Starting phenix.real_space_refine on Mon May 12 21:50:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jvv_61844/05_2025/9jvv_61844.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jvv_61844/05_2025/9jvv_61844.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jvv_61844/05_2025/9jvv_61844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jvv_61844/05_2025/9jvv_61844.map" model { file = "/net/cci-nas-00/data/ceres_data/9jvv_61844/05_2025/9jvv_61844.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jvv_61844/05_2025/9jvv_61844.cif" } resolution = 2.82 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= 0.004 sd= 0.141 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 72 5.16 5 C 6201 2.51 5 N 1497 2.21 5 O 1635 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9405 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3107 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 13, 'TRANS': 401} Chain breaks: 2 Chain: "B" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3107 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 13, 'TRANS': 401} Chain breaks: 2 Chain: "C" Number of atoms: 3107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3107 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 13, 'TRANS': 401} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.03, per 1000 atoms: 0.64 Number of scatterers: 9405 At special positions: 0 Unit cell: (115.239, 113.085, 81.852, 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 72 16.00 O 1635 8.00 N 1497 7.00 C 6201 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 - 3.00 Amino acid : True - 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: 2.73 Conformation dependent library (CDL) restraints added in 1.3 seconds 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2250 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 3 sheets defined 82.2% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 46 through 66 removed outlier: 3.595A pdb=" N LEU A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 91 Proline residue: A 81 - end of helix Processing helix chain 'A' and resid 92 through 106 Processing helix chain 'A' and resid 114 through 142 removed outlier: 4.348A pdb=" N THR A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 120 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A 128 " --> pdb=" O TYR A 124 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE A 129 " --> pdb=" O MET A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 176 removed outlier: 3.625A pdb=" N PHE A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 184 Processing helix chain 'A' and resid 241 through 258 Processing helix chain 'A' and resid 263 through 302 removed outlier: 3.631A pdb=" N VAL A 267 " --> pdb=" O ALA A 263 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 275 " --> pdb=" O ASN A 271 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR A 287 " --> pdb=" O MET A 283 " (cutoff:3.500A) Proline residue: A 289 - end of helix removed outlier: 3.707A pdb=" N ALA A 293 " --> pdb=" O PRO A 289 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS A 294 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 338 removed outlier: 3.625A pdb=" N MET A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Proline residue: A 333 - end of helix Processing helix chain 'A' and resid 343 through 351 removed outlier: 4.036A pdb=" N PHE A 347 " --> pdb=" O ASN A 343 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 362 Processing helix chain 'A' and resid 367 through 379 removed outlier: 3.671A pdb=" N GLU A 377 " --> pdb=" O ARG A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 397 removed outlier: 3.503A pdb=" N THR A 386 " --> pdb=" O ASP A 382 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE A 388 " --> pdb=" O ARG A 384 " (cutoff:3.500A) Proline residue: A 391 - end of helix removed outlier: 3.980A pdb=" N THR A 395 " --> pdb=" O PRO A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 416 removed outlier: 3.574A pdb=" N ALA A 402 " --> pdb=" O MET A 398 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 403 " --> pdb=" O ASP A 399 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE A 410 " --> pdb=" O ALA A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 442 removed outlier: 3.791A pdb=" N VAL A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR A 433 " --> pdb=" O SER A 429 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 437 " --> pdb=" O THR A 433 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 441 " --> pdb=" O VAL A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 458 removed outlier: 3.569A pdb=" N LEU A 451 " --> pdb=" O LEU A 447 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 469 removed outlier: 3.937A pdb=" N LEU A 467 " --> pdb=" O ASP A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 473 Processing helix chain 'A' and resid 474 through 497 removed outlier: 4.033A pdb=" N SER A 480 " --> pdb=" O ARG A 476 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS A 495 " --> pdb=" O GLY A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 506 removed outlier: 3.522A pdb=" N SER A 506 " --> pdb=" O ASP A 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 66 removed outlier: 3.596A pdb=" N LEU B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 91 Proline residue: B 81 - end of helix Processing helix chain 'B' and resid 92 through 106 Processing helix chain 'B' and resid 114 through 142 removed outlier: 4.348A pdb=" N THR B 118 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 120 " --> pdb=" O LEU B 116 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N THR B 128 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 129 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 176 