Starting phenix.real_space_refine on Sun Apr 7 01:38:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0j_35904/04_2024/8j0j_35904_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0j_35904/04_2024/8j0j_35904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0j_35904/04_2024/8j0j_35904.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0j_35904/04_2024/8j0j_35904.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0j_35904/04_2024/8j0j_35904_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j0j_35904/04_2024/8j0j_35904_trim.pdb" } resolution = 2.7 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= 0.003 sd= 0.059 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 S 48 5.16 5 Cl 3 4.86 5 C 6174 2.51 5 N 1419 2.21 5 O 1494 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9138 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3010 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 354} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3010 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 354} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3010 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 354} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {' CL': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {' CL': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 36 Unusual residues: {' CL': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.10, per 1000 atoms: 0.56 Number of scatterers: 9138 At special positions: 0 Unit cell: (104.676, 100.386, 77.22, 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) Cl 3 17.00 S 48 16.00 O 1494 8.00 N 1419 7.00 C 6174 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: 3.25 Conformation dependent library (CDL) restraints added in 1.7 seconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 3 sheets defined 76.1% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 152 through 159 removed outlier: 3.577A pdb=" N TYR A 156 " --> pdb=" O ASP A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 Processing helix chain 'A' and resid 189 through 192 removed outlier: 3.601A pdb=" N CYS A 192 " --> pdb=" O PRO A 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 189 through 192' Processing helix chain 'A' and resid 193 through 210 removed outlier: 3.934A pdb=" N GLN A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL A 204 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU A 205 " --> pdb=" O SER A 201 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA A 210 " --> pdb=" O TRP A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.555A pdb=" N ASN A 216 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 250 removed outlier: 3.679A pdb=" N LEU A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 259 removed outlier: 3.824A pdb=" N VAL A 254 " --> pdb=" O TYR A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 267 removed outlier: 3.540A pdb=" N ASN A 265 " --> pdb=" O VAL A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 279 removed outlier: 3.662A pdb=" N VAL A 272 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N CYS A 274 " --> pdb=" O PRO A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 293 through 316 removed outlier: 4.378A pdb=" N TRP A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) Proline residue: A 303 - end of helix removed outlier: 3.621A pdb=" N LYS A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 327 Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.773A pdb=" N HIS A 332 " --> pdb=" O PRO A 329 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER A 334 " --> pdb=" O SER A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 348 removed outlier: 4.254A pdb=" N PHE A 339 " --> pdb=" O VAL A 335 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 343 " --> pdb=" O PHE A 339 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 344 " --> pdb=" O VAL A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 372 removed outlier: 3.682A pdb=" N LEU A 366 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 367 " --> pdb=" O ALA A 363 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 372 " --> pdb=" O VAL A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 393 Processing helix chain 'A' and resid 394 through 409 Processing helix chain 'A' and resid 412 through 431 removed outlier: 3.622A pdb=" N THR A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 424 " --> pdb=" O PHE A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 438 Processing helix chain 'A' and resid 442 through 448 Processing helix chain 'A' and resid 449 through 466 removed