Starting phenix.real_space_refine on Wed Sep 17 15:23:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jvv_61844/09_2025/9jvv_61844.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jvv_61844/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9jvv_61844/09_2025/9jvv_61844.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jvv_61844/09_2025/9jvv_61844.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jvv_61844/09_2025/9jvv_61844.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jvv_61844/09_2025/9jvv_61844.map" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.11, per 1000 atoms: 0.22 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: 0.77 Conformation dependent library (CDL) restraints added in 244.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2250 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 3 sheets defined 82.2% alpha, 1.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 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: 1.37 Time building geometry restraints manager: 0.98 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.400 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.000 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.001 0.000 ARG C 387 TYR 0.007 0.001 TYR C 494 PHE 0.010 0.001 PHE B 249 TRP 0.008 0.001 TRP B 472 HIS 0.002 0.001 HIS C 327 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 9558) covalent geometry : angle 0.66942 (12984) hydrogen bonds : bond 0.17354 ( 660) hydrogen bonds : angle 7.39066 ( 1953) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2454 Ramachandran restraints generated. 1227 Oldfield, 0 Emsley, 1227 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 0.354 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: 0.7818 (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: 0.5688 time to fit residues: 112.8467 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 : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.4980 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 0.0270 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 117 optimal weight: 0.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- 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 = 0.3761 r_free = 0.3761 target = 0.146084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.113454 restraints weight = 10839.061| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.82 r_work: 0.3246 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1549 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= 0.124 Angle : 0.531 8.264 12984 Z= 0.266 Chirality : 0.040 0.129 1656 Planarity : 0.004 0.039 1560 Dihedral : 4.784 48.563 1488 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.16 % Allowed : 8.85 % Favored : 88.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.24), residues: 1227 helix: 0.97 (0.17), residues: 948 sheet: -2.29 (0.80), residues: 30 loop : -1.44 (0.37), residues: 249 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 311 TYR 0.011 0.002 TYR C 316 PHE 0.013 0.001 PHE B 249 TRP 0.006 0.001 TRP A 472 HIS 0.003 0.001 HIS C 327 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9558) covalent geometry : angle 0.53124 (12984) hydrogen bonds : bond 0.04385 ( 660) hydrogen bonds : angle 4.58805 ( 1953) *********************** 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 167 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.357 Fit side-chains REVERT: A 235 GLU cc_start: 0.8161 (tt0) cc_final: 0.7849 (tt0) REVERT: A 325 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.8024 (mt) REVERT: A 382 ASP cc_start: 0.7257 (t0) cc_final: 0.7042 (t0) REVERT: A 498 LYS cc_start: 0.6986 (ttmt) cc_final: 0.6736 (ttmm) REVERT: B 52 PHE cc_start: 0.7054 (m-10) cc_final: 0.6658 (t80) REVERT: B 86 MET cc_start: 0.8103 (mmt) cc_final: 0.7785 (mmt) REVERT: B 166 ASP cc_start: 0.7838 (m-30) cc_final: 0.7564 (m-30) REVERT: B 182 GLN cc_start: 0.8777 (tt0) cc_final: 0.8575 (tt0) REVERT: B 325 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.8000 (mt) REVERT: B 341 ARG cc_start: 0.8270 (mtp-110) cc_final: 0.7710 (mtt180) REVERT: B 353 GLN cc_start: 0.7788 (mm-40) cc_final: 0.7586 (tp-100) REVERT: B 450 MET cc_start: 0.8390 (tpp) cc_final: 0.8136 (mmm) REVERT: C 52 PHE cc_start: 0.6883 (m-10) cc_final: 0.6484 (t80) REVERT: C 259 MET cc_start: 0.9076 (mtp) cc_final: 0.8824 (mtm) REVERT: C 285 MET cc_start: 0.8795 (mmm) cc_final: 0.8373 (mmm) REVERT: C 325 ILE cc_start: 0.8446 (OUTLIER) cc_final: 0.8143 (mt) outliers start: 22 outliers final: 3 residues processed: 152 average