Starting phenix.real_space_refine on Sun Jun 8 07:51:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jvv_61844/06_2025/9jvv_61844.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jvv_61844/06_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_61844/06_2025/9jvv_61844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jvv_61844/06_2025/9jvv_61844.map" model { file = "/net/cci-nas-00/data/ceres_data/9jvv_61844/06_2025/9jvv_61844.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jvv_61844/06_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-5710/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: 6.18, per 1000 atoms: 0.66 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: 2.81 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: 1.05 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: 2.65 Time building geometry restraints manager: 3.27 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: 0.07 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: 0.750 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 25.630 Find NCS groups from input model: 0.200 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:11.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.560 ------------------------------------------------------------------------------- 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 : 1.036 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: 1.2511 time to fit residues: 248.3347 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 : 0.971 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.112779 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: 0.3109 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 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 : 0.963 Fit side-chains REVERT: A 235 GLU cc_start: 0.8153 (tt0) cc_final: 0.7838 (tt0) REVERT: A 325 ILE cc_start: 0.8236 (OUTLIER) cc_final: 0.7996 (mt) REVERT: A 382 ASP cc_start: 0.7391 (t0) cc_final: 0.7154 (t0) REVERT: A 498 LYS cc_start: 0.7002 (ttmt) cc_final: 0.6750 (ttmm) REVERT: B 52 PHE cc_start: 0.7062 (m-10) cc_final: 0.6655 (t80) REVERT: B 86 MET cc_start: 0.8134 (mmt) cc_final: 0.7806 (mmt) REVERT: B 166 ASP cc_start: 0.7861 (m-30) cc_final: 0.7588 (m-30) REVERT: B 182 GLN cc_start: 0.8785 (tt0) cc_final: 0.8584 (tt0) REVERT: B 325 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.8009 (mt) REVERT: B 341 ARG cc_start: 0.8286 (mtp-110) cc_final: 0.7729 (mtt180) REVERT: B 353 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7599 (tp-100) REVERT: B 398 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.7808 (mmp) REVERT: B 450 MET cc_start: 0.8417 (tpp) cc_final: 0.8164 (mmm) REVERT: C 259 MET cc_start: 0.9076 (mtp) cc_final: 0.8829 (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: 0.8658 (p-90) cc_final: 0.8436 (p-90) outliers start: 22 outliers final: 5 residues processed: 153 average time/residue: 1.1942 time to fit residues: 195.3293 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 : 0.965 ------------------------------------------------------------------------------- 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: 1.9990 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: 0.9990 chunk 108 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- 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 = 0.3533 r_free = 0.3533 target = 0.133323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.097410 restraints weight = 10896.828| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.98 r_work: 0.2902 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9558 Z= 0.191 Angle : 0.564 6.960 12984 Z= 0.288 Chirality : 0.042 0.138 1656 Planarity : 0.004 0.036 1560 Dihedral : 4.909 50.679 1488 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 3.05 % Allowed : 11.60 % 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: 0.68 (0.24), residues: 1227 helix: 1.07 (0.17), residues: 951 sheet: -2.55 (0.74), residues: 30 loop : -1.39 (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 0.020 0.002 PHE B 249 TYR 0.011 0.002 TYR B 316 ARG 0.002 0.000 ARG B 387 Details of bonding type rmsd hydrogen bonds : bond 0.05154 ( 660) hydrogen bonds : angle 4.53002 ( 1953) covalent geometry : bond 0.00479 ( 9558) covalent geometry : angle 0.56394 (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 168 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 1.046 Fit side-chains REVERT: A 268 ASP cc_start: 0.7551 (m-30) cc_final: 0.7342 (m-30) REVERT: A 307 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7289 (tm-30) REVERT: A 325 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8161 (mt) REVERT: A 498 LYS cc_start: 0.7244 (ttmt) cc_final: 0.7043 (ttmm) REVERT: B 52 PHE cc_start: 0.7135 (m-10) cc_final: 0.6613 (t80) REVERT: B 86 MET cc_start: 0.8414 (mmt) cc_final: 0.8164 (mmt) REVERT: B 166 ASP cc_start: 0.8106 (m-30) cc_final: 0.7834 (m-30) REVERT: B 275 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: B 325 ILE cc_start: 0.8513 (OUTLIER) cc_final: 0.8194 (mt) REVERT: B 341 ARG cc_start: 0.8295 (mtp-110) cc_final: 0.7764 (mtt180) REVERT: C 259 MET cc_start: 0.9121 (mtp) cc_final: 0.8899 (mtm) REVERT: C 325 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8288 (mt) outliers start: 31 outliers final: 11 residues processed: 151 average time/residue: 1.2355 time to fit residues: 199.4006 Evaluate side-chains 144 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 129 time to evaluate : 0.963 ------------------------------------------------------------------------------- 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 59 VAL Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 275 GLU 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 436 SER Chi-restraints excluded: chain C residue 126 SER 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: 0.9990 chunk 65 optimal weight: 0.7980 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: 1.9990 chunk 22 optimal weight: 0.5980 chunk 69 optimal weight: 0.2980 chunk 100 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3743 r_free = 0.3743 target = 0.145007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.112546 restraints weight = 10788.922| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 1.81 r_work: 0.3223 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9558 Z= 0.111 Angle : 0.491 9.369 12984 Z= 0.246 Chirality : 0.039 0.126 1656 Planarity : 0.004 0.034 1560 Dihedral : 4.702 51.716 1488 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.46 % Allowed : 13.37 % Favored : 84.17 % 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: 1.18 (0.25), residues: 1227 helix: 1.43 (0.17), residues: 963 sheet: -2.45 (0.74), residues: 30 loop : -1.41 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 472 HIS 0.003 0.001 HIS B 327 PHE 0.011 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 0.03842 ( 660) hydrogen bonds : angle 4.26095 ( 1953) covalent geometry : bond 0.00249 ( 9558) covalent geometry : angle 0.49066 (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 155 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.963 Fit side-chains REVERT: A 52 PHE cc_start: 0.7101 (m-10) cc_final: 0.6579 (t80) REVERT: A 275 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7279 (mp0) REVERT: A 307 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7071 (tm-30) REVERT: A 311 ARG cc_start: 0.7650 (ttm-80) cc_final: 0.7421 (ttm-80) REVERT: A 498 LYS cc_start: 0.7152 (ttmt) cc_final: 0.6941 (ttmm) REVERT: B 52 PHE cc_start: 0.6977 (m-10) cc_final: 0.6592 (t80) REVERT: B 86 MET cc_start: 0.8100 (mmt) cc_final: 0.7880 (mmt) REVERT: B 125 MET cc_start: 0.7571 (OUTLIER) cc_final: 0.6781 (mmp) REVERT: B 166 ASP cc_start: 0.7858 (m-30) cc_final: 0.7578 (m-30) REVERT: B 285 MET cc_start: 0.8682 (mmm) cc_final: 0.8440 (mmt) REVERT: B 341 ARG cc_start: 0.8196 (mtp-110) cc_final: 0.7668 (mtt180) REVERT: B 378 ASN cc_start: 0.7313 (m110) cc_final: 0.7058 (m110) REVERT: B 398 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.7708 (mmp) REVERT: C 52 PHE cc_start: 0.6817 (m-10) cc_final: 0.6425 (t80) REVERT: C 275 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.6919 (mp0) REVERT: C 285 MET cc_start: 0.8780 (mmm) cc_final: 0.8288 (mmm) REVERT: C 325 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8078 (mt) outliers start: 25 outliers final: 8 residues processed: 144 average time/residue: 1.2005 time to fit residues: 185.0424 Evaluate side-chains 141 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 128 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 477 MET Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 398 MET 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 477 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 75 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 108 optimal weight: 0.6980 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.143723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111214 restraints weight = 10911.801| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.81 r_work: 0.3204 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9558 Z= 0.131 Angle : 0.502 7.210 12984 Z= 0.254 Chirality : 0.040 0.127 1656 Planarity : 0.004 0.035 1560 Dihedral : 4.703 50.799 1488 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.95 % Allowed : 13.47 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.25), residues: 1227 helix: 1.53 (0.17), residues: 963 sheet: -2.96 (0.67), residues: 42 loop : -1.30 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 