outlier: 3.530A pdb=" N ALA A 455 " --> pdb=" O PRO A 451 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 465 " --> pdb=" O LYS A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 499 removed outlier: 3.627A pdb=" N LEU A 474 " --> pdb=" O PRO A 470 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 489 " --> pdb=" O MET A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 511 removed outlier: 3.791A pdb=" N ILE A 510 " --> pdb=" O ASP A 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 159 removed outlier: 3.577A pdb=" N TYR B 156 " --> pdb=" O ASP B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 189 through 192 removed outlier: 3.602A pdb=" N CYS B 192 " --> pdb=" O PRO B 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 189 through 192' Processing helix chain 'B' and resid 193 through 210 removed outlier: 3.935A pdb=" N GLN B 202 " --> pdb=" O GLY B 198 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B 203 " --> pdb=" O LEU B 199 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 204 " --> pdb=" O SER B 200 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 205 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA B 210 " --> pdb=" O TRP B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 216 removed outlier: 3.554A pdb=" N ASN B 216 " --> pdb=" O PRO B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 250 removed outlier: 3.680A pdb=" N LEU B 226 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 259 removed outlier: 3.824A pdb=" N VAL B 254 " --> pdb=" O TYR B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 267 removed outlier: 3.540A pdb=" N ASN B 265 " --> pdb=" O VAL B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 279 removed outlier: 3.662A pdb=" N VAL B 272 " --> pdb=" O PHE B 268 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N CYS B 274 " --> pdb=" O PRO B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 Processing helix chain 'B' and resid 293 through 316 removed outlier: 4.378A pdb=" N TRP B 297 " --> pdb=" O HIS B 293 " (cutoff:3.500A) Proline residue: B 303 - end of helix removed outlier: 3.622A pdb=" N LYS B 310 " --> pdb=" O PHE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 327 Processing helix chain 'B' and resid 328 through 334 removed outlier: 3.774A pdb=" N HIS B 332 " --> pdb=" O PRO B 329 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER B 334 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 348 removed outlier: 4.253A pdb=" N PHE B 339 " --> pdb=" O VAL B 335 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 343 " --> pdb=" O PHE B 339 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 344 " --> pdb=" O VAL B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 372 removed outlier: 3.682A pdb=" N LEU B 366 " --> pdb=" O PHE B 362 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL B 367 " --> pdb=" O ALA B 363 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 372 " --> pdb=" O VAL B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 393 Processing helix chain 'B' and resid 394 through 409 Processing helix chain 'B' and resid 412 through 431 removed outlier: 3.622A pdb=" N THR B 417 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE B 424 " --> pdb=" O PHE B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 442 through 448 Processing helix chain 'B' and resid 449 through 466 removed outlier: 3.530A pdb=" N ALA B 455 " --> pdb=" O PRO B 451 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL B 457 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 465 " --> pdb=" O LYS B 461 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 499 removed outlier: 3.626A pdb=" N LEU B 474 " --> pdb=" O PRO B 470 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU B 489 " --> pdb=" O MET B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 507 through 511 removed outlier: 3.790A pdb=" N ILE B 510 " --> pdb=" O ASP B 507 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 159 removed outlier: 3.577A pdb=" N TYR C 156 " --> pdb=" O ASP C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 187 Processing helix chain 'C' and resid 189 through 192 removed outlier: 3.601A pdb=" N CYS C 192 " --> pdb=" O PRO C 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 189 through 192' Processing helix chain 'C' and resid 193 through 210 removed outlier: 3.935A pdb=" N GLN C 202 " --> pdb=" O GLY C 198 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA C 203 " --> pdb=" O LEU C 199 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL C 204 " --> pdb=" O SER C 200 