Starting phenix.real_space_refine on Thu Mar 14 19:54:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rvy_10018/03_2024/6rvy_10018.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rvy_10018/03_2024/6rvy_10018.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rvy_10018/03_2024/6rvy_10018.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rvy_10018/03_2024/6rvy_10018.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rvy_10018/03_2024/6rvy_10018.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rvy_10018/03_2024/6rvy_10018.pdb" } resolution = 4.13 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= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 6300 2.51 5 N 1602 2.21 5 O 1680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 50": "NH1" <-> "NH2" Residue "A ASP 120": "OD1" <-> "OD2" Residue "A ARG 189": "NH1" <-> "NH2" Residue "A ARG 202": "NH1" <-> "NH2" Residue "A ARG 217": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 365": "OE1" <-> "OE2" Residue "A ASP 388": "OD1" <-> "OD2" Residue "A ARG 465": "NH1" <-> "NH2" Residue "B ARG 50": "NH1" <-> "NH2" Residue "B ASP 120": "OD1" <-> "OD2" Residue "B ARG 189": "NH1" <-> "NH2" Residue "B ARG 202": "NH1" <-> "NH2" Residue "B ARG 217": "NH1" <-> "NH2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 365": "OE1" <-> "OE2" Residue "B ASP 388": "OD1" <-> "OD2" Residue "B ARG 465": "NH1" <-> "NH2" Residue "C ARG 50": "NH1" <-> "NH2" Residue "C ASP 120": "OD1" <-> "OD2" Residue "C ARG 189": "NH1" <-> "NH2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "C ARG 246": "NH1" <-> "NH2" Residue "C PHE 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 334": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 365": "OE1" <-> "OE2" Residue "C ASP 388": "OD1" <-> "OD2" Residue "C ARG 465": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9627 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3209 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 16, 'TRANS': 413} Chain breaks: 1 Chain: "B" Number of atoms: 3209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3209 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 16, 'TRANS': 413} Chain breaks: 1 Chain: "C" Number of atoms: 3209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3209 Classifications: {'peptide': 430} Link IDs: {'PTRANS': 16, 'TRANS': 413} Chain breaks: 1 Time building chain proxies: 5.69, per 1000 atoms: 0.59 Number of scatterers: 9627 At special positions: 0 Unit cell: (119.416, 122.452, 85.008, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 1680 8.00 N 1602 7.00 C 6300 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: 3.95 Conformation dependent library (CDL) restraints added in 1.7 seconds 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2334 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 3 sheets defined 78.6% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 44 through 51 removed outlier: 3.831A pdb=" N CYS A 48 " --> pdb=" O GLN A 44 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 74 removed outlier: 3.701A pdb=" N ALA A 64 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 90 through 117 removed outlier: 3.782A pdb=" N GLU A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Proline residue: A 106 - end of helix Processing helix chain 'A' and resid 125 through 154 removed outlier: 4.171A pdb=" N ALA A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 192 Processing helix chain 'A' and resid 197 through 200 Processing helix chain 'A' and resid 230 through 249 removed outlier: 3.935A pdb=" N VAL A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 293 removed outlier: 3.596A pdb=" N SER A 261 " --> pdb=" O ARG A 257 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU A 264 " --> pdb=" O ASN A 260 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL A 268 " --> pdb=" O GLU A 264 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N LEU A 269 " --> pdb=" O ALA A 265 " (cutoff:3.500A) Proline residue: A 278 - end of helix removed outlier: 3.513A pdb=" N GLU A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 327 removed outlier: 4.453A pdb=" N ALA A 300 " --> pdb=" O GLY A 296 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU A 321 " --> pdb=" O GLY A 317 " (cutoff:3.500A) Proline residue: A 322 - end of helix Processing helix chain 'A' and resid 332 through 340 removed outlier: 3.659A pdb=" N PHE A 336 " --> pdb=" O ASN A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 351 removed outlier: 3.852A pdb=" N LEU A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 367 removed outlier: 3.602A pdb=" N GLU A 365 " --> pdb=" O MET A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 386 removed outlier: 4.175A pdb=" N LEU A 379 " --> pdb=" O SER A 375 " (cutoff:3.500A) Proline residue: A 380 - end of helix removed outlier: 3.631A pdb=" N ALA A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR A 384 " --> pdb=" O PRO A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 406 removed outlier: 3.606A pdb=" N VAL A 399 " --> pdb=" O CYS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 424 removed outlier: 3.731A pdb=" N THR A 420 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA A 421 " --> pdb=" O ILE A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 445 removed outlier: 3.636A pdb=" N LEU A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 452 through 459 removed outlier: 3.861A pdb=" N ILE A 456 " --> pdb=" O HIS A 452 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 459 " --> pdb=" O LEU A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 480 removed outlier: 3.734A pdb=" N VAL A 463 " --> pdb=" O