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 0.002 0.000 ARG B 387 Details of bonding type rmsd hydrogen bonds : bond 0.04153 ( 660) hydrogen bonds : angle 4.23871 ( 1953) covalent geometry : bond 0.00313 ( 9558) covalent geometry : angle 0.50160 (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 157 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.970 Fit side-chains REVERT: A 52 PHE cc_start: 0.7087 (m-10) cc_final: 0.6542 (t80) REVERT: A 275 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7286 (mp0) REVERT: A 307 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7456 (tm-30) REVERT: A 498 LYS cc_start: 0.7176 (ttmt) cc_final: 0.6962 (ttmm) REVERT: B 52 PHE cc_start: 0.6944 (m-10) cc_final: 0.6547 (t80) REVERT: B 125 MET cc_start: 0.7511 (OUTLIER) cc_final: 0.6734 (mmp) REVERT: B 166 ASP cc_start: 0.7856 (m-30) cc_final: 0.7585 (m-30) REVERT: B 275 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7546 (mp0) REVERT: B 285 MET cc_start: 0.8697 (mmm) cc_final: 0.8445 (mmt) REVERT: B 341 ARG cc_start: 0.8155 (mtp-110) cc_final: 0.7635 (mtt180) REVERT: B 398 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.7674 (mmp) REVERT: C 52 PHE cc_start: 0.6829 (m-10) cc_final: 0.6415 (t80) REVERT: C 275 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.6943 (mp0) REVERT: C 285 MET cc_start: 0.8801 (mmm) cc_final: 0.8326 (mmm) REVERT: C 325 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.7989 (mt) outliers start: 30 outliers final: 12 residues processed: 143 average time/residue: 1.1335 time to fit residues: 174.0166 Evaluate side-chains 142 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.987 ------------------------------------------------------------------------------- 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 477 MET Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 275 GLU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 108 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3739 r_free = 0.3739 target = 0.144502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112106 restraints weight = 10865.758| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.81 r_work: 0.3214 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9558 Z= 0.120 Angle : 0.496 9.907 12984 Z= 0.249 Chirality : 0.039 0.129 1656 Planarity : 0.004 0.034 1560 Dihedral : 4.658 51.498 1488 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.65 % Allowed : 14.85 % Favored : 82.50 % 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: 1.46 (0.25), residues: 1227 helix: 1.66 (0.17), residues: 966 sheet: -2.97 (0.67), residues: 42 loop : -1.21 (0.40), residues: 219 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 0.013 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 0.03921 ( 660) hydrogen bonds : angle 4.16738 ( 1953) covalent geometry : bond 0.00280 ( 9558) covalent geometry : angle 0.49608 (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: 27 poor density : 128 time to evaluate : 0.980 Fit side-chains REVERT: A 52 PHE cc_start: 0.7089 (m-10) cc_final: 0.6550 (t80) REVERT: A 275 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7138 (mp0) REVERT: A 307 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7296 (tm-30) REVERT: A 398 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.7452 (mmp) REVERT: A 498 LYS cc_start: 0.7181 (ttmt) cc_final: 0.6966 (ttmm) REVERT: B 52 PHE cc_start: 0.6940 (m-10) cc_final: 0.6555 (t80) REVERT: B 121 MET cc_start: 0.8014 (tpp) cc_final: 0.7764 (mmm) REVERT: B 125 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.6722 (mmp) REVERT: B 166 ASP cc_start: 0.7846 (m-30) cc_final: 0.7575 (m-30) REVERT: B 275 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: B 285 MET cc_start: 0.8675 (mmm) cc_final: 0.8424 (mmt) REVERT: B 341 ARG cc_start: 0.8153 (mtp-110) cc_final: 0.7655 (mtt180) REVERT: B 378 ASN cc_start: 0.7170 (m110) cc_final: 0.6914 (m110) REVERT: B 398 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.7722 (mmp) REVERT: C 52 PHE cc_start: 0.6836 (m-10) cc_final: 0.6430 (t80) REVERT: C 86 MET cc_start: 0.8275 (mmt) cc_final: 0.7900 (mtp) REVERT: C 275 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.6923 (mp0) REVERT: C 285 MET cc_start: 0.8802 (mmm) cc_final: 0.8314 (mmm) REVERT: C 325 ILE cc_start: 0.8366 (OUTLIER) cc_final: 0.8048 (mt) REVERT: C 348 PHE cc_start: 0.8217 (OUTLIER) cc_final: 0.7902 (m-10) outliers start: 27 outliers final: 14 residues processed: 140 average time/residue: 1.3170 time to fit residues: 197.6286 Evaluate side-chains 146 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 THR 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 398 MET Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 125 