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C 205 " --> pdb=" O SER C 201 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA C 210 " --> pdb=" O TRP C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 216 removed outlier: 3.555A pdb=" N ASN C 216 " --> pdb=" O PRO C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 250 removed outlier: 3.680A pdb=" N LEU C 226 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 259 removed outlier: 3.824A pdb=" N VAL C 254 " --> pdb=" O TYR C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 267 removed outlier: 3.540A pdb=" N ASN C 265 " --> pdb=" O VAL C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 279 removed outlier: 3.663A pdb=" N VAL C 272 " --> pdb=" O PHE C 268 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N CYS C 274 " --> pdb=" O PRO C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 286 Processing helix chain 'C' and resid 293 through 316 removed outlier: 4.378A pdb=" N TRP C 297 " --> pdb=" O HIS C 293 " (cutoff:3.500A) Proline residue: C 303 - end of helix removed outlier: 3.622A pdb=" N LYS C 310 " --> pdb=" O PHE C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 327 Processing helix chain 'C' and resid 328 through 334 removed outlier: 3.774A pdb=" N HIS C 332 " --> pdb=" O PRO C 329 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER C 334 " --> pdb=" O SER C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 348 removed outlier: 4.254A pdb=" N PHE C 339 " --> pdb=" O VAL C 335 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE C 343 " --> pdb=" O PHE C 339 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU C 344 " --> pdb=" O VAL C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 372 removed outlier: 3.682A pdb=" N LEU C 366 " --> pdb=" O PHE C 362 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL C 367 " --> pdb=" O ALA C 363 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU C 372 " --> pdb=" O VAL C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 393 Processing helix chain 'C' and resid 394 through 409 Processing helix chain 'C' and resid 412 through 431 removed outlier: 3.623A pdb=" N THR C 417 " --> pdb=" O GLY C 413 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 424 " --> pdb=" O PHE C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 438 Processing helix chain 'C' and resid 442 through 448 Processing helix chain 'C' and resid 449 through 466 removed outlier: 3.530A pdb=" N ALA C 455 " --> pdb=" O PRO C 451 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL C 457 " --> pdb=" O THR C 453 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 465 " --> pdb=" O LYS C 461 " (cutoff:3.500A) Processing helix chain 'C' and resid 468 through 499 removed outlier: 3.627A pdb=" N LEU C 474 " --> pdb=" O PRO C 470 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU C 489 " --> pdb=" O MET C 485 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 511 removed outlier: 3.791A pdb=" N ILE C 510 " --> pdb=" O ASP C 507 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 161 removed outlier: 3.583A pdb=" N GLU A 167 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 161 removed outlier: 3.584A pdb=" N GLU B 167 " --> pdb=" O ARG B 161 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 160 through 161 removed outlier: 3.583A pdb=" N GLU C 167 " --> pdb=" O ARG C 161 " (cutoff:3.500A) 513 hydrogen bonds defined for protein. 1377 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: 2.39 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1601 1.33 - 1.45: 2648 1.45 - 1.57: 5138 1.57 - 1.69: 0 1.69 - 1.81: 69 Bond restraints: 9456 Sorted by residual: bond pdb=" CBD Y01 A 902 " pdb=" CBF Y01 A 902 " ideal model delta sigma weight residual 1.536 1.404 0.132 2.00e-02 2.50e+03 4.37e+01 bond pdb=" CBD Y01 B 901 " pdb=" CBF Y01 B 901 " ideal model delta sigma weight residual 1.536 1.404 0.132 2.00e-02 2.50e+03 4.36e+01 bond pdb=" CBD Y01 C 901 " pdb=" CBF Y01 C 901 " ideal model delta sigma weight residual 1.536 1.404 0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" CAV Y01 B 901 " pdb=" CBC Y01 B 901 " ideal model delta sigma weight residual 1.523 1.434 0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" CAV Y01 C 901 " pdb=" CBC Y01 C 901 " ideal model delta sigma weight residual 1.523 1.434 0.089 2.00e-02 2.50e+03 1.99e+01 ... (remaining 9451 not shown) Histogram of bond angle deviations from ideal: 98.98 - 105.99: 292 105.99 - 112.99: 4923 112.99 - 120.00: 3534 120.00 - 127.01: 4012 127.01 - 134.01: 169 Bond angle restraints: 12930 Sorted by residual: angle pdb=" CAR Y01 B 901 " pdb=" CBC Y01 B 901 " pdb=" OAW Y01 B 901 " ideal model delta sigma weight residual 107.47 122.18 -14.71 3.00e+00 1.11e-01 2.41e+01 angle pdb=" CAR Y01 A 902 " pdb=" CBC Y01 A 902 " pdb=" OAW Y01 A 902 " ideal model delta sigma weight residual 107.47 122.18 -14.71 3.00e+00 1.11e-01 2.41e+01 angle pdb=" CAR Y01 C 901 " pdb=" CBC Y01 C 901 " pdb=" OAW Y01 C 901 " ideal model delta sigma weight residual 107.47 122.15 -14.68 3.00e+00 1.11e-01 2.40e+01 angle pdb=" CAR Y01 A 902 " pdb=" CBC Y01 A 902 " pdb=" CAV Y01 A 902 " ideal model delta sigma weight residual 110.42 99.65 10.77 3.00e+00 1.11e-01 1.29e+01 angle pdb=" CAK Y01 C 901 " pdb=" CAI Y01 C 901 " pdb=" CAZ Y01 C 901 " ideal model delta sigma weight residual 124.96 114.21 10.75 3.00e+00 1.11e-01 1.28e+01 ... (remaining 12925 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 4830 17.59 - 35.19: 516 35.19 - 52.78: 168 52.78 - 70.38: 18 70.38 - 87.97: 6 Dihedral angle restraints: 5538 sinusoidal: 2208 harmonic: 3330 Sorted by residual: dihedral pdb=" CB GLU C 257 " pdb=" CG GLU C 257 " pdb=" CD GLU C 257 " pdb=" OE1 GLU C 257 " ideal model delta sinusoidal sigma weight residual 0.00 87.97 -87.97 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU A 257 " pdb=" CG GLU A 257 " pdb=" CD GLU A 257 " pdb=" OE1 GLU A 257 " ideal model delta sinusoidal sigma weight residual 0.00 87.95 -87.95 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CB GLU B 257 " pdb=" CG GLU B 257 " pdb=" CD GLU B 257 " pdb=" OE1 GLU B 257 " ideal model delta sinusoidal sigma weight residual 0.00 87.95 -87.95 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 5535 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 1440 0.127 - 0.253: 0 0.253 - 0.380: 6 0.380 - 0.506: 3 0.506 - 0.633: 6 Chirality restraints: 1455 Sorted by residual: chirality pdb=" CBF Y01 A 902 " pdb=" CAS Y01 A 902 " pdb=" CBD Y01 A 902 " pdb=" CBH Y01 A 902 " both_signs ideal model delta sigma weight residual False -2.45 -1.81 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CBF Y01 C 901 " pdb=" CAS Y01 C 901 " pdb=" CBD Y01 C 901 " pdb=" CBH Y01 C 901 " both_signs ideal model delta sigma weight residual False -2.45 -1.81 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" CBF Y01 B 901 " pdb=" CAS Y01 B 901 " pdb=" CBD Y01 B 901 " pdb=" CBH Y01 B 901 " both_signs ideal model delta sigma weight residual False -2.45 -1.82 -0.63 2.00e-01 2.50e+01 9.91e+00 ... (remaining 1452 not shown) Planarity restraints: 1563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 469 " 0.037 5.00e-02 4.00e+02 5.62e-02 5.05e+00 pdb=" N PRO C 470 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO C 470 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 470 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 469 " 0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO B 470 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 470 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 470 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 469 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO A 470 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 470 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 470 " -0.031 5.00e-02 4.00e+02 ... (remaining 1560 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1897 2.77 - 3.30: 8034 3.30 - 3.84: 14001 3.84 - 4.37: 17824 4.37 - 4.90: 29815 Nonbonded interactions: 71571 Sorted by model distance: nonbonded pdb=" OE2 GLU C 164 " pdb=" OH TYR C 448 " model vdw 2.238 2.440 nonbonded pdb=" OE2 GLU B 164 " pdb=" OH TYR B 448 " model vdw 2.238 2.440 nonbonded pdb=" OE2 GLU A 164 " pdb=" OH TYR A 448 " model vdw 2.239 2.440 nonbonded pdb=" OD1 ASP A 166 " pdb=" NH2 ARG A 263 " model vdw 2.264 2.520 nonbonded pdb=" OD1 ASP C 166 " pdb=" NH2 ARG C 263 " model vdw 2.264 2.520 ... (remaining 71566 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 105 through 516) selection = (chain 'B' and resid 105 through 516) selection = (chain 'C' and resid 105 through 516) } 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: 1.650 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: 5.850 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.180 Find NCS groups from input model: 0.570 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:11.