VAL A 459 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N VAL A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 470 " --> pdb=" O SER A 466 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN A 471 " --> pdb=" O ARG A 467 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL A 472 " --> pdb=" O THR A 468 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP A 475 " --> pdb=" O ASN A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 488 removed outlier: 3.703A pdb=" N ASP A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 51 removed outlier: 3.830A pdb=" N CYS B 48 " --> pdb=" O GLN B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 74 removed outlier: 3.701A pdb=" N ALA B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 85 through 90 Processing helix chain 'B' and resid 90 through 117 removed outlier: 3.783A pdb=" N GLU B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET B 102 " --> pdb=" O ARG B 98 " (cutoff:3.500A) Proline residue: B 106 - end of helix Processing helix chain 'B' and resid 125 through 154 removed outlier: 4.171A pdb=" N ALA B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 192 Processing helix chain 'B' and resid 197 through 200 Processing helix chain 'B' and resid 230 through 249 removed outlier: 3.934A pdb=" N VAL B 236 " --> pdb=" O LEU B 232 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE B 237 " --> pdb=" O GLY B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 293 removed outlier: 3.596A pdb=" N SER B 261 " --> pdb=" O ARG B 257 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL B 268 " --> pdb=" O GLU B 264 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LEU B 269 " --> pdb=" O ALA B 265 " (cutoff:3.500A) Proline residue: B 278 - end of helix removed outlier: 3.513A pdb=" N GLU B 293 " --> pdb=" O ILE B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 327 removed outlier: 4.453A pdb=" N ALA B 300 " --> pdb=" O GLY B 296 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU B 321 " --> pdb=" O GLY B 317 " (cutoff:3.500A) Proline residue: B 322 - end of helix Processing helix chain 'B' and resid 332 through 340 removed outlier: 3.660A pdb=" N PHE B 336 " --> pdb=" O ASN B 332 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 351 removed outlier: 3.852A pdb=" N LEU B 344 " --> pdb=" O ILE B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 367 removed outlier: 3.602A pdb=" N GLU B 365 " --> pdb=" O MET B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 386 removed outlier: 4.175A pdb=" N LEU B 379 " --> pdb=" O SER B 375 " (cutoff:3.500A) Proline residue: B 380 - end of helix removed outlier: 3.630A pdb=" N ALA B 383 " --> pdb=" O LEU B 379 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N THR B 384 " --> pdb=" O PRO B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 406 removed outlier: 3.605A pdb=" N VAL B 399 " --> pdb=" O CYS B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 424 removed outlier: 3.731A pdb=" N THR B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA B 421 " --> pdb=" O ILE B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 445 removed outlier: 3.636A pdb=" N LEU B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 451 No H-bonds generated for 'chain 'B' and resid 449 through 451' Processing helix chain 'B' and resid 452 through 459 removed outlier: 3.862A pdb=" N ILE B 456 " --> pdb=" O HIS B 452 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 459 " --> pdb=" O LEU B 455 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 480 removed outlier: 3.734A pdb=" N VAL B 463 " --> pdb=" O VAL B 459 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL B 469 " --> pdb=" O ARG B 465 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU B 470 " --> pdb=" O SER B 466 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASN B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL B 472 " --> pdb=" O THR B 468 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 488 removed outlier: 3.704A pdb=" N ASP B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 51 removed outlier: 3.830A pdb=" N CYS C 48 " --> pdb=" O GLN C 44 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 74 removed outlier: 3.700A pdb=" N ALA C 64 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C 67 " --> pdb=" O VAL C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 90 through 117 removed outlier: 3.782A pdb=" N GLU C 94 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N MET C 102 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Proline residue: C 106 - end of helix Processing helix chain 'C' and resid 125 through 154 removed outlier: 4.171A pdb=" N ALA C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 192 Processing helix chain 'C' and resid 197 through 200 Processing helix chain 'C' and resid 230 through 249 removed outlier: 3.934A pdb=" N VAL C 236 " --> pdb=" O LEU C 232 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N PHE C 237 " --> pdb=" O GLY C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 293 removed outlier: 3.597A pdb=" N SER C 261 " --> pdb=" O ARG C 257 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VAL C 268 " --> pdb=" O GLU C 264 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LEU C 269 " --> pdb=" O ALA C 265 " (cutoff:3.500A) Proline residue: C 278 - end of helix removed outlier: 3.512A pdb=" N GLU C 293 " --> pdb=" O ILE C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 327 removed outlier: 4.452A pdb=" N ALA C 300 " --> pdb=" O GLY C 296 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N LEU C 321 " --> pdb=" O GLY C 317 " (cutoff:3.500A) Proline residue: C 322 - end of helix Processing helix chain 'C' and resid 332 through 340 removed outlier: 3.660A pdb=" N PHE C 336 " --> pdb=" O ASN C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 351 removed outlier: 3.853A pdb=" N LEU C 344 " --> pdb=" O ILE C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 367 removed outlier: 3.602A pdb=" N GLU C 365 " --> pdb=" O MET C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 373 through 386 removed outlier: 4.175A pdb=" N LEU C 379 " --> pdb=" O SER C 375 " (cutoff:3.500A) Proline residue: C 380 - end of helix removed outlier: 3.631A pdb=" N ALA C 383 " --> pdb=" O LEU C 379 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N THR C 384 " --> pdb=" O PRO C 380 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 406 removed outlier: 3.605A pdb=" N VAL C 399 " --> pdb=" O CYS C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 424 removed outlier: 3.731A pdb=" N THR C 420 " --> pdb=" O THR C 416 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA C 421 " --> pdb=" O ILE C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 445 removed outlier: 3.636A pdb=" N LEU C 437 " --> pdb=" O ALA C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 449 through 451 No H-bonds generated for 'chain 'C' and resid 449 through 451' Processing helix chain 'C' and resid 452 through 459 removed outlier: 3.862A pdb=" N ILE C 456 " --> pdb=" O HIS C 452 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL C 459 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 480 removed outlier: 3.735A pdb=" N VAL C 463 " --> pdb=" O VAL C 459 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N SER C 466 " --> pdb=" O LEU C 462 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N VAL C 469 " --> pdb=" O ARG C 465 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU C 470 " --> pdb=" O SER C 466 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASN C 471 " --> pdb=" O ARG C 467 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL C 472 " --> pdb=" O THR C 468 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ASP C 475 " --> pdb=" O ASN C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 483 through 488 removed outlier: 3.704A pdb=" N ASP C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 210 Processing sheet with id=AA2, first strand: chain 'B' and resid 202 through 210 Processing sheet with id=AA3, first strand: chain 'C' and resid 202 through 210 651 hydrogen bonds defined for protein. 1944 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: 2.53 Time building geometry restraints manager: 4.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2987 1.34 - 1.46: 1399 1.46 - 1.57: 5340 1.57 - 1.69: 0 1.69 - 1.80: 72 Bond restraints: 9798 Sorted by residual: bond pdb=" CG LEU C 112 " pdb=" CD1 LEU C 112 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.09e+00 bond pdb=" CG LEU A 112 " pdb=" CD1 LEU A 112 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.07e+00 bond pdb=" CG LEU B 112 " pdb=" CD1 LEU B 112 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.00e+00 bond pdb=" C LEU C 105 " pdb=" N PRO C 106 " ideal model delta sigma weight residual 1.336 1.352 -0.017 1.23e-02 6.61e+03 1.88e+00 bond pdb=" C LEU B 105 " pdb=" N PRO B 106 " ideal model delta sigma weight residual 1.336 1.352 -0.017 1.23e-02 6.61e+03 1.84e+00 ... (remaining 9793 not shown) Histogram of bond angle deviations from ideal: 100.24 - 107.02: 242 107.02 - 113.80: 5770 113.80 - 120.57: 4220 120.57 - 127.35: 3025 127.35 - 134.13: 87 Bond angle restraints: 13344 Sorted by residual: angle pdb=" N ALA C 277 " pdb=" CA ALA C 277 " pdb=" C ALA C 277 " ideal model delta sigma weight residual 109.81 120.59 -10.78 2.21e+00 2.05e-01 2.38e+01 angle pdb=" N ALA B 277 " pdb=" CA ALA B 277 " pdb=" C ALA B 277 " ideal model delta sigma weight residual 109.81 120.54 -10.73 2.21e+00 2.05e-01 2.36e+01 angle pdb=" N ALA A 277 " pdb=" CA ALA A 277 " pdb=" C ALA A 277 " ideal model delta sigma weight residual 109.81 120.49 -10.68 2.21e+00 2.05e-01 2.34e+01 angle pdb=" N THR B 342 " pdb=" CA THR B 342 " pdb=" C THR B 342 " ideal model delta sigma weight residual 109.81 118.00 -8.19 2.21e+00 2.05e-01 1.37e+01 angle pdb=" N THR A 342 " pdb=" CA THR A 342 " pdb=" C THR A 342 " ideal model delta sigma weight residual 109.81 118.00 -8.19 2.21e+00 2.05e-01 1.37e+01 ... (remaining 13339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.03: 4963 15.03 - 30.07: 599 30.07 - 45.10: 159 45.10 - 60.14: 39 60.14 - 75.17: 6 Dihedral angle restraints: 5766 sinusoidal: 2127 harmonic: 3639 Sorted by residual: dihedral pdb=" CA VAL A 90 " pdb=" C VAL A 90 " pdb=" N PHE A 91 " pdb=" CA PHE A 91 " ideal model delta harmonic sigma weight residual -180.00 -153.67 -26.33 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA VAL B 90 " pdb=" C VAL B 90 " pdb=" N PHE B 91 " pdb=" CA PHE B 91 " ideal model delta harmonic sigma weight residual -180.00 -153.68 -26.32 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA VAL C 90 " pdb=" C VAL C 90 " pdb=" N PHE C 91 " pdb=" CA PHE C 91 " ideal model delta harmonic sigma weight residual 180.00 -153.70 -26.30 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 5763 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1220 0.051 - 0.101: 327 0.101 - 0.151: 79 0.151 - 0.202: 33 0.202 - 0.252: 9 Chirality restraints: 1668 Sorted by residual: chirality pdb=" CA THR C 342 " pdb=" N THR C 342 " pdb=" C THR C 342 " pdb=" CB THR C 342 " both_signs ideal model delta sigma weight residual False 2.53 2.27 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CA THR B 342 " pdb=" N THR B 342 " pdb=" C THR B 342 " pdb=" CB THR