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 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 348 PHE 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: 0.5980 chunk 88 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 41 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 108 optimal weight: 0.0670 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.145245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.112860 restraints weight = 10982.491| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.81 r_work: 0.3223 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2334 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= 0.114 Angle : 0.490 10.770 12984 Z= 0.245 Chirality : 0.039 0.127 1656 Planarity : 0.003 0.033 1560 Dihedral : 4.614 51.945 1488 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.15 % Allowed : 14.65 % Favored : 82.20 % 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: 1.65 (0.25), residues: 1227 helix: 1.80 (0.17), residues: 966 sheet: -2.94 (0.67), residues: 42 loop : -1.18 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 472 HIS 0.003 0.001 HIS B 327 PHE 0.012 0.001 PHE B 249 TYR 0.008 0.001 TYR B 316 ARG 0.001 0.000 ARG B 387 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 660) hydrogen bonds : angle 4.11074 ( 1953) covalent geometry : bond 0.00259 ( 9558) covalent geometry : angle 0.48982 (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 160 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 1.098 Fit side-chains REVERT: A 52 PHE cc_start: 0.7081 (m-10) cc_final: 0.6555 (t80) REVERT: A 235 GLU cc_start: 0.8145 (tt0) cc_final: 0.7755 (tt0) REVERT: A 275 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7172 (mp0) REVERT: A 307 GLU cc_start: 0.7568 (tm-30) cc_final: 0.7256 (tm-30) REVERT: A 353 GLN cc_start: 0.7681 (mm-40) cc_final: 0.7356 (mm-40) REVERT: A 387 ARG cc_start: 0.7870 (mmm160) cc_final: 0.7555 (mmm160) REVERT: A 398 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.7412 (mmp) REVERT: A 498 LYS cc_start: 0.7229 (ttmt) cc_final: 0.6984 (ttmm) REVERT: B 52 PHE cc_start: 0.6955 (m-10) cc_final: 0.6575 (t80) REVERT: B 125 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.6724 (mmp) REVERT: B 166 ASP cc_start: 0.7824 (m-30) cc_final: 0.7549 (m-30) REVERT: B 275 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7475 (mp0) REVERT: B 285 MET cc_start: 0.8652 (mmm) cc_final: 0.8414 (mmt) REVERT: B 341 ARG cc_start: 0.8068 (mtp-110) cc_final: 0.7576 (mtt180) REVERT: B 378 ASN cc_start: 0.7222 (m110) cc_final: 0.7010 (m110) REVERT: B 387 ARG cc_start: 0.7785 (mmm160) cc_final: 0.7565 (mmm160) REVERT: B 398 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.7691 (mmp) REVERT: C 52 PHE cc_start: 0.6912 (m-10) cc_final: 0.6444 (t80) REVERT: C 86 MET cc_start: 0.8285 (mmt) cc_final: 0.7921 (mtp) REVERT: C 275 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: C 285 MET cc_start: 0.8808 (mmm) cc_final: 0.8381 (mmm) REVERT: C 325 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8067 (mt) outliers start: 32 outliers final: 14 residues processed: 145 average time/residue: 1.2971 time to fit residues: 201.3201 Evaluate side-chains 144 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 THR 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 367 THR 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 125 MET Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 275 GLU 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 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: 0.9990 chunk 71 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 116 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 HIS C 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.144261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.111821 restraints weight = 11102.263| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.81 r_work: 0.3209 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9558 Z= 0.130 Angle : 0.509 9.724 12984 Z= 0.254 Chirality : 0.040 0.126 1656 Planarity : 0.004 0.034 1560 Dihedral : 4.652 52.937 1488 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.46 % Allowed : 15.83 % 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: 1.61 (0.25), residues: 1227 helix: 1.75 (0.17), residues: 969 sheet: -2.99 (0.66), residues: 42 loop : -1.12 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 472 HIS 0.003 0.001 HIS A 327 PHE 0.014 0.001 PHE B 249 TYR 0.009 0.001 TYR B 316 ARG 0.001 0.000 ARG B 387 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 660) hydrogen bonds : angle 4.14498 ( 1953) covalent geometry : bond 0.00309 ( 9558) covalent geometry : angle 0.50930 (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 151 