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 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 0.132 9456 Z= 0.334 Angle : 0.700 14.713 12930 Z= 0.281 Chirality : 0.059 0.633 1455 Planarity : 0.005 0.056 1563 Dihedral : 16.091 87.973 3378 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.25 % Allowed : 21.94 % Favored : 76.80 % 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: -2.18 (0.23), residues: 1119 helix: -1.73 (0.17), residues: 705 sheet: None (None), residues: 0 loop : -0.53 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 404 HIS 0.009 0.001 HIS C 387 PHE 0.010 0.001 PHE B 217 TYR 0.012 0.001 TYR A 365 ARG 0.002 0.000 ARG B 472 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 1.001 Fit side-chains REVERT: A 366 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8173 (mt) REVERT: B 168 VAL cc_start: 0.8493 (t) cc_final: 0.8282 (m) REVERT: B 450 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.7467 (t80) REVERT: C 216 ASN cc_start: 0.7809 (t0) cc_final: 0.7501 (t0) REVERT: C 366 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8142 (mt) REVERT: C 405 ASN cc_start: 0.8770 (t0) cc_final: 0.8474 (t160) outliers start: 12 outliers final: 5 residues processed: 101 average time/residue: 0.8409 time to fit residues: 93.7213 Evaluate side-chains 95 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 450 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.0980 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 387 HIS C 387 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9456 Z= 0.195 Angle : 0.654 7.637 12930 Z= 0.330 Chirality : 0.043 0.182 1455 Planarity : 0.006 0.047 1563 Dihedral : 7.996 59.956 1435 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.13 % Allowed : 18.60 % Favored : 78.27 % 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: -0.00 (0.25), residues: 1119 helix: 0.26 (0.20), residues: 711 sheet: None (None), residues: 0 loop : -0.23 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 229 HIS 0.006 0.001 HIS C 387 PHE 0.019 0.002 PHE C 450 TYR 0.013 0.002 TYR B 408 ARG 0.006 0.001 ARG C 472 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 90 time to evaluate : 1.017 Fit side-chains REVERT: A 180 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6827 (pt0) REVERT: A 322 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7541 (ptp-170) REVERT: B 166 ASP cc_start: 0.7220 (OUTLIER) cc_final: 0.7009 (t70) REVERT: B 322 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7439 (ptp-170) REVERT: B 410 GLN cc_start: 0.8167 (OUTLIER) cc_final: 0.7771 (pm20) REVERT: C 161 ARG cc_start: 0.8109 (ptt90) cc_final: 0.7854 (ptt-90) REVERT: C 216 ASN cc_start: 0.8007 (t0) cc_final: 0.7726 (t0) REVERT: C 450 PHE cc_start: 0.8099 (OUTLIER) cc_final: 0.7876 (p90) REVERT: C 452 MET cc_start: 0.8160 (mtp) cc_final: 0.7909 (mtt) outliers start: 30 outliers final: 9 residues processed: 113 average time/residue: 1.1142 time to fit residues: 136.3849 Evaluate side-chains 87 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 72 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 450 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 387 HIS C 314 GLN C 387 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9456 Z= 0.274 Angle : 0.732 8.011 12930 Z= 0.373 Chirality : 0.047 0.188 1455 Planarity : 0.007 0.050 1563 Dihedral : 7.357 52.723 1431 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.03 % Allowed : 17.35 % Favored : 79.62 % 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: 0.52 (0.25), residues: 1119 helix: 0.81 (0.20), residues: 687 sheet: None (None), residues: 0 loop : -0.27 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 206 HIS 0.009 0.002 HIS B 387 PHE 0.018 0.002 PHE C 450 TYR 0.014 0.002 TYR B 408 ARG 0.004 0.001 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 78 time to evaluate : 0.984 Fit side-chains REVERT: A 322 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7420 (ptp-170) REVERT: B 190 ILE cc_start: 0.8488 (OUTLIER) cc_final: 0.8267 (tp) REVERT: B 322 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7395 (ptp-170) REVERT: B 429 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8129 (tp) REVERT: C 161 ARG cc_start: 0.8171 (ptt90) cc_final: 0.7896 (ptt-90) REVERT: C 180 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7199 (pt0) REVERT: C 216 ASN cc_start: 0.8100 (t0) cc_final: 0.7846 (t0) REVERT: C 452 MET cc_start: 0.8422 (mtp) cc_final: 0.8136 (mtm) outliers start: 29 outliers final: 17 residues processed: 102 average time/residue: 1.0538 time to fit residues: 116.6058 Evaluate side-chains 98 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 76 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 429 LEU Chi-restraints excluded: chain B residue 450 PHE Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 218 LEU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 410 