time/residue: 0.6136 time to fit residues: 99.5751 Evaluate side-chains 141 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 135 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 325 ILE Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 325 ILE 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 7 optimal weight: 5.9990 chunk 106 optimal weight: 0.8980 chunk 110 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 48 optimal weight: 5.9990 chunk 27 optimal weight: 0.3980 chunk 61 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 99 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3750 r_free = 0.3750 target = 0.145395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.112683 restraints weight = 10836.802| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.82 r_work: 0.3228 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.1907 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= 0.123 Angle : 0.501 6.651 12984 Z= 0.253 Chirality : 0.039 0.128 1656 Planarity : 0.004 0.034 1560 Dihedral : 4.700 51.725 1488 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.46 % Allowed : 12.39 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.25), residues: 1227 helix: 1.38 (0.17), residues: 957 sheet: -2.27 (0.78), residues: 30 loop : -1.50 (0.38), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 311 TYR 0.009 0.001 TYR C 316 PHE 0.014 0.001 PHE B 249 TRP 0.007 0.001 TRP C 472 HIS 0.003 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 9558) covalent geometry : angle 0.50092 (12984) hydrogen bonds : bond 0.04154 ( 660) hydrogen bonds : angle 4.30724 ( 1953) *********************** 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 164 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.374 Fit side-chains REVERT: A 52 PHE cc_start: 0.7184 (m-10) cc_final: 0.6648 (t80) REVERT: A 325 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.8021 (mt) REVERT: A 498 LYS cc_start: 0.7114 (ttmt) cc_final: 0.6883 (ttmm) REVERT: B 52 PHE cc_start: 0.7030 (m-10) cc_final: 0.6637 (t80) REVERT: B 86 MET cc_start: 0.8184 (mmt) cc_final: 0.7911 (mmt) REVERT: B 166 ASP cc_start: 0.7894 (m-30) cc_final: 0.7616 (m-30) REVERT: B 182 GLN cc_start: 0.8808 (tt0) cc_final: 0.8589 (tt0) REVERT: B 275 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: B 285 MET cc_start: 0.8812 (mmm) cc_final: 0.8581 (mmt) REVERT: B 325 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.8073 (mt) REVERT: B 341 ARG cc_start: 0.8272 (mtp-110) cc_final: 0.7789 (mtt180) REVERT: B 378 ASN cc_start: 0.7357 (m110) cc_final: 0.7114 (m110) REVERT: B 398 MET cc_start: 0.8697 (OUTLIER) cc_final: 0.7820 (mmp) REVERT: B 450 MET cc_start: 0.8469 (tpp) cc_final: 0.8136 (mmm) REVERT: C 52 PHE cc_start: 0.6873 (m-10) cc_final: 0.6462 (t80) REVERT: C 259 MET cc_start: 0.9061 (mtp) cc_final: 0.8852 (mtm) REVERT: C 285 MET cc_start: 0.8789 (mmm) cc_final: 0.8560 (mmm) REVERT: C 325 ILE cc_start: 0.8453 (OUTLIER) cc_final: 0.8149 (mt) outliers start: 25 outliers final: 8 residues processed: 150 average time/residue: 0.6098 time to fit residues: 97.7577 Evaluate side-chains 146 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 325 ILE Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 325 ILE Chi-restraints excluded: chain B residue 356 ILE Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 325 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 43 optimal weight: 0.0670 chunk 118 optimal weight: 0.6980 chunk 106 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.145502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112971 restraints weight = 10869.362| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 1.82 r_work: 0.3226 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2076 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= 0.116 Angle : 0.491 9.178 12984 Z= 0.246 Chirality : 0.039 0.127 1656 Planarity : 0.004 0.034 1560 Dihedral : 4.619 49.902 1488 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.85 % Allowed : 13.08 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.25), residues: 1227 helix: 1.53 (0.17), residues: 966 sheet: -2.30 (0.77), residues: 30 loop : -1.26 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 311 TYR 0.008 0.001 TYR B 316 PHE 0.012 0.001 PHE B 249 TRP 0.007 0.001 TRP C 472 HIS 0.003 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 9558) covalent geometry : angle 0.49108 (12984) hydrogen bonds : bond 0.03878 ( 660) hydrogen bonds : angle 4.19866 ( 1953) *********************** 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 