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 126 time to evaluate : 1.055 Fit side-chains REVERT: A 52 PHE cc_start: 0.7140 (m-10) cc_final: 0.6608 (t80) REVERT: A 275 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: A 307 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7278 (tm-30) REVERT: A 387 ARG cc_start: 0.7898 (mmm160) cc_final: 0.7570 (mmm160) REVERT: A 398 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.7412 (mmp) REVERT: A 498 LYS cc_start: 0.7274 (ttmt) cc_final: 0.7032 (ttmm) REVERT: B 52 PHE cc_start: 0.6986 (m-10) cc_final: 0.6602 (t80) REVERT: B 125 MET cc_start: 0.7534 (OUTLIER) cc_final: 0.6785 (mmp) REVERT: B 166 ASP cc_start: 0.7880 (m-30) cc_final: 0.7606 (m-30) REVERT: B 271 ASN cc_start: 0.8379 (t0) cc_final: 0.8168 (t0) REVERT: B 275 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: B 285 MET cc_start: 0.8777 (mmm) cc_final: 0.8532 (mmt) REVERT: B 341 ARG cc_start: 0.8063 (mtp-110) cc_final: 0.7532 (mtt180) REVERT: B 378 ASN cc_start: 0.7323 (m110) cc_final: 0.7088 (m110) REVERT: B 387 ARG cc_start: 0.7826 (mmm160) cc_final: 0.7573 (mmm160) REVERT: B 398 MET cc_start: 0.8716 (OUTLIER) cc_final: 0.7737 (mmp) REVERT: C 52 PHE cc_start: 0.6969 (m-10) cc_final: 0.6495 (t80) REVERT: C 86 MET cc_start: 0.8186 (mmt) cc_final: 0.7920 (mmt) REVERT: C 275 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.6992 (mp0) REVERT: C 285 MET cc_start: 0.8856 (mmm) cc_final: 0.8585 (mmm) REVERT: C 325 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.8034 (mt) outliers start: 25 outliers final: 16 residues processed: 140 average time/residue: 1.1967 time to fit residues: 179.4816 Evaluate side-chains 149 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 THR 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 398 MET 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 125 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 98 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 2 optimal weight: 0.0870 chunk 120 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN C 143 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.144441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.112023 restraints weight = 10905.577| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.80 r_work: 0.3211 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9558 Z= 0.124 Angle : 0.509 10.991 12984 Z= 0.253 Chirality : 0.040 0.126 1656 Planarity : 0.003 0.034 1560 Dihedral : 4.639 52.881 1488 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.75 % Allowed : 15.63 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.25), residues: 1227 helix: 1.78 (0.17), residues: 969 sheet: -2.97 (0.66), residues: 42 loop : -1.12 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 472 HIS 0.003 0.001 HIS A 327 PHE 0.013 0.001 PHE B 249 TYR 0.008 0.001 TYR C 316 ARG 0.001 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 660) hydrogen bonds : angle 4.13076 ( 1953) covalent geometry : bond 0.00291 ( 9558) covalent geometry : angle 0.50894 (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: 28 poor density : 124 time to evaluate : 0.956 Fit side-chains REVERT: A 52 PHE cc_start: 0.7102 (m-10) cc_final: 0.6567 (t80) REVERT: A 235 GLU cc_start: 0.8140 (tt0) cc_final: 0.7664 (tt0) REVERT: A 275 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: A 290 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7615 (tp) REVERT: A 307 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7269 (tm-30) REVERT: A 387 ARG cc_start: 0.7874 (mmm160) cc_final: 0.7599 (mmm160) REVERT: A 498 LYS cc_start: 0.7237 (ttmt) cc_final: 0.6996 (ttmm) REVERT: B 52 PHE cc_start: 0.6938 (m-10) cc_final: 0.6553 (t80) REVERT: B 125 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.6721 (mmp) REVERT: B 166 ASP cc_start: 0.7839 (m-30) cc_final: 0.7561 (m-30) REVERT: B 271 ASN cc_start: 0.8325 (t0) cc_final: 0.8110 (t0) REVERT: B 275 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7570 (mp0) REVERT: B 285 MET cc_start: 0.8707 (mmm) cc_final: 0.8469 (mmt) REVERT: B 341 ARG cc_start: 0.8051 (mtp-110) cc_final: 0.7525 (mtt180) REVERT: B 378 ASN cc_start: 0.7287 (m110) cc_final: 0.7057 (m110) REVERT: B 387 ARG cc_start: 0.7767 (mmm160) cc_final: 0.7495 (mmm160) REVERT: B 398 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.7727 (mmp) REVERT: C 52 PHE cc_start: 0.6931 (m-10) cc_final: 0.6444 (t80) REVERT: C 275 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.6930 (mp0) REVERT: C 325 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.8022 (mt) outliers start: 28 outliers final: 17 residues processed: 139 average time/residue: 1.2197 time to fit residues: 181.8456 Evaluate side-chains 147 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 THR 