removed outlier: 3.625A pdb=" N PHE B 176 " --> pdb=" O ILE B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 184 Processing helix chain 'B' and resid 241 through 258 Processing helix chain 'B' and resid 263 through 302 removed outlier: 3.631A pdb=" N VAL B 267 " --> pdb=" O ALA B 263 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU B 275 " --> pdb=" O ASN B 271 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP B 286 " --> pdb=" O ILE B 282 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR B 287 " --> pdb=" O MET B 283 " (cutoff:3.500A) Proline residue: B 289 - end of helix removed outlier: 3.707A pdb=" N ALA B 293 " --> pdb=" O PRO B 289 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA B 302 " --> pdb=" O GLY B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 338 removed outlier: 3.625A pdb=" N MET B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) Proline residue: B 333 - end of helix Processing helix chain 'B' and resid 343 through 351 removed outlier: 4.036A pdb=" N PHE B 347 " --> pdb=" O ASN B 343 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 362 Processing helix chain 'B' and resid 367 through 379 removed outlier: 3.670A pdb=" N GLU B 377 " --> pdb=" O ARG B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 397 removed outlier: 3.503A pdb=" N THR B 386 " --> pdb=" O ASP B 382 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE B 388 " --> pdb=" O ARG B 384 " (cutoff:3.500A) Proline residue: B 391 - end of helix removed outlier: 3.979A pdb=" N THR B 395 " --> pdb=" O PRO B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 416 removed outlier: 3.574A pdb=" N ALA B 402 " --> pdb=" O MET B 398 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU B 403 " --> pdb=" O ASP B 399 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE B 410 " --> pdb=" O ALA B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 442 removed outlier: 3.791A pdb=" N VAL B 426 " --> pdb=" O GLY B 422 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N THR B 427 " --> pdb=" O GLY B 423 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR B 433 " --> pdb=" O SER B 429 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B 437 " --> pdb=" O THR B 433 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA B 440 " --> pdb=" O SER B 436 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER B 441 " --> pdb=" O VAL B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 458 removed outlier: 3.569A pdb=" N LEU B 451 " --> pdb=" O LEU B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 removed outlier: 3.937A pdb=" N LEU B 467 " --> pdb=" O ASP B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 473 Processing helix chain 'B' and resid 474 through 497 removed outlier: 4.034A pdb=" N SER B 480 " --> pdb=" O ARG B 476 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR B 494 " --> pdb=" O ALA B 490 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS B 495 " --> pdb=" O GLY B 491 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 506 removed outlier: 3.523A pdb=" N SER B 506 " --> pdb=" O ASP B 502 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 66 removed outlier: 3.595A pdb=" N LEU C 66 " --> pdb=" O GLY C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 91 Proline residue: C 81 - end of helix Processing helix chain 'C' and resid 92 through 106 Processing helix chain 'C' and resid 114 through 142 removed outlier: 4.347A pdb=" N THR C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA C 120 " --> pdb=" O LEU C 116 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR C 128 " --> pdb=" O TYR C 124 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE C 129 " --> pdb=" O MET C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 176 removed outlier: 3.625A pdb=" N PHE C 176 " --> pdb=" O ILE C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 184 Processing helix chain 'C' and resid 241 through 258 Processing helix chain 'C' and resid 263 through 302 removed outlier: 3.632A pdb=" N VAL C 267 " --> pdb=" O ALA C 263 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU C 275 " --> pdb=" O ASN C 271 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP C 286 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR C 287 " --> pdb=" O MET C 283 " (cutoff:3.500A) Proline residue: C 289 - end of helix removed outlier: 3.707A pdb=" N ALA C 293 " --> pdb=" O PRO C 289 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N CYS C 294 " --> pdb=" O LEU C 290 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ALA C 302 " --> pdb=" O GLY C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 338 removed outlier: 3.625A pdb=" N MET C 317 " --> pdb=" O LEU C 313 " (cutoff:3.500A) Proline residue: C 333 - end of helix Processing helix chain 'C' and resid 343 through 351 removed outlier: 4.036A pdb=" N PHE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE C 348 " --> pdb=" O PRO C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 362 Processing helix chain 'C' and resid 367 through 379 removed outlier: 3.671A pdb=" N GLU C 377 " --> pdb=" O ARG C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 382 through 397 removed outlier: 3.502A pdb=" N THR C 386 " --> pdb=" O ASP C 382 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N PHE C 388 " --> pdb=" O ARG C 384 " (cutoff:3.500A) Proline residue: C 391 - end of helix removed outlier: 3.980A pdb=" N THR C 395 " --> pdb=" O PRO C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 416 removed outlier: 3.575A pdb=" N ALA C 402 " --> pdb=" O MET C 398 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE C 410 " --> pdb=" O ALA C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 442 removed outlier: 3.790A pdb=" N VAL C 426 " --> pdb=" O GLY C 