Starting phenix.real_space_refine on Wed Mar 4 12:58:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fhl_31586/03_2026/7fhl_31586.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fhl_31586/03_2026/7fhl_31586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7fhl_31586/03_2026/7fhl_31586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fhl_31586/03_2026/7fhl_31586.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fhl_31586/03_2026/7fhl_31586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fhl_31586/03_2026/7fhl_31586.map" } resolution = 3.1 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3394 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 44 5.16 5 C 7346 2.51 5 N 1710 2.21 5 O 1954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11058 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5467 Classifications: {'peptide': 663} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 642} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 5467 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5467 Classifications: {'peptide': 663} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 642} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 60 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 11} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'UNK:plan-1': 12} Unresolved non-hydrogen planarities: 12 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.49, per 1000 atoms: 0.23 Number of scatterers: 11058 At special positions: 0 Unit cell: (88.218, 120.666, 117.624, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 44 16.00 O 1954 8.00 N 1710 7.00 C 7346 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS A 101 " distance=2.03 Simple disulfide: pdb=" SG CYS C 93 " - pdb=" SG CYS C 101 " distance=2.03 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: 0.62 Conformation dependent library (CDL) restraints added in 425.5 milliseconds 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2584 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 0 sheets defined 87.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 20 through 27 Processing helix chain 'A' and resid 29 through 44 Processing helix chain 'A' and resid 48 through 54 removed outlier: 3.582A pdb=" N LEU A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLN A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 69 Processing helix chain 'A' and resid 70 through 88 Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.790A pdb=" N GLU A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 90 through 95' Processing helix chain 'A' and resid 116 through 137 Processing helix chain 'A' and resid 138 through 143 removed outlier: 3.700A pdb=" N GLY A 143 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 150 through 174 Processing helix chain 'A' and resid 186 through 199 removed outlier: 3.763A pdb=" N ILE A 199 " --> pdb=" O PHE A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 239 removed outlier: 3.595A pdb=" N GLY A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLY A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N THR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ASN A 218 " --> pdb=" O GLY A 214 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ILE A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 222 " --> pdb=" O ASN A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 247 removed outlier: 3.596A pdb=" N LEU A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.802A pdb=" N THR A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 3.975A pdb=" N VAL A 270 " --> pdb=" O ASN A 266 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TRP A 271 " --> pdb=" O ASN A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 271' Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 280 through 294 removed outlier: 4.352A pdb=" N PHE A 284 " --> pdb=" O TRP A 280 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N PHE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 335 removed outlier: 3.503A pdb=" N LYS A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 330 " --> pdb=" O MET A 326 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 358 removed outlier: 4.513A pdb=" N LYS A 349 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU A 350 " --> pdb=" O GLN A 346 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR A 357 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 376 removed outlier: 3.584A pdb=" N ASP A 373 " --> pdb=" O GLY A 369 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 399 removed outlier: 3.649A pdb=" N ALA A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA A 396 " --> pdb=" O CYS A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 416 Processing helix chain 'A' and resid 417 through 429 removed outlier: 3.510A pdb=" N GLN A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 457 removed outlier: 3.504A pdb=" N TYR A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 487 removed outlier: 3.837A pdb=" N TRP A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 469 " --> pdb=" O GLN A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 494 removed outlier: 3.982A pdb=" N GLU A 494 " --> pdb=" O ASN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 517 Processing helix chain 'A' and resid 528 through 538 removed outlier: 4.514A pdb=" N TYR A 532 " --> pdb=" O GLU A 528 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 