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 125 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 122 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 32 optimal weight: 0.0060 chunk 68 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 113 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 96 optimal weight: 0.4980 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.146053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.113679 restraints weight = 10890.815| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.81 r_work: 0.3234 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2433 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= 0.108 Angle : 0.493 10.534 12984 Z= 0.244 Chirality : 0.039 0.126 1656 Planarity : 0.003 0.033 1560 Dihedral : 4.572 52.520 1488 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.56 % Allowed : 15.93 % Favored : 81.51 % 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: 1.80 (0.25), residues: 1227 helix: 1.89 (0.17), residues: 969 sheet: -2.95 (0.67), residues: 42 loop : -1.09 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 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 B 316 ARG 0.001 0.000 ARG C 87 Details of bonding type rmsd hydrogen bonds : bond 0.03608 ( 660) hydrogen bonds : angle 4.06071 ( 1953) covalent geometry : bond 0.00239 ( 9558) covalent geometry : angle 0.49313 (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 154 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 1.027 Fit side-chains REVERT: A 52 PHE cc_start: 0.7036 (m-10) cc_final: 0.6582 (t80) REVERT: A 235 GLU cc_start: 0.8171 (tt0) cc_final: 0.7702 (tt0) REVERT: A 275 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: A 290 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7596 (tp) REVERT: A 307 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7311 (tm-30) REVERT: A 387 ARG cc_start: 0.7840 (mmm160) cc_final: 0.7566 (mmm160) REVERT: A 498 LYS cc_start: 0.7227 (ttmt) cc_final: 0.6998 (ttmm) REVERT: B 52 PHE cc_start: 0.6967 (m-10) cc_final: 0.6592 (t80) REVERT: B 125 MET cc_start: 0.7490 (OUTLIER) cc_final: 0.6729 (mmp) REVERT: B 166 ASP cc_start: 0.7834 (m-30) cc_final: 0.7558 (m-30) REVERT: B 275 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: B 285 MET cc_start: 0.8711 (mmm) cc_final: 0.8486 (mmt) REVERT: B 341 ARG cc_start: 0.8051 (mtp-110) cc_final: 0.7539 (mtt180) REVERT: B 378 ASN cc_start: 0.7262 (m110) cc_final: 0.7042 (m110) REVERT: B 387 ARG cc_start: 0.7662 (mmm160) cc_final: 0.7409 (mmm160) REVERT: B 398 MET cc_start: 0.8703 (OUTLIER) cc_final: 0.7729 (mmp) REVERT: C 52 PHE cc_start: 0.6949 (m-10) cc_final: 0.6484 (t80) REVERT: C 86 MET cc_start: 0.8140 (mmt) cc_final: 0.7918 (mtm) REVERT: C 275 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.6943 (mp0) REVERT: C 325 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8120 (mt) outliers start: 26 outliers final: 13 residues processed: 143 average time/residue: 1.4206 time to fit residues: 217.1983 Evaluate side-chains 147 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 THR 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 367 THR Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 275 GLU 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 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 477 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 98 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 117 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 116 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN B 416 ASN C 353 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.144087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111648 restraints weight = 10945.491| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.81 r_work: 0.3205 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2451 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= 0.135 Angle : 0.528 10.349 12984 Z= 0.263 Chirality : 0.040 0.125 1656 Planarity : 0.004 0.035 1560 Dihedral : 4.624 53.440 1488 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.26 % Allowed : 16.72 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.25), residues: 1227 helix: 1.77 (0.17), residues: 969 sheet: -2.98 (0.66), residues: 42 loop : -1.10 (0.41), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 472 HIS 0.003 0.001 HIS A 327 PHE 0.014 0.001 PHE B 249 TYR 0.009 0.001 TYR C 316 ARG 0.001 0.000 ARG A 387 Details of bonding type rmsd hydrogen bonds : bond 0.04082 ( 660) hydrogen bonds : angle 4.13293 ( 1953) covalent geometry : bond 0.00322 ( 9558) covalent geometry : angle 0.52832 (12984) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6857.03 seconds wall clock time: 119 minutes 48.04 seconds (7188.04 seconds total)