B 342 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA THR A 342 " pdb=" N THR A 342 " pdb=" C THR A 342 " pdb=" CB THR A 342 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1665 not shown) Planarity restraints: 1656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 321 " 0.045 5.00e-02 4.00e+02 6.64e-02 7.06e+00 pdb=" N PRO C 322 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO C 322 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 322 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 321 " 0.044 5.00e-02 4.00e+02 6.62e-02 7.02e+00 pdb=" N PRO A 322 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO A 322 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 322 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 321 " 0.044 5.00e-02 4.00e+02 6.59e-02 6.95e+00 pdb=" N PRO B 322 " -0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 322 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 322 " 0.037 5.00e-02 4.00e+02 ... (remaining 1653 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2841 2.81 - 3.33: 9719 3.33 - 3.86: 16133 3.86 - 4.38: 18328 4.38 - 4.90: 30139 Nonbonded interactions: 77160 Sorted by model distance: nonbonded pdb=" O SER C 177 " pdb=" OG SER C 177 " model vdw 2.290 2.440 nonbonded pdb=" O SER A 177 " pdb=" OG SER A 177 " model vdw 2.291 2.440 nonbonded pdb=" O SER B 177 " pdb=" OG SER B 177 " model vdw 2.291 2.440 nonbonded pdb=" O GLY C 69 " pdb=" OG SER C 73 " model vdw 2.327 2.440 nonbonded pdb=" O GLY A 69 " pdb=" OG SER A 73 " model vdw 2.328 2.440 ... (remaining 77155 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.340 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: 2.200 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 28.100 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 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 : 0.006 0.057 9798 Z= 0.387 Angle : 1.030 10.778 13344 Z= 0.538 Chirality : 0.056 0.252 1668 Planarity : 0.008 0.066 1656 Dihedral : 14.692 75.172 3432 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.49 % Allowed : 13.04 % Favored : 86.47 % 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: -5.00 (0.17), residues: 1278 helix: -3.03 (0.11), residues: 963 sheet: -3.60 (0.57), residues: 42 loop : -3.25 (0.34), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 461 HIS 0.003 0.001 HIS C 316 PHE 0.013 0.002 PHE A 258 TYR 0.006 0.002 TYR A 305 ARG 0.005 0.001 ARG C 465 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 200 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.8581 (p90) cc_final: 0.8375 (p90) REVERT: A 279 VAL cc_start: 0.9209 (m) cc_final: 0.8901 (p) REVERT: A 297 LEU cc_start: 0.8964 (tp) cc_final: 0.8706 (mp) REVERT: A 325 TYR cc_start: 0.8860 (t80) cc_final: 0.8634 (t80) REVERT: A 394 GLN cc_start: 0.8426 (mt0) cc_final: 0.8080 (mp10) REVERT: A 439 LEU cc_start: 0.9410 (tp) cc_final: 0.9070 (tp) REVERT: A 461 TRP cc_start: 0.8008 (p-90) cc_final: 0.7579 (p-90) REVERT: A 473 GLU cc_start: 0.8720 (tt0) cc_final: 0.8270 (tt0) REVERT: B 89 PHE cc_start: 0.7543 (t80) cc_final: 0.7338 (t80) REVERT: B 178 LYS cc_start: 0.6864 (tptt) cc_final: 0.6525 (mppt) REVERT: B 201 PHE cc_start: 0.8381 (p90) cc_final: 0.7916 (p90) REVERT: B 279 VAL cc_start: 0.9119 (m) cc_final: 0.8919 (p) REVERT: B 297 LEU cc_start: 0.8982 (tp) cc_final: 0.8738 (tp) REVERT: B 305 TYR cc_start: 0.8954 (t80) cc_final: 0.8681 (t80) REVERT: B 313 HIS cc_start: 0.8100 (m90) cc_final: 0.7794 (m90) REVERT: B 325 TYR cc_start: 0.8723 (t80) cc_final: 0.8141 (t80) REVERT: B 379 LEU cc_start: 0.9227 (tp) cc_final: 0.9017 (tp) REVERT: B 439 LEU cc_start: 0.9379 (tp) cc_final: 0.9117 (tp) REVERT: B 461 TRP cc_start: 0.8141 (p-90) cc_final: 0.7075 (p-90) REVERT: B 473 GLU cc_start: 0.8796 (tt0) cc_final: 0.8408 (tt0) REVERT: C 89 PHE cc_start: 0.7841 (t80) cc_final: 0.7449 (t80) REVERT: C 100 LEU cc_start: 0.9130 (mt) cc_final: 0.8926 (mt) REVERT: C 178 LYS cc_start: 0.6830 (tptt) cc_final: 0.6375 (mppt) REVERT: C 201 PHE cc_start: 0.8345 (p90) cc_final: 0.7869 (p90) REVERT: C 297 LEU cc_start: 0.8847 (tp) cc_final: 0.8584 (mp) REVERT: C 313 HIS cc_start: 0.8158 (m90) cc_final: 0.7843 (m90) REVERT: C 325 TYR cc_start: 0.8626 (t80) cc_final: 0.8330 (t80) REVERT: C 395 CYS cc_start: 0.8202 (m) cc_final: 0.7891 (m) REVERT: C 461 TRP cc_start: 0.8180 (p-90) cc_final: 0.6951 (p-90) REVERT: C 473 GLU cc_start: 0.8812 (tt0) cc_final: 0.8400 (tt0) outliers start: 5 outliers final: 0 residues processed: 203 average time/residue: 0.1941 time to fit residues: 55.9143 Evaluate side-chains 141 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 54 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 117 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN A 452 HIS B 212 ASN C 212 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9798 Z= 0.187 Angle : 0.669 8.088 13344 Z= 0.336 Chirality : 0.039 0.168 1668 Planarity : 0.005 0.044 1656 Dihedral : 4.930 18.351 1365 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.21), residues: 1278 helix: -1.18 (0.15), residues: 993 sheet: -2.99 (0.69), residues: 42 loop : -3.05 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 130 HIS 0.004 0.001 HIS B 316 PHE 0.011 0.001 PHE C 237 TYR 0.013 0.002 TYR A 276 ARG 0.003 0.000 ARG A 376 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.062 Fit side-chains revert: symmetry clash REVERT: A 279 VAL cc_start: 0.9239 (m) cc_final: 0.8930 (p) REVERT: A 282 MET cc_start: 0.8706 (tmm) cc_final: 0.8299 (tmm) REVERT: A 297 LEU cc_start: 0.9016 (tp) cc_final: 0.8711 (mp) REVERT: A 313 HIS cc_start: 0.7936 (m90) cc_final: 0.7284 (m90) REVERT: A 325 TYR cc_start: 0.8911 (t80) cc_final: 0.8620 (t80) REVERT: A 376 ARG cc_start: 0.8562 (mpt180) cc_final: 0.7881 (mpt180) REVERT: A 394 GLN cc_start: 0.8544 (mt0) cc_final: 0.8103 (mp10) REVERT: A 439 LEU cc_start: 0.9395 (tp) cc_final: 0.9007 (tt) REVERT: A 461 TRP cc_start: 0.8146 (p-90) cc_final: 0.7338 (p-90) REVERT: B 89 PHE cc_start: 0.7588 (t80) cc_final: 0.7376 (t80) REVERT: B 91 PHE cc_start: 0.8283 (t80) cc_final: 0.7848 (t80) REVERT: B 201 PHE cc_start: 0.8309 (p90) cc_final: 0.7783 (p90) REVERT: B 282 MET cc_start: 0.8798 (tmm) cc_final: 0.8504 (tmm) REVERT: B 297 LEU cc_start: 0.8925 (tp) cc_final: 0.8642 (mp) REVERT: B 313 HIS cc_start: 0.7948 (m90) cc_final: 0.7740 (m90) REVERT: B 325 TYR cc_start: 0.8684 (t80) cc_final: 0.8081 (t80) REVERT: B 439 LEU cc_start: 0.9379 (tp) cc_final: 0.9097 (tp) REVERT: B 461 TRP cc_start: 0.8199 (p-90) cc_final: 0.7124 (p-90) REVERT: B 473 GLU cc_start: 0.8836 (tt0) cc_final: 0.8386 (tt0) REVERT: C 89 PHE cc_start: 0.7818 (t80) cc_final: 0.7336 (t80) REVERT: C 178 LYS cc_start: 0.6643 (tptt) cc_final: 0.6286 (mppt) REVERT: C 282 MET cc_start: 0.8698 (tmm) cc_final: 0.8280 (tmm) REVERT: C 297 LEU cc_start: 0.8820 (tp) cc_final: 0.8530 (mp) REVERT: C 313 HIS cc_start: 0.8148 (m90) cc_final: 0.7933 (m90) REVERT: C 325 TYR cc_start: 0.8666 (t80) cc_final: 0.8335 (t80) REVERT: C 395 CYS cc_start: 0.8311 (m) cc_final: 0.8090 (m) REVERT: C 439 LEU cc_start: 0.9411 (tp) cc_final: 0.9072 (tp) REVERT: C 473 GLU cc_start: 0.8768 (tt0) cc_final: 0.8391 (tt0) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1744 time to fit residues: 52.8342 Evaluate side-chains 144 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 0.0010 chunk 97 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 32 optimal weight: 20.0000 chunk 117 optimal weight: 5.9990 chunk 126 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 116 optimal weight: 10.0000 chunk 40 optimal weight: 0.8980 chunk 94 optimal weight: 30.0000 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 452 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9798 Z= 0.167 Angle : 0.638 8.919 13344 Z= 0.315 Chirality : 0.039 0.171 1668 Planarity : 0.004 0.037 1656 Dihedral : 4.525 17.284 1365 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.23), residues: 1278 helix: -0.40 (0.16), residues: 993 sheet: -2.54 (0.71), residues: 42 loop : -2.64 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 130 HIS 0.004 0.001 HIS C 316 PHE 0.015 0.001 PHE A 241 TYR 0.018 0.001 TYR C 305 ARG 0.003 0.000 ARG B 98 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 PHE cc_start: 0.8609 (p90) cc_final: 0.8377 (p90) REVERT: A 279 VAL cc_start: 0.9277 (m) cc_final: 0.8911 (p) REVERT: A 282 MET cc_start: 0.8632 (tmm) cc_final: 0.8303 (tmm) REVERT: A 297 LEU cc_start: 0.8967 (tp) cc_final: 0.8623 (mp) REVERT: A 309 CYS cc_start: 0.7762 (t) cc_final: 0.7209 (t) REVERT: A 313 HIS cc_start: 0.7778 (m90) cc_final: 0.7178 (m90) REVERT: A 325 TYR cc_start: 0.8824 (t80) cc_final: 0.8510 (t80) REVERT: A 394 GLN cc_start: 0.8427 (mt0) cc_final: 0.8033 (mp10) REVERT: A 461 TRP cc_start: 0.8206 (p-90) cc_final: 0.7359 (p-90) REVERT: B 89 PHE cc_start: 0.7704 (t80) cc_final: 0.7495 (t80) REVERT: B 91 PHE cc_start: 0.8255 (t80) cc_final: 0.7810 (t80) REVERT: B 201 PHE cc_start: 0.8324 (p90) cc_final: 0.7781 (p90) REVERT: B 282 MET cc_start: 0.8718 (tmm) cc_final: 0.8425 (tmm) REVERT: B 297 LEU cc_start: 0.8957 (tp) cc_final: 0.8610 (mp) REVERT: B 325 TYR cc_start: 0.8684 (t80) cc_final: 0.8142 (t80) REVERT: B 394 GLN cc_start: 0.8205 (mt0) cc_final: 0.7994 (mt0) REVERT: B 395 CYS cc_start: 0.8109 (m) cc_final: 0.7814 (m) REVERT: B 461 TRP cc_start: 0.8266 (p-90) cc_final: 0.7023 (p-90) REVERT: B 473 GLU cc_start: 0.8847 (tt0) cc_final: 0.8415 (tt0) REVERT: C 89 PHE cc_start: 0.7845 (t80) cc_final: 0.7313 (t80) REVERT: C 178 LYS cc_start: 0.6607 (tptt) cc_final: 0.6282 (mppt) REVERT: C 190 ASN cc_start: 0.8815 (m-40) cc_final: 0.7933 (m110) REVERT: C 282 MET cc_start: 0.8604 (tmm) cc_final: 0.8221 (tmm) REVERT: C 325 TYR cc_start: 0.8587 (t80) cc_final: 0.8258 (t80) REVERT: C 387 MET cc_start: 0.8969 (mmm) cc_final: 0.8754 (mmt) REVERT: C 395 CYS cc_start: 0.8206 (m) cc_final: 0.7999 (m) REVERT: C 473 GLU cc_start: 0.8764 (tt0) cc_final: 0.8365 (tt0) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1762 time to fit residues: 52.8938 Evaluate side-chains 152 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 9.9990 chunk 88 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 56 optimal weight: 0.9980 chunk 78 optimal weight: 0.9990 chunk 117 optimal weight: 20.0000 chunk 124 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 313 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9798 Z= 0.164 Angle : 0.640 8.138 13344 Z= 0.312 Chirality : 0.039 0.170 1668 Planarity : 0.004 0.034 1656 Dihedral : 4.308 17.182 1365 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % 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: -0.98 (0.24), residues: 1278 helix: 0.00 (0.17), residues: 993 sheet: None (None), residues: 0 loop : -2.73 (0.36), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 461 HIS 0.003 0.001 HIS A 316 PHE 0.009 0.001 PHE A 241 TYR 0.022 0.002 TYR A 305 ARG 0.003 0.000 ARG C 376 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 279 VAL cc_start: 0.9275 (m) cc_final: 0.8949 (p) REVERT: A 282 MET cc_start: 0.8589 (tmm) cc_final: 0.8246 (tmm) REVERT: A 309 CYS cc_start: 0.7752 (t) cc_final: 0.7236 (t) REVERT: A 313 HIS cc_start: 0.7591 (m90) cc_final: 0.7172 (m90) REVERT: A 325 TYR cc_start: 0.8657 (t80) cc_final: 0.8325 (t80) REVERT: A 379 LEU cc_start: 0.8956 (tp) cc_final: 0.8342 (tp) REVERT: A 387 MET cc_start: 0.8878 (mmt) cc_final: 0.8655 (mmm) REVERT: A 394 GLN cc_start: 0.8469 (mt0) cc_final: 0.8057 (mp10) REVERT: A 439 LEU cc_start: 0.9364 (tp) cc_final: 0.9040 (tp) REVERT: A 461 TRP cc_start: 0.8184 (p-90) cc_final: 0.7285 (p-90) REVERT: B 89 PHE cc_start: 0.7690 (t80) cc_final: 0.7459 (t80) REVERT: B 91 PHE cc_start: 0.8261 (t80) cc_final: 0.7791 (t80) REVERT: B 201 PHE cc_start: 0.8263 (p90) cc_final: 0.7576 (p90) REVERT: B 282 MET cc_start: 0.8652 (tmm) cc_final: 0.8363 (tmm) REVERT: B 297 LEU cc_start: 0.8976 (tp) cc_final: 0.8662 (mp) REVERT: B 325 TYR cc_start: 0.8601 (t80) cc_final: 0.8068 (t80) REVERT: B 461 TRP cc_start: 0.8229 (p-90) cc_final: 0.7019 (p-90) REVERT: B 473 GLU cc_start: 0.8860 (tt0) cc_final: 0.8405 (tt0) REVERT: C 89 PHE cc_start: 0.7802 (t80) cc_final: 0.7398 (t80) REVERT: C 178 LYS cc_start: 0.6584 (tptt) cc_final: 0.6293 (mppt) REVERT: C 190 ASN cc_start: 0.8742 (m-40) cc_final: 0.7835 (m110) REVERT: C 282 MET cc_start: 0.8562 (tmm) cc_final: 0.8235 (tmm) REVERT: C 288 LYS cc_start: 0.8807 (mmmt) cc_final: 0.8194 (mmtt) REVERT: C 325 TYR cc_start: 0.8439 (t80) cc_final: 0.8090 (t80) REVERT: C 387 MET cc_start: 0.9004 (mmm) cc_final: 0.8792 (mmt) REVERT: C 439 LEU cc_start: 0.9329 (tp) cc_final: 0.9020 (tt) REVERT: C 473 GLU cc_start: 0.8767 (tt0) cc_final: 0.8332 (tt0) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1797 time to fit residues: 53.6033 Evaluate side-chains 160 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 30.0000 chunk 106 optimal weight: 0.8980 chunk 86 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 ASN C 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9798 Z= 0.186 Angle : 0.650 9.746 13344 Z= 0.315 Chirality : 0.039 0.172 1668 Planarity : 0.004 0.033 1656 Dihedral : 4.224 15.862 1365 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.24), residues: 1278 helix: 0.26 (0.17), residues: 978 sheet: None (None), residues: 0 loop : -2.48 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 461 HIS 0.005 0.001 HIS A 316 PHE 0.010 0.001 PHE A 91 TYR 0.022 0.002 TYR A 305 ARG 0.002 0.000 ARG A 376 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ASN cc_start: 0.9125 (m-40) cc_final: 0.8861 (m110) REVERT: A 279 VAL cc_start: 0.9337 (m) cc_final: 0.8996 (p) REVERT: A 282 MET cc_start: 0.8573 (tmm) cc_final: 0.8281 (tmm) REVERT: A 309 CYS cc_start: 0.7759 (t) cc_final: 0.7226 (t) REVERT: A 313 HIS cc_start: 0.7779 (m90) cc_final: 0.7400 (m90) REVERT: A 325 TYR cc_start: 0.8647 (t80) cc_final: 0.8343 (t80) REVERT: A 394 GLN cc_start: 0.8393 (mt0) cc_final: 0.8064 (mp10) REVERT: A 439 LEU cc_start: 0.9351 (tp) cc_final: 0.9068 (tp) REVERT: A 461 TRP cc_start: 0.8209 (p-90) cc_final: 0.7241 (p-90) REVERT: B 89 PHE cc_start: 0.7692 (t80) cc_final: 0.7492 (t80) REVERT: B 91 PHE cc_start: 0.8266 (t80) cc_final: 0.7777 (t80) REVERT: B 201 PHE cc_start: 0.8342 (p90) cc_final: 0.7712 (p90) REVERT: B 282 MET cc_start: 0.8666 (tmm) cc_final: 0.8379 (tmm) REVERT: B 325 TYR cc_start: 0.8623 (t80) cc_final: 0.8071 (t80) REVERT: B 379 LEU cc_start: 0.8864 (tp) cc_final: 0.8362 (tp) REVERT: B 461 TRP cc_start: 0.8224 (p-90) cc_final: 0.7015 (p-90) REVERT: B 473 GLU cc_start: 0.8907 (tt0) cc_final: 0.8396 (tt0) REVERT: C 89 PHE cc_start: 0.7851 (t80) cc_final: 0.7426 (t80) REVERT: C 178 LYS cc_start: 0.6724 (tptt) cc_final: 0.6334 (mppt) REVERT: C 190 ASN cc_start: 0.8786 (m-40) cc_final: 0.7900 (m110) REVERT: C 282 MET cc_start: 0.8567 (tmm) cc_final: 0.8284 (tmm) REVERT: C 316 HIS cc_start: 0.8390 (t-90) cc_final: 0.8142 (t-90) REVERT: C 325 TYR cc_start: 0.8456 (t80) cc_final: 0.8081 (t80) REVERT: C 387 MET cc_start: 0.8983 (mmm) cc_final: 0.8744 (mmt) REVERT: C 473 GLU cc_start: 0.8786 (tt0) cc_final: 0.8338 (tt0) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.1941 time to fit residues: 58.6806 Evaluate side-chains 151 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 5.9990 chunk 112 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 73 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 120 optimal weight: 9.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 407 GLN B 407 GLN C 407 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9798 Z= 0.196 Angle : 0.648 8.003 13344 Z= 0.315 Chirality : 0.039 0.166 1668 Planarity : 0.004 0.031 1656 Dihedral : 4.207 17.610 1365 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % 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: -0.48 (0.24), residues: 1278 helix: 0.37 (0.17), residues: 981 sheet: -1.95 (0.81), residues: 42 loop : -2.42 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 461 HIS 0.004 0.001 HIS B 316 PHE 0.018 0.001 PHE A 91 TYR 0.022 0.002 TYR C 305 ARG 0.002 0.000 ARG B 376 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ASN cc_start: 0.9095 (m-40) cc_final: 0.8857 (m110) REVERT: A 279 VAL cc_start: 0.9321 (m) cc_final: 0.9014 (p) REVERT: A 309 CYS cc_start: 0.7764 (t) cc_final: 0.7174 (t) REVERT: A 313 HIS cc_start: 0.7809 (m90) cc_final: 0.7477 (m90) REVERT: A 325 TYR cc_start: 0.8656 (t80) cc_final: 0.8386 (t80) REVERT: A 394 GLN cc_start: 0.8497 (mt0) cc_final: 0.8029 (mp10) REVERT: A 439 LEU cc_start: 0.9393 (tp) cc_final: 0.9073 (tp) REVERT: A 461 TRP cc_start: 0.8212 (p-90) cc_final: 0.7193 (p-90) REVERT: B 89 PHE cc_start: 0.7581 (t80) cc_final: 0.7366 (t80) REVERT: B 91 PHE cc_start: 0.8262 (t80) cc_final: 0.7790 (t80) REVERT: B 201 PHE cc_start: 0.8281 (p90) cc_final: 0.7701 (p90) REVERT: B 282 MET cc_start: 0.8638 (tmm) cc_final: 0.8393 (tmm) REVERT: B 325 TYR cc_start: 0.8632 (t80) cc_final: 0.8161 (t80) REVERT: B 461 TRP cc_start: 0.8302 (p-90) cc_final: 