422 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR C 427 " --> pdb=" O GLY C 423 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR C 433 " --> pdb=" O SER C 429 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL C 437 " --> pdb=" O THR C 433 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA C 440 " --> pdb=" O SER C 436 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 441 " --> pdb=" O VAL C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 458 removed outlier: 3.568A pdb=" N LEU C 451 " --> pdb=" O LEU C 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 469 removed outlier: 3.937A pdb=" N LEU C 467 " --> pdb=" O ASP C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 473 Processing helix chain 'C' and resid 474 through 497 removed outlier: 4.034A pdb=" N SER C 480 " --> pdb=" O ARG C 476 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR C 494 " --> pdb=" O ALA C 490 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N HIS C 495 " --> pdb=" O GLY C 491 " (cutoff:3.500A) Processing helix chain 'C' and resid 497 through 506 removed outlier: 3.522A pdb=" N SER C 506 " --> pdb=" O ASP C 502 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 189 Processing sheet with id=AA2, first strand: chain 'B' and resid 186 through 189 Processing sheet with id=AA3, first strand: chain 'C' and resid 186 through 189 660 hydrogen bonds defined for protein. 1953 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: 2.59 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2895 1.34 - 1.46: 1768 1.46 - 1.58: 4766 1.58 - 1.69: 0 1.69 - 1.81: 129 Bond restraints: 9558 Sorted by residual: bond pdb=" C13 CLR A1001 " pdb=" C18 CLR A1001 " ideal model delta sigma weight residual 1.532 1.494 0.038 2.00e-02 2.50e+03 3.67e+00 bond pdb=" C17 CLR A1001 " pdb=" C20 CLR A1001 " ideal model delta sigma weight residual 1.535 1.497 0.038 2.00e-02 2.50e+03 3.60e+00 bond pdb=" C13 CLR A1001 " pdb=" C17 CLR A1001 " ideal model delta sigma weight residual 1.550 1.513 0.037 2.00e-02 2.50e+03 3.48e+00 bond pdb=" C13 CLR A1001 " pdb=" C14 CLR A1001 " ideal model delta sigma weight residual 1.537 1.502 0.035 2.00e-02 2.50e+03 3.00e+00 bond pdb=" C16 CLR A1001 " pdb=" C17 CLR A1001 " ideal model delta sigma weight residual 1.554 1.520 0.034 2.00e-02 2.50e+03 2.91e+00 ... (remaining 9553 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 12796 2.31 - 4.62: 159 4.62 - 6.92: 25 6.92 - 9.23: 1 9.23 - 11.54: 3 Bond angle restraints: 12984 Sorted by residual: angle pdb=" C TYR A 287 " pdb=" N SER A 288 " pdb=" CA SER A 288 " ideal model delta sigma weight residual 120.09 124.63 -4.54 1.25e+00 6.40e-01 1.32e+01 angle pdb=" C TYR C 287 " pdb=" N SER C 288 " pdb=" CA SER C 288 " ideal model delta sigma weight residual 120.09 124.63 -4.54 1.25e+00 6.40e-01 1.32e+01 angle pdb=" C TYR B 287 " pdb=" N SER B 288 " pdb=" CA SER B 288 " ideal model delta sigma weight residual 120.09 124.58 -4.49 1.25e+00 6.40e-01 1.29e+01 angle pdb=" CA LEU B 45 " pdb=" CB LEU B 45 " pdb=" CG LEU B 45 " ideal model delta sigma weight residual 116.30 127.84 -11.54 3.50e+00 8.16e-02 1.09e+01 angle pdb=" CA LEU C 45 " pdb=" CB LEU C 45 " pdb=" CG LEU C 45 " ideal model delta sigma weight residual 116.30 127.84 -11.54 3.50e+00 8.16e-02 1.09e+01 ... (remaining 12979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.66: 5047 12.66 - 25.32: 539 25.32 - 37.98: 174 37.98 - 50.64: 38 50.64 - 63.30: 16 Dihedral angle restraints: 5814 sinusoidal: 2307 harmonic: 3507 Sorted by residual: dihedral pdb=" CA MET B 477 " pdb=" C MET B 477 " pdb=" N ARG B 478 " pdb=" CA ARG B 478 " ideal model delta harmonic sigma weight residual 180.00 159.14 20.86 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA MET C 477 " pdb=" C MET C 477 " pdb=" N ARG C 478 " pdb=" CA ARG C 478 " ideal model delta harmonic sigma weight residual 180.00 159.16 20.84 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA MET A 477 " pdb=" C MET A 477 " pdb=" N ARG A 478 " pdb=" CA ARG A 478 " ideal model delta harmonic sigma weight residual 180.00 159.16 20.84 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 5811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1561 0.082 - 0.164: 87 0.164 - 0.246: 6 0.246 - 0.328: 1 0.328 - 0.410: 1 Chirality restraints: 1656 Sorted by residual: chirality pdb=" C13 CLR A1001 " pdb=" C12 CLR A1001 " pdb=" C14 CLR A1001 " pdb=" C17 CLR A1001 " both_signs ideal model delta sigma weight residual False -2.93 -2.52 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" C10 CLR A1001 " pdb=" C1 CLR A1001 " pdb=" C5 CLR A1001 " pdb=" C9 CLR A1001 " both_signs ideal model delta sigma weight residual False -2.85 -2.56 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C13 CLR B1001 " pdb=" C12 CLR B1001 " pdb=" C14 CLR B1001 " pdb=" C17 CLR B1001 " both_signs ideal model delta sigma weight residual False -2.93 -2.71 -0.22 2.00e-01 2.50e+01 1.19e+00 ... (remaining 1653 not shown) Planarity restraints: 1560 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY C 328 " -0.010 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" C GLY C 328 " 0.033 2.00e-02 2.50e+03 pdb=" O GLY C 328 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY C 329 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 332 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.59e+00 pdb=" N PRO C 333 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 333 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 333 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 332 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.57e+00 pdb=" N PRO A 333 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 333 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 333 " 0.027 5.00e-02 4.00e+02 ... (remaining 