GLN Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 450 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 60 optimal weight: 0.5980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 387 HIS C 387 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9456 Z= 0.186 Angle : 0.614 6.698 12930 Z= 0.311 Chirality : 0.043 0.176 1455 Planarity : 0.006 0.053 1563 Dihedral : 6.663 48.820 1431 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.72 % Allowed : 17.45 % Favored : 79.83 % 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: 1.07 (0.25), residues: 1119 helix: 1.28 (0.20), residues: 687 sheet: None (None), residues: 0 loop : -0.11 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 229 HIS 0.008 0.001 HIS C 387 PHE 0.019 0.002 PHE C 450 TYR 0.012 0.002 TYR B 408 ARG 0.004 0.000 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 80 time to evaluate : 0.991 Fit side-chains REVERT: A 322 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7396 (ptp-170) REVERT: A 333 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8374 (tt) REVERT: B 180 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6967 (pt0) REVERT: B 190 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8241 (tp) REVERT: B 322 ARG cc_start: 0.8019 (OUTLIER) cc_final: 0.7238 (ptp-170) REVERT: B 410 GLN cc_start: 0.8194 (OUTLIER) cc_final: 0.7647 (pm20) REVERT: C 161 ARG cc_start: 0.8156 (ptt90) cc_final: 0.7901 (ptt-90) REVERT: C 180 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.7182 (pt0) REVERT: C 216 ASN cc_start: 0.8074 (t0) cc_final: 0.7795 (t0) REVERT: C 392 MET cc_start: 0.8689 (mmm) cc_final: 0.8463 (mmt) REVERT: C 452 MET cc_start: 0.8258 (mtp) cc_final: 0.7965 (mtt) outliers start: 26 outliers final: 11 residues processed: 101 average time/residue: 1.0498 time to fit residues: 115.0912 Evaluate side-chains 94 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 76 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 429 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.0570 chunk 79 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 54 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 387 HIS C 387 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9456 Z= 0.254 Angle : 0.690 7.472 12930 Z= 0.352 Chirality : 0.046 0.183 1455 Planarity : 0.007 0.053 1563 Dihedral : 6.320 47.332 1421 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 3.13 % Allowed : 16.51 % Favored : 80.36 % 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: 0.94 (0.25), residues: 1119 helix: 1.20 (0.20), residues: 687 sheet: None (None), residues: 0 loop : -0.21 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 206 HIS 0.007 0.002 HIS C 387 PHE 0.020 0.002 PHE B 450 TYR 0.014 0.002 TYR B 408 ARG 0.003 0.001 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 77 time to evaluate : 1.088 Fit side-chains REVERT: A 180 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.6998 (pt0) REVERT: A 322 ARG cc_start: 0.8148 (OUTLIER) cc_final: 0.7355 (ptp-170) REVERT: B 180 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7016 (pt0) REVERT: B 322 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7315 (ptp-170) REVERT: C 161 ARG cc_start: 0.8184 (ptt90) cc_final: 0.7914 (ptt-90) REVERT: C 180 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7287 (pt0) REVERT: C 216 ASN cc_start: 0.8120 (t0) cc_final: 0.7856 (t0) REVERT: C 325 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7967 (mtpp) REVERT: C 452 MET cc_start: 0.8364 (mtp) cc_final: 0.8044 (mtt) outliers start: 30 outliers final: 17 residues processed: 101 average time/residue: 1.0667 time to fit residues: 117.1515 Evaluate side-chains 100 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 77 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 322 ARG Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 410 GLN Chi-restraints excluded: chain A residue 450 PHE Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 322 ARG Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 325 LYS Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 410 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 0.0870 chunk 103 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 387 HIS C 387 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9456 Z= 0.145 Angle : 0.535 6.247 12930 Z= 0.271 Chirality : 0.040 0.180 1455 Planarity : 0.006 0.053 1563 Dihedral : 5.868 47.989 1421 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 1.99 % Allowed : 17.66 % Favored : 80.36 % 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: 1.45 (0.26), residues: 1119 helix: 1.55 (0.21), residues: 708 sheet: None (None), residues: 0 loop : 0.05 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 229 HIS 0.007 0.001 HIS B 387 PHE 0.018 0.001 PHE B 450 TYR 0.011 0.001 TYR B 408 ARG 0.004 0.000 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 1.000 Fit side-chains REVERT: A 180 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6888 (pt0) REVERT: B 112 LYS cc_start: 0.8062 (mttp) cc_final: 0.7245 (mmtt) REVERT: B 180 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6878 (pt0) REVERT: B 410 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7549 (pm20) REVERT: C 161 ARG cc_start: 0.8171 (ptt90) cc_final: 0.7922 (ptt-90) REVERT: C 180 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7070 (pt0) REVERT: C 216 ASN cc_start: 0.8128 (t0) cc_final: 0.7823 (t0) REVERT: C 392 MET cc_start: 0.8626 (mmm) cc_final: 0.8404 (mmt) REVERT: C 452 MET cc_start: 0.8038 (mtp) cc_final: 0.7811 (mtt) REVERT: C 514 LYS cc_start: 0.8041 (ttpt) cc_final: 0.7837 (tttm) outliers start: 19 outliers final: 7 residues processed: 100 average time/residue: 1.1688 time to fit residues: 125.9416 Evaluate side-chains 87 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 366 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 5.9990 chunk 60 optimal weight: 0.4980 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 9456 Z= 0.223 Angle : 0.648 10.081 12930 Z= 0.329 Chirality : 0.044 0.183 1455 Planarity : 0.006 0.052 1563 Dihedral : 5.929 44.294 1419 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 2.40 % Allowed : 17.55 % Favored : 80.04 % 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: 1.35 (0.25), residues: 1119 helix: 1.54 (0.20), residues: 687 sheet: None (None), residues: 0 loop : -0.06 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 206 HIS 0.010 0.002 HIS B 387 PHE 0.018 0.002 PHE B 450 TYR 0.013 0.002 TYR B 408 ARG 0.003 0.000 ARG A 472 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 77 time to evaluate : 0.991 Fit side-chains REVERT: A 180 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6966 (pt0) REVERT: B 180 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.6970 (pt0) REVERT: C 161 ARG cc_start: 0.8178 (ptt90) cc_final: 0.7918 (ptt-90) REVERT: C 180 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7216 (pt0) REVERT: C 216 ASN cc_start: 0.8133 (t0) cc_final: 0.7865 (t0) REVERT: C 392 MET cc_start: 0.8699 (mmm) cc_final: 0.8479 (mmt) REVERT: C 452 MET cc_start: 0.8290 (mtp) cc_final: 0.8006 (mtt) outliers start: 23 outliers final: 13 residues processed: 94 average time/residue: 0.9749 time to fit residues: 100.4155 Evaluate side-chains 93 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 77 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 366 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 102 optimal weight: 0.4980 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 387 HIS C 314 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9456 Z= 0.267 Angle : 0.698 9.539 12930 Z= 0.357 Chirality : 0.046 0.191 1455 Planarity : 0.006 0.051 1563 Dihedral : 6.134 40.106 1419 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.40 % Allowed : 17.55 % Favored : 80.04 % 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: 1.08 (0.25), residues: 1119 helix: 1.33 (0.20), residues: 687 sheet: None (None), residues: 0 loop : -0.18 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 206 HIS 0.010 0.002 HIS B 387 PHE 0.017 0.002 PHE B 450 TYR 0.014 0.002 TYR B 408 ARG 0.002 0.000 ARG A 416 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 80 time to evaluate : 0.979 Fit side-chains REVERT: A 180 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6997 (pt0) REVERT: B 180 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7053 (pt0) REVERT: C 161 ARG cc_start: 0.8191 (ptt90) cc_final: 0.7932 (ptt-90) REVERT: C 180 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7319 (pt0) REVERT: C 216 ASN cc_start: 0.8125 (t0) cc_final: 0.7869 (t0) REVERT: C 325 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7920 (mtpp) REVERT: C 452 MET cc_start: 0.8345 (mtp) cc_final: 0.8037 (mtt) outliers start: 23 outliers final: 16 residues processed: 97 average time/residue: 0.9632 time to fit residues: 102.3005 Evaluate side-chains 97 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 77 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 325 LYS Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 410 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9456 Z= 0.165 Angle : 0.579 8.685 12930 Z= 0.294 Chirality : 0.042 0.185 1455 Planarity : 0.006 0.054 1563 Dihedral : 5.774 