0.7036 (p-90) REVERT: B 473 GLU cc_start: 0.8852 (tt0) cc_final: 0.8374 (tt0) REVERT: C 89 PHE cc_start: 0.7904 (t80) cc_final: 0.7441 (t80) REVERT: C 178 LYS cc_start: 0.6707 (tptt) cc_final: 0.6367 (mppt) REVERT: C 190 ASN cc_start: 0.8797 (m-40) cc_final: 0.7872 (m110) REVERT: C 282 MET cc_start: 0.8616 (tmm) cc_final: 0.8395 (tmm) REVERT: C 325 TYR cc_start: 0.8490 (t80) cc_final: 0.8173 (t80) REVERT: C 387 MET cc_start: 0.8967 (mmm) cc_final: 0.8767 (mmt) REVERT: C 473 GLU cc_start: 0.8841 (tt0) cc_final: 0.8312 (tt0) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1739 time to fit residues: 49.4899 Evaluate side-chains 148 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 9.9990 chunk 71 optimal weight: 0.5980 chunk 91 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 57 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 313 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9798 Z= 0.174 Angle : 0.658 8.110 13344 Z= 0.317 Chirality : 0.039 0.172 1668 Planarity : 0.004 0.031 1656 Dihedral : 4.153 16.549 1365 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: -0.40 (0.24), residues: 1278 helix: 0.39 (0.17), residues: 981 sheet: -1.72 (0.84), residues: 42 loop : -2.32 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 130 HIS 0.007 0.001 HIS C 452 PHE 0.015 0.001 PHE A 91 TYR 0.021 0.002 TYR A 305 ARG 0.002 0.000 ARG C 98 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 ASN cc_start: 0.8859 (m-40) cc_final: 0.7915 (m110) REVERT: A 279 VAL cc_start: 0.9306 (m) cc_final: 0.9024 (p) REVERT: A 282 MET cc_start: 0.8658 (tmm) cc_final: 0.7912 (tmm) REVERT: A 309 CYS cc_start: 0.7813 (t) cc_final: 0.7187 (t) REVERT: A 313 HIS cc_start: 0.7707 (m90) cc_final: 0.7433 (m90) REVERT: A 325 TYR cc_start: 0.8610 (t80) cc_final: 0.8335 (t80) REVERT: A 394 GLN cc_start: 0.8483 (mt0) cc_final: 0.7981 (mp10) REVERT: A 461 TRP cc_start: 0.8273 (p-90) cc_final: 0.7201 (p-90) REVERT: B 91 PHE cc_start: 0.8214 (t80) cc_final: 0.7740 (t80) REVERT: B 201 PHE cc_start: 0.8238 (p90) cc_final: 0.7612 (p90) REVERT: B 309 CYS cc_start: 0.8300 (p) cc_final: 0.7646 (t) REVERT: B 313 HIS cc_start: 0.8025 (m90) cc_final: 0.7387 (m90) REVERT: B 325 TYR cc_start: 0.8607 (t80) cc_final: 0.8070 (t80) REVERT: B 376 ARG cc_start: 0.8533 (mpt180) cc_final: 0.8010 (mmt-90) REVERT: B 461 TRP cc_start: 0.8285 (p-90) cc_final: 0.7011 (p-90) REVERT: B 473 GLU cc_start: 0.8877 (tt0) cc_final: 0.8364 (tt0) REVERT: C 89 PHE cc_start: 0.7835 (t80) cc_final: 0.7381 (t80) REVERT: C 178 LYS cc_start: 0.6705 (tptt) cc_final: 0.6343 (mppt) REVERT: C 190 ASN cc_start: 0.8802 (m-40) cc_final: 0.7894 (m110) REVERT: C 325 TYR cc_start: 0.8443 (t80) cc_final: 0.8123 (t80) REVERT: C 387 MET cc_start: 0.8993 (mmm) cc_final: 0.8744 (mmt) REVERT: C 473 GLU cc_start: 0.8827 (tt0) cc_final: 0.8294 (tt0) outliers start: 0 outliers final: 0 residues processed: 199 average time/residue: 0.1808 time to fit residues: 52.3057 Evaluate side-chains 150 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 97 optimal weight: 0.0050 chunk 113 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 overall best weight: 1.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9798 Z= 0.180 Angle : 0.661 8.055 13344 Z= 0.318 Chirality : 0.039 0.168 1668 Planarity : 0.004 0.032 1656 Dihedral : 4.130 18.132 1365 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % 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 (0.24), residues: 1278 helix: 0.48 (0.17), residues: 981 sheet: -1.61 (0.85), residues: 42 loop : -2.36 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP C 130 HIS 0.007 0.002 HIS C 452 PHE 0.021 0.001 PHE B 89 TYR 0.022 0.002 TYR A 276 ARG 0.003 0.000 ARG C 376 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 186 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: A 190 ASN cc_start: 0.8841 (m-40) cc_final: 0.8020 (m-40) REVERT: A 279 VAL cc_start: 0.9327 (m) cc_final: 0.9041 (p) REVERT: A 282 MET cc_start: 0.8640 (tmm) cc_final: 0.7927 (tmm) REVERT: A 309 CYS cc_start: 0.7856 (t) cc_final: 0.7177 (t) REVERT: A 313 HIS cc_start: 0.7788 (m90) cc_final: 0.7560 (m90) REVERT: A 325 TYR cc_start: 0.8587 (t80) cc_final: 0.8311 (t80) REVERT: A 394 GLN cc_start: 0.8396 (mt0) cc_final: 0.7952 (mp10) REVERT: A 461 TRP cc_start: 0.8298 (p-90) cc_final: 0.7243 (p-90) REVERT: B 91 PHE cc_start: 0.8257 (t80) cc_final: 0.7815 (t80) REVERT: B 282 MET cc_start: 0.8783 (tmm) cc_final: 0.8425 (tmm) REVERT: B 309 CYS cc_start: 0.8228 (p) cc_final: 0.7602 (t) REVERT: B 313 HIS cc_start: 0.8048 (m90) cc_final: 0.7372 (m90) REVERT: B 325 TYR cc_start: 0.8582 (t80) cc_final: 0.8078 (t80) REVERT: B 376 ARG cc_start: 0.8497 (mpt180) cc_final: 0.8015 (mmt-90) REVERT: C 89 PHE cc_start: 0.7832 (t80) cc_final: 0.7399 (t80) REVERT: C 178 LYS cc_start: 0.6699 (tptt) cc_final: 0.6363 (mppt) REVERT: C 190 ASN cc_start: 0.8857 (m-40) cc_final: 0.7935 (m110) REVERT: C 282 MET cc_start: 0.8718 (tmm) cc_final: 0.8502 (tmm) REVERT: C 325 TYR cc_start: 0.8413 (t80) cc_final: 0.8077 (t80) REVERT: C 387 MET cc_start: 0.8946 (mmm) cc_final: 0.8727 (mmt) REVERT: C 473 GLU cc_start: 0.8839 (tt0) cc_final: 0.8273 (tt0) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1779 time to fit residues: 48.9022 Evaluate side-chains 149 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 HIS ** C 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9798 Z= 0.184 Angle : 0.666 8.014 13344 Z= 0.321 Chirality : 0.040 0.172 1668 Planarity : 0.004 0.034 1656 Dihedral : 4.096 17.323 1365 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % 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 (0.24), residues: 1278 helix: 