1557 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 2294 2.79 - 3.32: 9525 3.32 - 3.85: 15123 3.85 - 4.37: 18205 4.37 - 4.90: 31169 Nonbonded interactions: 76316 Sorted by model distance: nonbonded pdb=" OH TYR B 404 " pdb=" OD1 ASP B 471 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR C 404 " pdb=" OD1 ASP C 471 " model vdw 2.269 3.040 nonbonded pdb=" OH TYR A 404 " pdb=" OD1 ASP A 471 " model vdw 2.277 3.040 nonbonded pdb=" NH1 ARG C 65 " pdb=" O ILE C 300 " model vdw 2.309 3.120 nonbonded pdb=" NH1 ARG A 65 " pdb=" O ILE A 300 " model vdw 2.310 3.120 ... (remaining 76311 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' } 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: 0.860 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.840 Find NCS groups from input model: 0.180 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: 0.000 Load rotamer database and sin/cos tables:10.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 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 : 0.003 0.057 9558 Z= 0.164 Angle : 0.669 11.542 12984 Z= 0.376 Chirality : 0.044 0.410 1656 Planarity : 0.005 0.047 1560 Dihedral : 12.391 63.303 3564 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.10 % Allowed : 0.49 % Favored : 99.41 % 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: -0.66 (0.24), residues: 1227 helix: 0.11 (0.18), residues: 876 sheet: -2.58 (0.78), residues: 30 loop : -1.48 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 472 HIS 0.002 0.001 HIS C 327 PHE 0.010 0.001 PHE B 249 TYR 0.007 0.001 TYR C 494 ARG 0.001 0.000 ARG C 387 Details of bonding type rmsd hydrogen bonds : bond 0.17354 ( 660) hydrogen bonds : angle 7.39066 ( 1953) covalent geometry : bond 0.00336 ( 9558) covalent geometry : angle 0.66942 (12984) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 0.982 Fit side-chains REVERT: A 235 GLU cc_start: 0.7632 (tt0) cc_final: 0.7412 (tt0) REVERT: A 307 GLU cc_start: 0.7068 (tm-30) cc_final: 0.6829 (tm-30) REVERT: B 86 MET cc_start: 0.7421 (mmt) cc_final: 0.6808 (mmt) REVERT: B 166 ASP cc_start: 0.7581 (m-30) cc_final: 0.7315 (m-30) REVERT: B 182 GLN cc_start: 0.8512 (tt0) cc_final: 0.8182 (tt0) REVERT: B 450 MET cc_start: 0.8082 (tpp) cc_final: 0.7819 (mmm) REVERT: C 86 MET cc_start: 0.7758 (mmt) cc_final: 0.7386 (mmt) REVERT: C 235 GLU cc_start: 0.7625 (tt0) cc_final: 0.7420 (tt0) REVERT: C 259 MET cc_start: 0.8977 (mtp) cc_final: 0.8492 (mtp) REVERT: C 285 MET cc_start: 0.8828 (mmm) cc_final: 0.8319 (mmm) REVERT: C 374 CYS cc_start: 0.8303 (m) cc_final: 0.7999 (m) outliers start: 1 outliers final: 0 residues processed: 186 average time/residue: 1.1646 time to fit residues: 232.1888 Evaluate side-chains 141 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.8980 chunk 93 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 96 optimal weight: 0.4980 chunk 37 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.145470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.112778 restraints weight = 10848.597| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.83 r_work: 0.3237 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9558 Z= 0.130 Angle : 0.537 8.185 12984 Z= 0.270 Chirality : 0.040 0.129 1656 Planarity : 0.004 0.039 1560 Dihedral : 4.803 48.939 1488 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.16 % Allowed : 9.05 % Favored : 88.79 % 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: 0.49 (0.24), residues: 1227 helix: 0.94 (0.17), residues: 948 sheet: -2.34 (0.79), residues: 30 loop : -1.47 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 472 HIS 0.003 0.001 HIS C 327 PHE 0.013 0.001 PHE B 249 TYR 0.011 0.002 TYR C 316 ARG 0.003 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.04466 ( 660) hydrogen bonds : angle 4.59638 ( 1953) covalent geometry : bond 0.00292 ( 9558) covalent geometry : angle 0.53739 (12984) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 1.077 Fit side-chains REVERT: A 235 GLU cc_start: 0.8154 (tt0) cc_final: 0.7839 (tt0) REVERT: A 325 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7993 (mt) REVERT: A 382 ASP cc_start: 0.7388 (t0) cc_final: 0.7150 (t0) REVERT: A 498 LYS cc_start: 0.6994 (ttmt) cc_final: 0.6743 (ttmm) REVERT: B 52 PHE cc_start: 0.7058 (m-10) cc_final: 0.6652 (t80) REVERT: B 86 MET cc_start: 0.8136 (mmt) cc_final: 0.7810 (mmt) REVERT: B 166 ASP cc_start: 0.7855 (m-30) cc_final: 0.7583 (m-30) REVERT: B 182 GLN cc_start: 0.8784 (tt0) cc_final: 0.8584 (tt0) REVERT: B 325 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.8008 (mt) REVERT: B 341 ARG cc_start: 0.8280 (mtp-110) cc_final: 0.7727 (mtt180) REVERT: B 353 GLN cc_start: 0.7796 (mm-40) cc_final: 0.7594 (tp-100) REVERT: B 398 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.7808 (mmp) REVERT: B 450 MET cc_start: 0.8418 (tpp) cc_final: 0.8166 (mmm) REVERT: C 259 MET cc_start: 0.9076 (mtp) cc_final: 0.8830 (mtm) REVERT: C 285 MET cc_start: 0.8832 (mmm) cc_final: 0.8551 (mmm) REVERT: C 325 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8132 (mt) REVERT: C 472 TRP cc_start: 0.8657 (p-90) cc_final: 0.8434 (p-90) outliers start: 22 outliers final: 5 residues processed: 153 average time/residue: 1.1726 time to fit residues: 192.1858 Evaluate side-chains 143 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain C residue 325 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 103 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.134156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.098020 restraints weight = 10871.003| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.02 r_work: 0.2922 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9558 Z= 0.169 Angle : 0.547 6.910 12984 Z= 0.279 Chirality : 0.042 0.134 1656 Planarity : 0.004 