167 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 138 time to evaluate : 0.377 Fit side-chains REVERT: A 52 PHE cc_start: 0.7129 (m-10) cc_final: 0.6602 (t80) REVERT: A 235 GLU cc_start: 0.8148 (tt0) cc_final: 0.7763 (tt0) REVERT: A 275 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: A 285 MET cc_start: 0.8603 (mmm) cc_final: 0.8381 (mmt) REVERT: A 290 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7648 (tp) REVERT: A 307 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7271 (tm-30) REVERT: A 498 LYS cc_start: 0.7143 (ttmt) cc_final: 0.6939 (ttmm) REVERT: B 52 PHE cc_start: 0.6976 (m-10) cc_final: 0.6586 (t80) REVERT: B 86 MET cc_start: 0.8123 (mmt) cc_final: 0.7866 (mmt) REVERT: B 166 ASP cc_start: 0.7851 (m-30) cc_final: 0.7563 (m-30) REVERT: B 182 GLN cc_start: 0.8752 (tt0) cc_final: 0.8524 (tt0) REVERT: B 285 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8518 (mmt) REVERT: B 341 ARG cc_start: 0.8172 (mtp-110) cc_final: 0.7661 (mtt180) REVERT: B 378 ASN cc_start: 0.7203 (m110) cc_final: 0.6985 (m110) REVERT: B 398 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.7728 (mmp) REVERT: B 450 MET cc_start: 0.8481 (tpp) cc_final: 0.8129 (mmm) REVERT: C 52 PHE cc_start: 0.6828 (m-10) cc_final: 0.6416 (t80) REVERT: C 275 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.6954 (mp0) REVERT: C 285 MET cc_start: 0.8731 (mmm) cc_final: 0.8478 (mmm) REVERT: C 325 ILE cc_start: 0.8389 (OUTLIER) cc_final: 0.8105 (mt) outliers start: 29 outliers final: 11 residues processed: 151 average time/residue: 0.6058 time to fit residues: 97.8263 Evaluate side-chains 151 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 334 LEU 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 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 32 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 96 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN C 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.144139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.111722 restraints weight = 10995.945| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.81 r_work: 0.3211 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.2224 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= 0.126 Angle : 0.492 7.083 12984 Z= 0.249 Chirality : 0.040 0.129 1656 Planarity : 0.004 0.035 1560 Dihedral : 4.658 51.274 1488 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.05 % Allowed : 13.47 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.47 (0.25), residues: 1227 helix: 1.61 (0.17), residues: 966 sheet: -2.39 (0.75), residues: 30 loop : -1.21 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 311 TYR 0.009 0.001 TYR B 316 PHE 0.014 0.001 PHE B 249 TRP 0.008 0.001 TRP C 472 HIS 0.003 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9558) covalent geometry : angle 0.49189 (12984) hydrogen bonds : bond 0.04079 ( 660) hydrogen bonds : angle 4.18100 ( 1953) *********************** 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 168 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 137 time to evaluate : 0.363 Fit side-chains REVERT: A 52 PHE cc_start: 0.7101 (m-10) cc_final: 0.6603 (t80) REVERT: A 235 GLU cc_start: 0.8154 (tt0) cc_final: 0.7799 (tt0) REVERT: A 275 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: A 290 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7722 (tp) REVERT: A 307 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7324 (tm-30) REVERT: A 311 ARG cc_start: 0.7693 (ttm-80) cc_final: 0.7460 (mtm-85) REVERT: A 398 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7553 (mmp) REVERT: A 498 LYS cc_start: 0.7210 (ttmt) cc_final: 0.6997 (ttmm) REVERT: B 52 PHE cc_start: 0.6991 (m-10) cc_final: 0.6597 (t80) REVERT: B 166 ASP cc_start: 0.7900 (m-30) cc_final: 0.7630 (m-30) REVERT: B 275 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: B 285 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8575 (mmt) REVERT: B 341 ARG cc_start: 0.8153 (mtp-110) cc_final: 0.7663 (mtt180) REVERT: B 378 ASN cc_start: 0.7226 (m110) cc_final: 0.6989 (m110) REVERT: B 398 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.7804 (mmp) REVERT: B 450 MET cc_start: 0.8539 (tpp) cc_final: 0.8198 (mmm) REVERT: C 52 PHE cc_start: 0.6860 (m-10) cc_final: 0.6441 (t80) REVERT: C 86 MET cc_start: 0.8048 (OUTLIER) cc_final: 0.7571 (mmt) REVERT: C 271 ASN cc_start: 0.8353 (t0) cc_final: 0.8101 (t0) REVERT: C 275 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7090 (mp0) REVERT: C 285 MET cc_start: 0.8868 (mmm) cc_final: 