46 residues processed: 247 average time/residue: 1.2098 time to fit residues: 332.5768 Evaluate side-chains 241 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 195 time to evaluate : 1.759 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 41 residues processed: 5 average time/residue: 0.1390 time to fit residues: 3.6952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 115 optimal weight: 0.9990 chunk 186 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 155 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- 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 C 484 HIS D 69 GLN D 389 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 15748 Z= 0.246 Angle : 0.521 6.491 21352 Z= 0.275 Chirality : 0.042 0.161 2364 Planarity : 0.004 0.035 2736 Dihedral : 5.365 54.955 2124 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 3.25 % 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: 0.22 (0.19), residues: 1964 helix: 0.87 (0.18), residues: 820 sheet: -0.17 (0.26), residues: 420 loop : -0.33 (0.24), residues: 724 ********************** 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 248 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 195 time to evaluate : 1.764 Fit side-chains outliers start: 53 outliers final: 40 residues processed: 240 average time/residue: 1.2635 time to fit residues: 337.3402 Evaluate side-chains 235 residues out of total 1632 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 195 time to evaluate : 1.704 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 39 residues processed: 1 average time/residue: 0.1391 time to fit residues: 2.5705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 123 optimal weight: 1.9990 chunk 165 optimal weight: 0.0970 chunk 47 optimal weight: 5.9990 chunk 143 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 484 HIS B 69 GLN B 262 ASN C 69 GLN C 262 ASN C 389 ASN C 484 HIS D 69 GLN D 389 ASN D 484 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.154857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.134902 restraints weight = 17737.102| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.10 r_work: 0.3572 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 15748 Z= 0.244 Angle : 0.524 6.406 21352 Z= 0.276 Chirality : 0.042 0.161 2364 Planarity : 0.004 0.035 2736 Dihedral : 5.385 56.476 2124 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer Outliers : 3.43 % 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: 0.21 (0.19), residues: 1964 helix: 0.86 (0.18), residues: 820 sheet: -0.16 (0.26), residues: 420 loop : -0.33 (0.24), residues: 724 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5935.98 seconds wall clock time: 106 minutes 20.35 seconds (6380.35 seconds total)