0.036 1560 Dihedral : 4.874 50.322 1488 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.95 % Allowed : 11.70 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.24), residues: 1227 helix: 1.15 (0.17), residues: 951 sheet: -2.51 (0.74), residues: 30 loop : -1.38 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 355 HIS 0.003 0.001 HIS C 327 PHE 0.019 0.002 PHE B 249 TYR 0.010 0.001 TYR C 316 ARG 0.002 0.000 ARG B 387 Details of bonding type rmsd hydrogen bonds : bond 0.04913 ( 660) hydrogen bonds : angle 4.47658 ( 1953) covalent geometry : bond 0.00419 ( 9558) covalent geometry : angle 0.54734 (12984) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 1.025 Fit side-chains REVERT: A 268 ASP cc_start: 0.7413 (m-30) cc_final: 0.7209 (m-30) REVERT: A 307 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7144 (tm-30) REVERT: A 311 ARG cc_start: 0.7780 (ttp-170) cc_final: 0.7572 (ttm-80) REVERT: A 325 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.8043 (mt) REVERT: A 498 LYS cc_start: 0.7157 (ttmt) cc_final: 0.6950 (ttmm) REVERT: B 52 PHE cc_start: 0.7041 (m-10) cc_final: 0.6508 (t80) REVERT: B 86 MET cc_start: 0.8287 (mmt) cc_final: 0.8020 (mmt) REVERT: B 166 ASP cc_start: 0.8006 (m-30) cc_final: 0.7727 (m-30) REVERT: B 325 ILE cc_start: 0.8415 (OUTLIER) cc_final: 0.8098 (mt) REVERT: B 341 ARG cc_start: 0.8247 (mtp-110) cc_final: 0.7697 (mtt180) REVERT: B 398 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.7860 (mmp) REVERT: C 259 MET cc_start: 0.9055 (mtp) cc_final: 0.8837 (mtm) REVERT: C 325 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8226 (mt) outliers start: 30 outliers final: 10 residues processed: 155 average time/residue: 1.1600 time to fit residues: 192.9622 Evaluate side-chains 144 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 436 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 3.9990 chunk 65 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 19 optimal weight: 0.0970 chunk 22 optimal weight: 0.5980 chunk 69 optimal weight: 0.0970 chunk 100 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 overall best weight: 0.3576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN C 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.147031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.114686 restraints weight = 10741.793| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.81 r_work: 0.3255 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9558 Z= 0.101 Angle : 0.479 9.571 12984 Z= 0.239 Chirality : 0.039 0.128 1656 Planarity : 0.003 0.032 1560 Dihedral : 4.627 51.758 1488 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.36 % Allowed : 13.18 % Favored : 84.46 % 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: 1.37 (0.25), residues: 1227 helix: 1.58 (0.17), residues: 960 sheet: -2.37 (0.75), residues: 30 loop : -1.34 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 472 HIS 0.003 0.001 HIS B 327 PHE 0.011 0.001 PHE A 248 TYR 0.007 0.001 TYR C 316 ARG 0.001 0.000 ARG A 173 Details of bonding type rmsd hydrogen bonds : bond 0.03490 ( 660) hydrogen bonds : angle 4.18401 ( 1953) covalent geometry : bond 0.00215 ( 9558) covalent geometry : angle 0.47943 (12984) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 1.073 Fit side-chains REVERT: A 52 PHE cc_start: 0.7125 (m-10) cc_final: 0.6637 (t80) REVERT: A 235 GLU cc_start: 0.8181 (tt0) cc_final: 0.7811 (tt0) REVERT: A 275 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: A 290 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7642 (tp) REVERT: A 307 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7113 (tm-30) REVERT: A 311 ARG cc_start: 0.7727 (ttp-170) cc_final: 0.7485 (ttm-80) REVERT: A 498 LYS cc_start: 0.7103 (ttmt) cc_final: 0.6882 (ttmm) REVERT: B 52 PHE cc_start: 0.7012 (m-10) cc_final: 0.6651 (t80) REVERT: B 86 MET cc_start: 0.8130 (mmt) cc_final: 0.7882 (mmt) REVERT: B 121 MET cc_start: 0.8167 (tpp) cc_final: 0.7928 (mmm) REVERT: B 166 ASP cc_start: 0.7878 (m-30) cc_final: 0.7604 (m-30) REVERT: B 182 GLN cc_start: 0.8764 (tt0) cc_final: 0.8546 (tt0) REVERT: B 275 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7492 (mp0) REVERT: B 285 MET cc_start: 0.8682 (mmm) cc_final: 0.8475 (mmt) REVERT: B 341 ARG cc_start: 0.8190 (mtp-110) cc_final: 0.7701 (mtt180) REVERT: C 52 PHE cc_start: 0.6853 (m-10) cc_final: 0.6486 (t80) REVERT: C 259 MET cc_start: 0.8995 (mtp) cc_final: 0.8786 (mtm) REVERT: C 275 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.6900 (mp0) REVERT: C 285 MET cc_start: 0.8802 (mmm) cc_final: 0.8385 (mmm) REVERT: C 325 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8137 (mt) outliers start: 24 outliers final: 7 residues processed: 148 average time/residue: 1.1865 time to fit residues: 187.9920 Evaluate side-chains 143 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 131 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 477 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 75 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 108 optimal weight: 0.5980 chunk 76 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 378 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.144268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111799 restraints weight = 10915.775| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.82 r_work: 0.3211 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9558 Z= 0.126 Angle : 0.494 7.338 12984 Z= 0.250 Chirality : 0.040 0.129 1656 Planarity : 0.004 0.034 1560 Dihedral : 4.639 50.541 1488 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.95 % Allowed : 13.57 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.25), residues: 1227 helix: 1.62 (0.17), residues: 966 sheet: -2.45 (0.75), residues: 30 loop : -1.27 