43.196 1419 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 2.51 % Allowed : 17.66 % Favored : 79.83 % 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: 1.36 (0.26), residues: 1119 helix: 1.47 (0.20), residues: 708 sheet: None (None), residues: 0 loop : 0.02 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 206 HIS 0.011 0.001 HIS B 387 PHE 0.019 0.001 PHE B 450 TYR 0.011 0.002 TYR B 408 ARG 0.003 0.000 ARG C 472 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 79 time to evaluate : 1.007 Fit side-chains REVERT: A 180 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.6906 (pt0) REVERT: B 112 LYS cc_start: 0.8063 (mttp) cc_final: 0.7233 (mmtt) REVERT: B 180 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6940 (pt0) REVERT: B 410 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7607 (pm20) REVERT: C 161 ARG cc_start: 0.8193 (ptt90) cc_final: 0.7939 (ptt-90) REVERT: C 166 ASP cc_start: 0.7189 (m-30) cc_final: 0.6962 (m-30) REVERT: C 180 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7210 (pt0) REVERT: C 216 ASN cc_start: 0.8134 (t0) cc_final: 0.7861 (t0) REVERT: C 392 MET cc_start: 0.8652 (mmm) cc_final: 0.8410 (mmt) REVERT: C 452 MET cc_start: 0.8142 (mtp) cc_final: 0.7855 (mtt) outliers start: 24 outliers final: 10 residues processed: 96 average time/residue: 1.0275 time to fit residues: 107.2412 Evaluate side-chains 94 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 111 THR Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 410 GLN Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 366 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.6980 chunk 73 optimal weight: 0.0170 chunk 110 optimal weight: 0.2980 chunk 101 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9456 Z= 0.142 Angle : 0.533 8.503 12930 Z= 0.269 Chirality : 0.040 0.183 1455 Planarity : 0.006 0.054 1563 Dihedral : 5.599 47.145 1419 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.88 % Allowed : 18.08 % Favored : 80.04 % 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: 1.70 (0.26), residues: 1119 helix: 1.69 (0.21), residues: 711 sheet: None (None), residues: 0 loop : 0.24 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 229 HIS 0.012 0.001 HIS B 387 PHE 0.019 0.001 PHE B 450 TYR 0.010 0.001 TYR B 408 ARG 0.003 0.000 ARG B 472 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 85 time to evaluate : 1.075 Fit side-chains REVERT: A 180 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6825 (pt0) REVERT: A 333 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8432 (tt) REVERT: B 112 LYS cc_start: 0.8052 (mttp) cc_final: 0.7332 (mmtt) REVERT: B 180 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.6859 (pt0) REVERT: C 161 ARG cc_start: 0.8189 (ptt90) cc_final: 0.7934 (ptt-90) REVERT: C 180 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7086 (pt0) REVERT: C 216 ASN cc_start: 0.8100 (t0) cc_final: 0.7719 (t0) REVERT: C 452 MET cc_start: 0.8052 (mtp) cc_final: 0.7828 (mtt) outliers start: 18 outliers final: 10 residues processed: 97 average time/residue: 1.0760 time to fit residues: 113.6697 Evaluate side-chains 92 residues out of total 972 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 78 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 485 MET Chi-restraints excluded: chain B residue 166 ASP Chi-restraints excluded: chain B residue 180 GLU Chi-restraints excluded: chain B residue 201 SER Chi-restraints excluded: chain B residue 428 SER Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 242 THR Chi-restraints excluded: chain C residue 366 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS B 387 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.140371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.116440 restraints weight = 8679.595| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 0.97 r_work: 0.2950 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 9456 Z= 0.170 Angle : 0.578 8.823 12930 Z= 0.292 Chirality : 0.042 0.182 1455 Planarity : 0.006 0.053 1563 Dihedral : 5.678 45.584 1419 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.78 % Allowed : 18.29 % Favored : 79.94 % 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: 1.58 (0.26), residues: 1119 helix: 1.62 (0.20), residues: 708 sheet: None (None), residues: 0 loop : 0.15 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 206 HIS 0.011 0.001 HIS B 387 PHE 0.018 0.001 PHE B 450 TYR 0.012 0.002 TYR B 408 ARG 0.003 0.000 ARG A 472 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2614.02 seconds wall clock time: 47 minutes 50.40 seconds (2870.40 seconds total)