0.8485 (mmm) REVERT: C 325 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8068 (mt) outliers start: 31 outliers final: 13 residues processed: 152 average time/residue: 0.5996 time to fit residues: 97.4580 Evaluate side-chains 155 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 398 MET Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain B residue 88 MET Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 278 MET Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 334 LEU 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 86 MET Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 436 SER Chi-restraints excluded: chain C residue 477 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 44 optimal weight: 0.0670 chunk 62 optimal weight: 0.0870 chunk 63 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 94 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 16 optimal weight: 0.3980 chunk 67 optimal weight: 0.1980 chunk 7 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.2296 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.148445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.116311 restraints weight = 10842.051| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 1.82 r_work: 0.3270 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2380 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= 0.096 Angle : 0.470 10.994 12984 Z= 0.234 Chirality : 0.038 0.127 1656 Planarity : 0.003 0.030 1560 Dihedral : 4.518 51.887 1488 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.06 % Allowed : 15.44 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.25), residues: 1227 helix: 1.95 (0.17), residues: 963 sheet: -2.32 (0.76), residues: 30 loop : -1.17 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 311 TYR 0.006 0.001 TYR B 316 PHE 0.012 0.001 PHE A 269 TRP 0.008 0.001 TRP C 472 HIS 0.003 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00197 ( 9558) covalent geometry : angle 0.47018 (12984) hydrogen bonds : bond 0.03215 ( 660) hydrogen bonds : angle 4.00216 ( 1953) *********************** 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 168 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 147 time to evaluate : 0.350 Fit side-chains REVERT: A 52 PHE cc_start: 0.7056 (m-10) cc_final: 0.6607 (t80) REVERT: A 235 GLU cc_start: 0.8157 (tt0) cc_final: 0.7738 (tt0) REVERT: A 275 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: A 290 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7426 (tp) REVERT: A 307 GLU cc_start: 0.7579 (tm-30) cc_final: 0.7208 (tm-30) REVERT: A 498 LYS cc_start: 0.7191 (ttmt) cc_final: 0.6958 (ttmm) REVERT: B 52 PHE cc_start: 0.6985 (m-10) cc_final: 0.6621 (t80) REVERT: B 166 ASP cc_start: 0.7827 (m-30) cc_final: 0.7554 (m-30) REVERT: B 182 GLN cc_start: 0.8752 (tt0) cc_final: 0.8532 (tt0) REVERT: B 275 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7393 (mp0) REVERT: B 285 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8419 (mmt) REVERT: B 341 ARG cc_start: 0.8135 (mtp-110) cc_final: 0.7552 (mtt180) REVERT: B 353 GLN cc_start: 0.7728 (mm-40) cc_final: 0.7499 (tp-100) REVERT: B 378 ASN cc_start: 0.7139 (m110) cc_final: 0.6857 (m-40) REVERT: B 398 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8173 (mmm) REVERT: B 450 MET cc_start: 0.8452 (tpp) cc_final: 0.8110 (mmm) REVERT: C 52 PHE cc_start: 0.6965 (m-10) cc_final: 0.6438 (t80) REVERT: C 86 MET cc_start: 0.7893 (OUTLIER) cc_final: 0.7658 (mmt) REVERT: C 275 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.6943 (mp0) REVERT: C 285 MET cc_start: 0.8528 (mmm) cc_final: 0.8254 (mmm) REVERT: C 325 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.8054 (mt) outliers start: 21 outliers final: 6 residues processed: 156 average time/residue: 0.5640 time to fit residues: 94.0387 Evaluate side-chains 146 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 325 ILE 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 100 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3747 r_free = 0.3747 target = 0.145372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.112985 restraints weight = 11006.688| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.82 r_work: 0.3223 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2381 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= 0.121 Angle : 0.503 10.747 12984 Z= 0.250 Chirality : 0.039 0.128 1656 Planarity : 0.003 0.033 1560 Dihedral : 4.574 52.358 1488 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.05 % Allowed : 15.