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 472 HIS 0.003 0.001 HIS C 327 PHE 0.014 0.001 PHE B 249 TYR 0.009 0.001 TYR B 316 ARG 0.001 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 660) hydrogen bonds : angle 4.18225 ( 1953) covalent geometry : bond 0.00300 ( 9558) covalent geometry : angle 0.49441 (12984) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 1.040 Fit side-chains REVERT: A 52 PHE cc_start: 0.7079 (m-10) cc_final: 0.6553 (t80) REVERT: A 275 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: A 290 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7639 (tp) REVERT: A 307 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7315 (tm-30) REVERT: A 498 LYS cc_start: 0.7173 (ttmt) cc_final: 0.6952 (ttmm) REVERT: B 52 PHE cc_start: 0.6939 (m-10) cc_final: 0.6546 (t80) REVERT: B 166 ASP cc_start: 0.7835 (m-30) cc_final: 0.7566 (m-30) REVERT: B 275 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: B 285 MET cc_start: 0.8684 (mmm) cc_final: 0.8426 (mmt) REVERT: B 341 ARG cc_start: 0.8166 (mtp-110) cc_final: 0.7654 (mtt180) REVERT: B 398 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.7692 (mmp) REVERT: C 52 PHE cc_start: 0.6783 (m-10) cc_final: 0.6392 (t80) REVERT: C 86 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7623 (mmt) REVERT: C 275 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.6867 (mp0) REVERT: C 285 MET cc_start: 0.8833 (mmm) cc_final: 0.8335 (mmm) REVERT: C 325 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.8017 (mt) outliers start: 30 outliers final: 11 residues processed: 146 average time/residue: 1.1612 time to fit residues: 181.9506 Evaluate side-chains 146 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 477 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 107 optimal weight: 0.0970 chunk 52 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 3 optimal weight: 0.3980 chunk 95 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.145695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113277 restraints weight = 10835.486| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.81 r_work: 0.3228 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9558 Z= 0.112 Angle : 0.485 9.949 12984 Z= 0.243 Chirality : 0.039 0.125 1656 Planarity : 0.003 0.033 1560 Dihedral : 4.603 51.595 1488 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.26 % Allowed : 15.14 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.25), residues: 1227 helix: 1.77 (0.17), residues: 966 sheet: -2.40 (0.74), residues: 30 loop : -1.24 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 472 HIS 0.003 0.001 HIS A 327 PHE 0.012 0.001 PHE A 248 TYR 0.008 0.001 TYR B 316 ARG 0.002 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 660) hydrogen bonds : angle 4.10530 ( 1953) covalent geometry : bond 0.00255 ( 9558) covalent geometry : angle 0.48505 (12984) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.960 Fit side-chains REVERT: A 52 PHE cc_start: 0.7095 (m-10) cc_final: 0.6589 (t80) REVERT: A 275 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: A 290 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7586 (tp) REVERT: A 307 GLU cc_start: 0.7591 (tm-30) cc_final: 0.7271 (tm-30) REVERT: A 387 ARG cc_start: 0.7870 (mmm160) cc_final: 0.7568 (mmm160) REVERT: A 398 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.7436 (mmp) REVERT: A 498 LYS cc_start: 0.7233 (ttmt) cc_final: 0.6988 (ttmm) REVERT: B 52 PHE cc_start: 0.6970 (m-10) cc_final: 0.6595 (t80) REVERT: B 121 MET cc_start: 0.8056 (tpp) cc_final: 0.7802 (mmm) REVERT: B 166 ASP cc_start: 0.7841 (m-30) cc_final: 0.7572 (m-30) REVERT: B 275 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: B 285 MET cc_start: 0.8664 (mmm) cc_final: 0.8430 (mmt) REVERT: B 341 ARG cc_start: 0.8164 (mtp-110) cc_final: 0.7657 (mtt180) REVERT: B 398 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.7719 (mmp) REVERT: C 52 PHE cc_start: 0.6781 (m-10) cc_final: 0.6416 (t80) REVERT: C 86 MET cc_start: 0.7996 (mtm) cc_final: 0.7641 (mmt) REVERT: C 275 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.6880 (mp0) REVERT: C 285 MET cc_start: 0.8817 (mmm) cc_final: 0.8416 (mmm) REVERT: C 325 ILE cc_start: 0.8358 (OUTLIER) cc_final: 0.8089 (mt) outliers start: 23 outliers final: 11 residues processed: 144 average time/residue: 1.1760 time to fit residues: 181.7090 Evaluate side-chains 145 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 477 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 9 optimal weight: 0.6980 chunk 88 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 108 optimal weight: 0.2980 chunk 43 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.145503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.112995 restraints weight = 10978.163| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.83 r_work: 0.3224 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9558 Z= 0.113 Angle : 0.487 10.612 12984 Z= 0.243 Chirality : 0.039 0.125 1656 Planarity : 0.003 0.032 1560 Dihedral : 4.581 51.743 1488 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.75 % Allowed : 15.54 % Favored : 81.71 % 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: 1.78 (0.25), residues: 1227 helix: 1.86 (0.17), residues: 966 sheet: -2.37 (0.75), residues: 30 loop : -1.21 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 472 HIS 0.003 0.001 HIS A 327 PHE 0.012 0.001 PHE B 249 TYR 0.008 0.001 TYR B 316 ARG 0.001 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.03741 ( 660) hydrogen bonds : angle 4.07935 ( 1953) covalent geometry : bond 0.00258 ( 9558) covalent geometry : angle 0.48739 (12984) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.983 Fit side-chains REVERT: A 52 PHE cc_start: 0.7074 (m-10) cc_final: 0.6562 (t80) REVERT: A 275 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7155 (mp0) REVERT: A 290 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7573 (tp) REVERT: A 307 GLU cc_start: 0.7531 (tm-30) cc_final: 0.7273 (tm-30) REVERT: A 498 LYS cc_start: 0.7231 (ttmt) cc_final: 0.6985 (ttmm) REVERT: B 52 PHE cc_start: 0.6946 (m-10) cc_final: 0.6565 (t80) REVERT: B 121 MET cc_start: 0.8108 (tpp) cc_final: 0.7875 (mmm) REVERT: B 166 ASP cc_start: 0.7810 (m-30) cc_final: 0.7533 (m-30) REVERT: B 275 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: B 285 MET cc_start: 0.8636 (mmm) cc_final: 0.8395 (mmt) REVERT: B 341 ARG cc_start: 0.8086 (mtp-110) cc_final: 0.7582 (mtt180) REVERT: B 398 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.7655 (mmp) REVERT: C 52 PHE cc_start: 0.6774 (m-10) cc_final: 0.6411 (t80) REVERT: C 86 MET cc_start: 0.7953 (mtm) cc_final: 0.7708 (mmt) REVERT: C 275 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.6841 (mp0) REVERT: C 285 MET cc_start: 0.8796 (mmm) cc_final: 0.8557 (mmt) REVERT: C 325 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.8081 (mt) outliers start: 28 outliers final: 15 residues processed: 141 average time/residue: 1.1421 time to fit residues: 173.0918 Evaluate side-chains 146 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 477 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 16 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 68 optimal weight: 0.0040 chunk 74 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 90 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 chunk 70 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.145989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113586 restraints weight = 11076.028| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.83 r_work: 0.3232 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3102 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9558 Z= 0.110 Angle : 0.491 9.732 12984 Z= 0.244 Chirality : 0.039 0.125 1656 Planarity : 0.003 0.032 1560 Dihedral : 4.565 52.326 1488 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.56 % Allowed : 16.13 % Favored : 81.32 % 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: 1.90 (0.25), residues: 1227 helix: 1.94 (0.17), residues: 966 sheet: -2.37 (0.74), residues: 30 loop : -1.18 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 472 HIS 0.003 0.001 HIS A 327 PHE 0.011 0.001 PHE B 248 TYR 0.008 0.001 TYR B 316 ARG 0.001 0.000 ARG A 311 Details of bonding type rmsd hydrogen bonds : bond 0.03638 ( 660) hydrogen bonds : angle 4.04889 ( 1953) covalent geometry : bond 0.00249 ( 9558) covalent geometry : angle 0.49126 (12984) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 129 time to evaluate : 0.973 Fit side-chains REVERT: A 52 PHE cc_start: 0.7088 (m-10) cc_final: 0.6577 (t80) REVERT: A 86 MET cc_start: 0.8205 (mmt) cc_final: 0.7853 (mtm) REVERT: A 275 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: A 290 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7533 (tp) REVERT: A 307 GLU cc_start: 0.7538 (tm-30) cc_final: 0.7274 (tm-30) REVERT: A 498 LYS cc_start: 0.7253 (ttmt) cc_final: 0.7007 (ttmm) REVERT: B 52 PHE cc_start: 0.6956 (m-10) cc_final: 0.6573 (t80) REVERT: B 166 ASP cc_start: 0.7810 (m-30) cc_final: 0.7536 (m-30) REVERT: B 182 GLN cc_start: 0.8733 (tt0) cc_final: 0.8516 (tt0) REVERT: B 275 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7480 (mp0) REVERT: B 285 MET cc_start: 0.8651 (mmm) cc_final: 0.8415 (mmt) REVERT: B 341 ARG cc_start: 0.8104 (mtp-110) cc_final: 0.7577 (mtt180) REVERT: B 398 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.7670 (mmp) REVERT: C 52 PHE cc_start: 0.6948 (m-10) cc_final: 0.6452 (t80) REVERT: C 86 MET cc_start: 0.8011 (mtm) cc_final: 0.7790 (mmt) REVERT: C 275 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.6821 (mp0) REVERT: C 285 MET cc_start: 0.8797 (mmm) cc_final: 0.8559 (mmt) REVERT: C 325 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.8082 (mt) outliers start: 26 outliers final: 15 residues processed: 143 average time/residue: 1.1308 time to fit residues: 173.8588 Evaluate side-chains 146 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 477 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 98 optimal weight: 0.7980 chunk 95 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 2 optimal weight: 0.0370 chunk 120 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.146291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.113927 restraints weight = 10888.351| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.81 r_work: 0.3237 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 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 : 0.002 0.030 9558 Z= 0.108 Angle : 0.499 11.253 12984 Z= 0.245 Chirality : 0.039 0.126 1656 Planarity : 0.003 0.032 1560 Dihedral : 4.541 52.437 1488 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.36 % Allowed : 16.72 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.25), residues: 1227 helix: 2.00 (0.17), residues: 966 sheet: -2.89 (0.68), residues: 42 loop : -1.06 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 472 HIS 0.003 0.001 HIS A 327 PHE 0.012 0.001 PHE B 248 TYR 0.008 0.001 TYR B 316 ARG 0.001 0.000 ARG A 384 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 660) hydrogen bonds : angle 4.03046 ( 1953) covalent geometry : bond 0.00241 ( 9558) covalent geometry : angle 0.49911 (12984) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 1.113 Fit side-chains REVERT: A 52 PHE cc_start: 0.6998 (m-10) cc_final: 0.6534 (t80) REVERT: A 275 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7132 (mp0) REVERT: A 290 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7491 (tp) REVERT: A 307 