0.55 (0.17), residues: 981 sheet: -1.52 (0.86), residues: 42 loop : -2.37 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP C 130 HIS 0.005 0.001 HIS C 452 PHE 0.018 0.001 PHE B 89 TYR 0.021 0.002 TYR C 305 ARG 0.002 0.000 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 196 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 ASN cc_start: 0.8848 (m-40) cc_final: 0.8027 (m-40) REVERT: A 279 VAL cc_start: 0.9318 (m) cc_final: 0.9016 (p) REVERT: A 282 MET cc_start: 0.8668 (tmm) cc_final: 0.7927 (tmm) REVERT: A 309 CYS cc_start: 0.7783 (t) cc_final: 0.7014 (t) REVERT: A 313 HIS cc_start: 0.7812 (m90) cc_final: 0.7554 (m90) REVERT: A 325 TYR cc_start: 0.8576 (t80) cc_final: 0.8299 (t80) REVERT: A 379 LEU cc_start: 0.8891 (tp) cc_final: 0.8607 (tp) REVERT: A 394 GLN cc_start: 0.8410 (mt0) cc_final: 0.8022 (mp10) REVERT: A 461 TRP cc_start: 0.8301 (p-90) cc_final: 0.7207 (p-90) REVERT: B 91 PHE cc_start: 0.8283 (t80) cc_final: 0.7824 (t80) REVERT: B 282 MET cc_start: 0.8737 (tmm) cc_final: 0.8303 (tmm) REVERT: B 325 TYR cc_start: 0.8566 (t80) cc_final: 0.8051 (t80) REVERT: B 376 ARG cc_start: 0.8445 (mpt180) cc_final: 0.7931 (mmt-90) REVERT: B 473 GLU cc_start: 0.8861 (tt0) cc_final: 0.8131 (tt0) REVERT: C 89 PHE cc_start: 0.7851 (t80) cc_final: 0.7399 (t80) REVERT: C 178 LYS cc_start: 0.6689 (tptt) cc_final: 0.6357 (mppt) REVERT: C 190 ASN cc_start: 0.8805 (m-40) cc_final: 0.7893 (m110) REVERT: C 313 HIS cc_start: 0.8108 (m90) cc_final: 0.7874 (m90) REVERT: C 325 TYR cc_start: 0.8391 (t80) cc_final: 0.8051 (t80) REVERT: C 376 ARG cc_start: 0.8570 (mpt180) cc_final: 0.8284 (mmt-90) REVERT: C 387 MET cc_start: 0.8979 (mmm) cc_final: 0.8759 (mmt) REVERT: C 473 GLU cc_start: 0.8853 (tt0) cc_final: 0.8292 (tt0) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.1722 time to fit residues: 50.0195 Evaluate side-chains 145 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 8.9990 chunk 58 optimal weight: 0.2980 chunk 85 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 118 optimal weight: 5.9990 chunk 102 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 81 optimal weight: 0.0870 chunk 109 optimal weight: 6.9990 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 452 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9798 Z= 0.171 Angle : 0.664 8.828 13344 Z= 0.316 Chirality : 0.039 0.169 1668 Planarity : 0.004 0.032 1656 Dihedral : 4.055 18.190 1365 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -0.13 (0.24), residues: 1278 helix: 0.63 (0.17), residues: 978 sheet: -1.54 (0.85), residues: 42 loop : -2.41 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 130 HIS 0.004 0.001 HIS B 316 PHE 0.012 0.001 PHE A 91 TYR 0.021 0.002 TYR A 305 ARG 0.002 0.000 ARG A 467 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2556 Ramachandran restraints generated. 1278 Oldfield, 0 Emsley, 1278 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 1.062 Fit side-chains REVERT: A 190 ASN cc_start: 0.8836 (m-40) cc_final: 0.7888 (m110) REVERT: A 279 VAL cc_start: 0.9302 (m) cc_final: 0.9022 (p) REVERT: A 282 MET cc_start: 0.8642 (tmm) cc_final: 0.7938 (tmm) REVERT: A 309 CYS cc_start: 0.7663 (t) cc_final: 0.6831 (t) REVERT: A 313 HIS cc_start: 0.7846 (m90) cc_final: 0.7612 (m90) REVERT: A 325 TYR cc_start: 0.8538 (t80) cc_final: 0.8262 (t80) REVERT: A 379 LEU cc_start: 0.8864 (tp) cc_final: 0.8446 (tp) REVERT: A 461 TRP cc_start: 0.8299 (p-90) cc_final: 0.7171 (p-90) REVERT: B 91 PHE cc_start: 0.8263 (t80) cc_final: 0.7821 (t80) REVERT: B 282 MET cc_start: 0.8729 (tmm) cc_final: 0.8285 (tmm) REVERT: B 325 TYR cc_start: 0.8496 (t80) cc_final: 0.8031 (t80) REVERT: B 376 ARG cc_start: 0.8485 (mpt180) cc_final: 0.8084 (mmt-90) REVERT: B 473 GLU cc_start: 0.8870 (tt0) cc_final: 0.8162 (tt0) REVERT: C 89 PHE cc_start: 0.7844 (t80) cc_final: 0.7380 (t80) REVERT: C 178 LYS cc_start: 0.6436 (tptt) cc_final: 0.6234 (mmtm) REVERT: C 190 ASN cc_start: 0.8858 (m-40) cc_final: 0.7907 (m110) REVERT: C 325 TYR cc_start: 0.8363 (t80) cc_final: 0.7995 (t80) REVERT: C 376 ARG cc_start: 0.8571 (mpt180) cc_final: 0.8326 (mmt-90) REVERT: C 387 MET cc_start: 0.8963 (mmm) cc_final: 0.8700 (mmt) REVERT: C 473 GLU cc_start: 0.8868 (tt0) cc_final: 0.8343 (tt0) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1683 time to fit residues: 47.4401 Evaluate side-chains 142 residues out of total 1020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 3.9990 chunk 94 optimal weight: 30.0000 chunk 15 optimal weight: 5.9990 chunk 28 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 105 optimal weight: 2.9990 chunk 12 optimal weight: 0.0980 chunk 18 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.076768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.061969 restraints weight = 41694.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.062621 restraints weight = 27322.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.062762 restraints weight = 21879.906| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9798 Z= 0.165 Angle : 0.664 9.997 13344 Z= 0.314 Chirality : 0.039 0.167 1668 Planarity : 0.004 0.033 1656 Dihedral : 4.020 17.796 1365 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % 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: -0.06 (0.24), residues: 1278 helix: 0.66 (0.17), residues: 978 sheet: -1.38 (0.83), residues: 42 loop : -2.31 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP C 130 HIS 0.005 0.002 HIS B 313 PHE 0.011 0.001 PHE A 91 TYR 0.021 0.002 TYR A 305 ARG 0.005 0.000 ARG B 85 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1759.64 seconds wall clock time: 32 minutes 48.97 seconds (1968.97 seconds total)