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.25), residues: 1227 helix: 1.94 (0.17), residues: 960 sheet: -2.86 (0.68), residues: 42 loop : -1.07 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 311 TYR 0.009 0.001 TYR B 316 PHE 0.013 0.001 PHE B 249 TRP 0.006 0.001 TRP C 472 HIS 0.002 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9558) covalent geometry : angle 0.50336 (12984) hydrogen bonds : bond 0.03819 ( 660) hydrogen bonds : angle 4.04637 ( 1953) *********************** 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 166 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 135 time to evaluate : 0.381 Fit side-chains REVERT: A 52 PHE cc_start: 0.7092 (m-10) cc_final: 0.6613 (t80) REVERT: A 235 GLU cc_start: 0.8144 (tt0) cc_final: 0.7725 (tt0) REVERT: A 275 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7218 (mp0) REVERT: A 290 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7599 (tp) REVERT: A 307 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7373 (tm-30) REVERT: A 398 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.7414 (mmp) REVERT: A 498 LYS cc_start: 0.7266 (ttmt) cc_final: 0.7021 (ttmm) REVERT: B 52 PHE cc_start: 0.6990 (m-10) cc_final: 0.6614 (t80) REVERT: B 166 ASP cc_start: 0.7863 (m-30) cc_final: 0.7590 (m-30) REVERT: B 275 GLU cc_start: 0.8017 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: B 285 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8506 (mmt) REVERT: B 341 ARG cc_start: 0.8133 (mtp-110) cc_final: 0.7565 (mtt180) REVERT: B 398 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.7728 (mmp) REVERT: B 450 MET cc_start: 0.8519 (tpp) cc_final: 0.8162 (mmm) REVERT: C 52 PHE cc_start: 0.6958 (m-10) cc_final: 0.6467 (t80) REVERT: C 86 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7822 (mmt) REVERT: C 271 ASN cc_start: 0.8306 (t0) cc_final: 0.8055 (t0) REVERT: C 275 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7054 (mp0) REVERT: C 285 MET cc_start: 0.8826 (mmm) cc_final: 0.8457 (mmm) REVERT: C 325 ILE cc_start: 0.8399 (OUTLIER) cc_final: 0.8119 (mt) outliers start: 31 outliers final: 13 residues processed: 148 average time/residue: 0.5684 time to fit residues: 89.9239 Evaluate side-chains 153 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 THR 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 398 MET Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 477 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 51 optimal weight: 0.8980 chunk 2 optimal weight: 0.0370 chunk 35 optimal weight: 4.9990 chunk 47 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 65 optimal weight: 0.0370 chunk 57 optimal weight: 0.6980 chunk 84 optimal weight: 7.9990 chunk 104 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN B 378 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.147443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.115330 restraints weight = 10972.240| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.82 r_work: 0.3257 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3125 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9558 Z= 0.101 Angle : 0.484 10.085 12984 Z= 0.239 Chirality : 0.038 0.128 1656 Planarity : 0.003 0.031 1560 Dihedral : 4.513 51.534 1488 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.65 % Allowed : 15.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.05 (0.25), residues: 1227 helix: 2.08 (0.17), residues: 960 sheet: -2.80 (0.68), residues: 42 loop : -1.00 (0.40), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 311 TYR 0.007 0.001 TYR B 316 PHE 0.012 0.001 PHE A 269 TRP 0.007 0.001 TRP C 472 HIS 0.003 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 9558) covalent geometry : angle 0.48358 (12984) hydrogen bonds : bond 0.03353 ( 660) hydrogen bonds : angle 3.95545 ( 1953) *********************** 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 164 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.404 Fit side-chains REVERT: A 52 PHE cc_start: 0.7066 (m-10) cc_final: 0.6624 (t80) REVERT: A 86 MET cc_start: 0.8178 (mmt) cc_final: 0.7831 (mtm) REVERT: A 235 GLU cc_start: 0.8142 (tt0) cc_final: 0.7708 (tt0) REVERT: A 275 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7215 (mp0) REVERT: A 307 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7311 (tm-30) REVERT: A 398 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.7379 (mmp) REVERT: A 498 LYS cc_start: 0.7189 (ttmt) cc_final: 0.6949 (ttmm) REVERT: B 52 PHE cc_start: 0.6981 (m-10) cc_final: 0.6617 (t80) REVERT: B 166 ASP cc_start: 0.7831 (m-30) cc_final: 0.7561 (m-30) REVERT: B 182 GLN cc_start: 0.8733 (tt0) cc_final: 0.8529 (tt0) REVERT: B 275 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: B 285 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8473 (mmt) REVERT: B 341 ARG cc_start: 0.8122 (mtp-110) cc_final: 0.7561 (mtt180) REVERT: B 398 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.8189 (mmm) REVERT: B 450 MET cc_start: 0.8523 (tpp) cc_final: 0.8182 (mmm) REVERT: C 52 PHE cc_start: 0.6983 (m-10) cc_final: 0.6472 (t80) REVERT: C 86 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7814 (mmt) REVERT: C 275 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7014 (mp0) REVERT: C 325 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.8067 (mt) outliers start: 27 outliers final: 12 residues processed: 147 average time/residue: 0.5676 time to fit residues: 89.3172 Evaluate side-chains 152 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 THR 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 180 LEU Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 477 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 64 optimal weight: 2.9990 chunk 107 optimal weight: 0.0270 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 117 optimal weight: 0.3980 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 353 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.145789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113546 restraints weight = 10985.001| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.82 r_work: 0.3233 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9558 Z= 0.114 Angle : 0.507 11.448 12984 Z= 0.249 Chirality : 0.039 0.128 1656 Planarity : 0.003 0.033 1560 Dihedral : 4.532 52.785 1488 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.16 % Allowed : 16.72 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.25), residues: 1227 helix: 2.03 (0.17), residues: 963 sheet: -2.80 (0.68), residues: 42 loop : -0.88 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 311 TYR 0.008 0.001 TYR B 316 PHE 0.012 0.001 PHE B 249 TRP 0.005 0.001 TRP A 472 HIS 0.002 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9558) covalent geometry : angle 0.50708 (12984) hydrogen bonds : bond 0.03668 ( 660) hydrogen bonds : angle 4.00157 ( 1953) *********************** 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 155 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.361 Fit side-chains REVERT: A 52 PHE cc_start: 0.7014 (m-10) cc_final: 0.6542 (t80) REVERT: A 235 GLU cc_start: 0.8103 (tt0) cc_final: 0.7657 (tt0) REVERT: A 275 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7169 (mp0) REVERT: A 307 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7337 (tm-30) REVERT: A 353 GLN cc_start: 0.7846 (mm-40) cc_final: 0.7639 (mm-40) REVERT: A 398 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.7357 (mmp) REVERT: A 498 LYS cc_start: 0.7176 (ttmt) cc_final: 0.6863 (ttmm) REVERT: B 52 PHE cc_start: 0.6930 (m-10) cc_final: 0.6549 (t80) REVERT: B 166 ASP cc_start: 0.7813 (m-30) cc_final: 0.7535 (m-30) REVERT: B 275 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7404 (mp0) REVERT: B 285 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8401 (mmt) REVERT: B 341 ARG cc_start: 0.8095 (mtp-110) cc_final: 0.7500 (mtt180) REVERT: B 387 ARG cc_start: 0.7632 (mmm160) cc_final: 0.7350 (mmm160) REVERT: B 398 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8198 (mmm) REVERT: B 450 MET cc_start: 0.8472 (tpp) cc_final: 0.8109 (mmm) REVERT: C 52 PHE cc_start: 0.6936 (m-10) cc_final: 0.6406 (t80) REVERT: C 86 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7742 (mmt) REVERT: C 271 ASN cc_start: 0.8215 (t0) cc_final: 0.7970 (t0) REVERT: C 275 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: C 325 ILE cc_start: 0.8299 (OUTLIER) cc_final: 0.8026 (mt) outliers start: 22 outliers final: 12 residues processed: 141 average time/residue: 0.5946 time to fit residues: 89.4789 Evaluate side-chains 151 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 THR 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 180 LEU Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 477 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 72 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 86 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 92 optimal weight: 0.0060 chunk 116 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 48 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 HIS B 353 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.145837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.113536 