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7255 (tm-30) REVERT: A 498 LYS cc_start: 0.7222 (ttmt) cc_final: 0.6989 (ttmm) REVERT: B 52 PHE cc_start: 0.6933 (m-10) cc_final: 0.6556 (t80) REVERT: B 166 ASP cc_start: 0.7789 (m-30) cc_final: 0.7514 (m-30) REVERT: B 182 GLN cc_start: 0.8720 (tt0) cc_final: 0.8495 (tt0) REVERT: B 275 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7501 (mp0) REVERT: B 285 MET cc_start: 0.8627 (mmm) cc_final: 0.8391 (mmt) REVERT: B 341 ARG cc_start: 0.8086 (mtp-110) cc_final: 0.7554 (mtt180) REVERT: B 387 ARG cc_start: 0.7632 (mmm160) cc_final: 0.7362 (mmm160) REVERT: B 398 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.7653 (mmp) REVERT: C 52 PHE cc_start: 0.6933 (m-10) cc_final: 0.6435 (t80) REVERT: C 86 MET cc_start: 0.8113 (mtm) cc_final: 0.7769 (mmt) REVERT: C 275 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.6801 (mp0) REVERT: C 285 MET cc_start: 0.8777 (mmm) cc_final: 0.8543 (mmt) REVERT: C 325 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8078 (mt) outliers start: 24 outliers final: 15 residues processed: 139 average time/residue: 1.2153 time to fit residues: 181.0618 Evaluate side-chains 147 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 126 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 477 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 122 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 32 optimal weight: 0.0040 chunk 68 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 113 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 HIS B 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.146026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.113592 restraints weight = 10922.698| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.82 r_work: 0.3232 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9558 Z= 0.115 Angle : 0.506 10.443 12984 Z= 0.249 Chirality : 0.039 0.125 1656 Planarity : 0.003 0.033 1560 Dihedral : 4.558 52.765 1488 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.46 % Allowed : 16.62 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.25), residues: 1227 helix: 1.93 (0.17), residues: 969 sheet: -2.92 (0.67), residues: 42 loop : -0.98 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 472 HIS 0.003 0.001 HIS A 327 PHE 0.012 0.001 PHE B 249 TYR 0.008 0.001 TYR B 316 ARG 0.001 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.03725 ( 660) hydrogen bonds : angle 4.05671 ( 1953) covalent geometry : bond 0.00264 ( 9558) covalent geometry : angle 0.50572 (12984) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 1.034 Fit side-chains REVERT: A 52 PHE cc_start: 0.7030 (m-10) cc_final: 0.6571 (t80) REVERT: A 86 MET cc_start: 0.8131 (mmt) cc_final: 0.7878 (mtm) REVERT: A 275 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7233 (mp0) REVERT: A 290 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7561 (tp) REVERT: A 307 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7295 (tm-30) REVERT: A 353 GLN cc_start: 0.7604 (mm-40) cc_final: 0.7388 (mm-40) REVERT: A 498 LYS cc_start: 0.7271 (ttmt) cc_final: 0.7030 (ttmm) REVERT: B 52 PHE cc_start: 0.6957 (m-10) cc_final: 0.6574 (t80) REVERT: B 166 ASP cc_start: 0.7838 (m-30) cc_final: 0.7564 (m-30) REVERT: B 275 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7565 (mp0) REVERT: B 285 MET cc_start: 0.8675 (mmm) cc_final: 0.8438 (mmt) REVERT: B 341 ARG cc_start: 0.8075 (mtp-110) cc_final: 0.7509 (mtt180) REVERT: B 387 ARG cc_start: 0.7658 (mmm160) cc_final: 0.7392 (mmm160) REVERT: B 398 MET cc_start: 0.8660 (OUTLIER) cc_final: 0.7712 (mmp) REVERT: C 52 PHE cc_start: 0.6974 (m-10) cc_final: 0.6475 (t80) REVERT: C 86 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7824 (mmt) REVERT: C 275 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: C 285 MET cc_start: 0.8815 (mmm) cc_final: 0.8578 (mmt) REVERT: C 325 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8103 (mt) outliers start: 25 outliers final: 16 residues processed: 138 average time/residue: 1.1937 time to fit residues: 176.4517 Evaluate side-chains 147 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 ASP Chi-restraints excluded: chain A residue 271 ASN Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 367 THR Chi-restraints excluded: chain A residue 436 SER Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 477 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 98 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 34 optimal weight: 0.2980 chunk 117 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 4 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 85 optimal weight: 0.4980 chunk 47 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.145668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113218 restraints weight = 10924.696| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 1.82 r_work: 0.3228 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9558 Z= 0.116 Angle : 0.512 10.437 12984 Z= 0.253 Chirality : 0.039 0.125 1656 Planarity : 0.003 0.033 1560 Dihedral : 4.565 52.833 1488 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.65 % Allowed : 16.52 % Favored : 80.83 % 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: 1.88 (0.25), residues: 1227 helix: 1.93 (0.17), residues: 969 sheet: -2.92 (0.67), residues: 42 loop : -0.98 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 472 HIS 0.003 0.001 HIS A 327 PHE 0.012 0.001 PHE B 249 TYR 0.008 0.001 TYR B 316 ARG 0.001 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 660) hydrogen bonds : angle 4.06084 ( 1953) covalent geometry : bond 0.00268 ( 9558) covalent geometry : angle 0.51229 (12984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6439.53 seconds wall clock time: 111 minutes 32.28 seconds (6692.28 seconds total)