restraints weight = 10917.463| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.82 r_work: 0.3234 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9558 Z= 0.114 Angle : 0.507 10.986 12984 Z= 0.249 Chirality : 0.039 0.127 1656 Planarity : 0.003 0.033 1560 Dihedral : 4.553 52.715 1488 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.36 % Allowed : 16.52 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.25), residues: 1227 helix: 2.00 (0.17), residues: 966 sheet: -2.80 (0.68), residues: 42 loop : -0.97 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 311 TYR 0.008 0.001 TYR B 316 PHE 0.012 0.001 PHE B 249 TRP 0.008 0.001 TRP A 472 HIS 0.002 0.001 HIS A 327 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 9558) covalent geometry : angle 0.50714 (12984) hydrogen bonds : bond 0.03692 ( 660) hydrogen bonds : angle 4.00755 ( 1953) ********************** 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: 24 poor density : 130 time to evaluate : 0.379 Fit side-chains REVERT: A 52 PHE cc_start: 0.7076 (m-10) cc_final: 0.6600 (t80) REVERT: A 86 MET cc_start: 0.8212 (mmt) cc_final: 0.7826 (mtm) REVERT: A 235 GLU cc_start: 0.8127 (tt0) cc_final: 0.7690 (tt0) REVERT: A 275 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7221 (mp0) REVERT: A 307 GLU cc_start: 0.7573 (tm-30) cc_final: 0.7292 (tm-30) REVERT: A 398 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.7371 (mmp) REVERT: A 498 LYS cc_start: 0.7260 (ttmt) cc_final: 0.7015 (ttmm) REVERT: B 52 PHE cc_start: 0.6974 (m-10) cc_final: 0.6591 (t80) REVERT: B 166 ASP cc_start: 0.7845 (m-30) cc_final: 0.7569 (m-30) REVERT: B 275 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7449 (mp0) REVERT: B 285 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8465 (mmt) REVERT: B 341 ARG cc_start: 0.8121 (mtp-110) cc_final: 0.7553 (mtt180) REVERT: B 387 ARG cc_start: 0.7642 (mmm160) cc_final: 0.7372 (mmm160) REVERT: B 398 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8231 (mmm) REVERT: B 450 MET cc_start: 0.8482 (tpp) cc_final: 0.8124 (mmm) REVERT: C 52 PHE cc_start: 0.6974 (m-10) cc_final: 0.6448 (t80) REVERT: C 86 MET cc_start: 0.8178 (OUTLIER) cc_final: 0.7794 (mmt) REVERT: C 275 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.6972 (mp0) REVERT: C 325 ILE cc_start: 0.8362 (OUTLIER) cc_final: 0.8105 (mt) outliers start: 24 outliers final: 13 residues processed: 140 average time/residue: 0.6086 time to fit residues: 90.9545 Evaluate side-chains 150 residues out of total 1017 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 THR 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 180 LEU Chi-restraints excluded: chain B residue 238 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 398 MET Chi-restraints excluded: chain B residue 436 SER Chi-restraints excluded: chain B residue 477 MET Chi-restraints excluded: chain C residue 86 MET Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain C residue 275 GLU Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 477 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.4980 chunk 36 optimal weight: 0.5980 chunk 116 optimal weight: 0.9980 chunk 94 optimal weight: 0.5980 chunk 50 optimal weight: 0.6980 chunk 100 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 58 optimal weight: 0.0770 chunk 119 optimal weight: 3.9990 chunk 19 optimal weight: 0.0270 chunk 7 optimal weight: 3.9990 overall best weight: 0.3596 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.147710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.115754 restraints weight = 10770.102| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.80 r_work: 0.3264 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9558 Z= 0.100 Angle : 0.494 11.095 12984 Z= 0.242 Chirality : 0.039 0.127 1656 Planarity : 0.003 0.032 1560 Dihedral : 4.498 51.955 1488 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.26 % Allowed : 16.62 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.25), residues: 1227 helix: 2.16 (0.17), residues: 963 sheet: -2.72 (0.69), residues: 42 loop : -0.90 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 311 TYR 0.006 0.001 TYR B 316 PHE 0.010 0.001 PHE A 269 TRP 0.009 0.001 TRP A 472 HIS 0.003 0.001 HIS B 327 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 9558) covalent geometry : angle 0.49379 (12984) hydrogen bonds : bond 0.03315 ( 660) hydrogen bonds : angle 3.92911 ( 1953) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3361.43 seconds wall clock time: 58 minutes 1.11 seconds (3481.11 seconds total)