533 " --> pdb=" O TRP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 545 removed outlier: 3.747A pdb=" N LEU A 544 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 545 " --> pdb=" O LEU A 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 540 through 545' Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 551 through 565 removed outlier: 3.686A pdb=" N ILE A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) Proline residue: A 563 - end of helix Processing helix chain 'A' and resid 565 through 587 removed outlier: 3.535A pdb=" N GLN A 585 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 600 Processing helix chain 'A' and resid 601 through 607 removed outlier: 3.700A pdb=" N GLU A 605 " --> pdb=" O THR A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 612 Processing helix chain 'A' and resid 615 through 628 removed outlier: 3.656A pdb=" N VAL A 621 " --> pdb=" O PRO A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 644 removed outlier: 3.823A pdb=" N MET A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 647 No H-bonds generated for 'chain 'A' and resid 645 through 647' Processing helix chain 'A' and resid 648 through 659 removed outlier: 4.081A pdb=" N PHE A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 684 Processing helix chain 'B' and resid 7 through 17 Processing helix chain 'C' and resid 20 through 27 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 48 through 54 removed outlier: 3.633A pdb=" N LEU C 52 " --> pdb=" O PRO C 48 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLN C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 69 Processing helix chain 'C' and resid 70 through 88 Processing helix chain 'C' and resid 90 through 95 removed outlier: 3.786A pdb=" N GLU C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 90 through 95' Processing helix chain 'C' and resid 116 through 137 Processing helix chain 'C' and resid 138 through 143 removed outlier: 3.716A pdb=" N GLY C 143 " --> pdb=" O ILE C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 150 Processing helix chain 'C' and resid 150 through 174 Processing helix chain 'C' and resid 186 through 199 removed outlier: 3.891A pdb=" N ILE C 199 " --> pdb=" O PHE C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 199 through 239 removed outlier: 4.478A pdb=" N GLY C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N THR C 215 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ASN C 218 " --> pdb=" O GLY C 214 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE C 219 " --> pdb=" O THR C 215 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 247 Processing helix chain 'C' and resid 250 through 263 removed outlier: 3.826A pdb=" N THR C 263 " --> pdb=" O PHE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 removed outlier: 3.982A pdb=" N VAL C 270 " --> pdb=" O ASN C 266 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N TRP C 271 " --> pdb=" O ASN C 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 271' Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'C' and resid 280 through 294 removed outlier: 4.152A pdb=" N PHE C 284 " --> pdb=" O TRP C 280 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 335 removed outlier: 3.538A pdb=" N ALA C 330 " --> pdb=" O MET C 326 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C 331 " --> pdb=" O LEU C 327 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP C 335 " --> pdb=" O PHE C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 358 removed outlier: 4.552A pdb=" N LYS C 349 " --> pdb=" O ASN C 345 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU C 350 " --> pdb=" O GLN C 346 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR C 357 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 376 Processing helix chain 'C' and resid 384 through 399 Processing helix chain 'C' and resid 411 through 416 removed outlier: 3.576A pdb=" N TYR C 415 " --> pdb=" O PHE C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 429 Processing helix chain 'C' and resid 430 through 457 Processing helix chain 'C' and resid 460 through 487 removed outlier: 3.997A pdb=" N TRP C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 487 through 494 removed outlier: 3.979A pdb=" N GLU C 494 " --> pdb=" O ASN C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 517 removed outlier: 3.586A pdb=" N PHE C 499 " --> pdb=" O GLY C 495 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR C 517 " --> pdb=" O ALA C 513 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 538 removed outlier: 4.295A pdb=" N TYR C 532 " --> pdb=" O GLU C 528 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 533 " --> pdb=" O TRP C 529 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 545 removed outlier: 4.022A pdb=" N ARG C 543 " --> pdb=" O LEU C 539 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU C 544 " --> pdb=" O ARG C 540 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU C 545 " --> pdb=" O LEU C 541 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 539 through 545' Processing helix chain 'C' and resid 548 through 565 removed outlier: 4.636A pdb=" N ALA C 553 " --> pdb=" O GLN C 549 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHE C 554 " --> pdb=" O ARG C 550 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE C 562 " --> pdb=" O PHE C 558 " (cutoff:3.500A) Proline residue: C 563 - end of helix Processing helix chain 'C' and resid 565 through 587 removed outlier: 3.806A pdb=" N GLN C 585 " --> pdb=" O SER C 581 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL C 586 " --> pdb=" O ILE C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 601 through 606 removed outlier: 3.659A pdb=" N GLU C 605 " --> pdb=" O THR C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 612 removed outlier: 3.524A pdb=" N ASN C 612 " --> pdb=" O LEU C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 628 Processing helix chain 'C' and resid 632 through 644 removed outlier: 3.617A pdb=" N MET C 636 " --> pdb=" O TRP C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 646 through 659 removed outlier: 4.151A pdb=" N THR C 650 " --> pdb=" O TRP C 646 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR C 651 " --> pdb=" O TRP C 647 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE C 652 " --> pdb=" O SER C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 684 Processing helix chain 'D' and resid 7 through 17 747 hydrogen bonds defined for protein. 2220 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: 1.45 Time building geometry restraints manager: 0.90 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: 3361 1.34 - 1.46: 2992 1.46 - 1.58: 4925 1.58 - 1.70: 0 1.70 - 1.82: 72 Bond restraints: 11350 Sorted by residual: bond pdb=" C LYS C 98 " pdb=" N PRO C 99 " ideal model delta sigma weight residual 1.333 1.347 -0.014 1.20e-02 6.94e+03 1.45e+00 bond pdb=" CA ILE A 562 " pdb=" CB ILE A 562 " ideal model delta sigma weight residual 1.539 1.545 -0.006 5.40e-03 3.43e+04 1.08e+00 bond pdb=" N THR A 517 " pdb=" CA THR A 517 " ideal model delta sigma weight residual 1.463 1.450 0.013 1.22e-02 6.72e+03 1.07e+00 bond pdb=" C LYS A 98 " pdb=" N PRO A 99 " ideal model delta sigma weight residual 1.333 1.345 -0.012 1.20e-02 6.94e+03 9.72e-01 bond pdb=" C ILE C 272 " pdb=" N PRO C 273 " ideal model delta sigma weight residual 1.336 1.348 -0.012 1.20e-02 6.94e+03 9.25e-01 ... (remaining 11345 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 15059 1.49 - 2.99: 307 2.99 - 4.48: 55 4.48 - 5.97: 16 5.97 - 7.46: 3 Bond angle restraints: 15440 Sorted by residual: angle pdb=" CB MET A 629 " pdb=" CG MET A 629 " pdb=" SD MET A 629 " ideal model delta sigma weight residual 112.70 120.16 -7.46 3.00e+00 1.11e-01 6.19e+00 angle pdb=" CA PRO A 97 " pdb=" C PRO A 97 " pdb=" N LYS A 98 " ideal model delta sigma weight residual 114.66 117.48 -2.82 1.34e+00 5.57e-01 4.42e+00 angle pdb=" C SER C 55 " pdb=" N SER C 56 " pdb=" CA SER C 56 " ideal model delta sigma weight residual 121.54 125.55 -4.01 1.91e+00 2.74e-01 4.41e+00 angle pdb=" C SER A 55 " pdb=" N SER A 56 " pdb=" CA SER A 56 " ideal model delta sigma weight residual 121.54 125.52 -3.98 1.91e+00 2.74e-01 4.34e+00 angle pdb=" CA PRO C 97 " pdb=" C PRO C 97 " pdb=" N LYS C 98 " ideal model delta sigma weight residual 114.66 117.44 -2.78 1.34e+00 5.57e-01 4.31e+00 ... (remaining 15435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 6049 17.64 - 35.29: 434 35.29 - 52.93: 68 52.93 - 70.58: 15 70.58 - 88.22: 6 Dihedral angle restraints: 6572 sinusoidal: 2576 harmonic: 3996 Sorted by residual: dihedral pdb=" CA LYS C 98 " pdb=" C LYS C 98 " pdb=" N PRO C 99 " pdb=" CA PRO C 99 " ideal model delta harmonic sigma weight residual 180.00 162.30 17.70 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA LYS A 98 " pdb=" C LYS A 98 " pdb=" N PRO A 99 " pdb=" CA PRO A 99 " ideal model delta harmonic sigma weight residual 180.00 162.71 17.29 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CB CYS A 93 " pdb=" SG CYS A 93 " pdb=" SG CYS A 101 " pdb=" CB CYS A 101 " ideal model delta sinusoidal sigma weight residual 93.00 65.17 27.83 1 1.00e+01 1.00e-02 1.11e+01 ... (remaining 6569 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1196 0.029 - 0.058: 368 0.058 - 0.087: 131 0.087 - 0.116: 46 0.116 - 0.145: 7 Chirality restraints: 1748 Sorted by residual: chirality pdb=" CB ILE C 272 " pdb=" CA ILE C 272 " pdb=" CG1 ILE C 272 " pdb=" CG2 ILE C 272 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" CA VAL C 404 " pdb=" N VAL C 404 " pdb=" C VAL C 404 " pdb=" CB VAL C 404 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.17e-01 chirality pdb=" CA VAL A 404 " pdb=" N VAL A 404 " pdb=" C VAL A 404 " pdb=" CB VAL A 404 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 1745 not shown) Planarity restraints: 1914 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE C 308 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.15e+00 pdb=" C PHE C 308 " -0.031 2.00e-02 2.50e+03 pdb=" O PHE C 308 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS C 309 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 314 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.08e+00 pdb=" C LYS C 314 " 0.030 2.00e-02 2.50e+03 pdb=" O LYS C 314 " -0.011 2.00e-02 2.50e+03 pdb=" N GLN C 315 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 317 " -0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" C SER C 317 " 0.029 2.00e-02 2.50e+03 pdb=" O SER C 317 " -0.011 2.00e-02 2.50e+03 pdb=" N GLY C 318 " -0.010 2.00e-02 2.50e+03 ... (remaining 1911 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 142 2.70 - 3.25: 12186 3.25 - 3.80: 17414 3.80 - 4.35: 21599 4.35 - 4.90: 35706 Nonbonded interactions: 87047 Sorted by model distance: nonbonded pdb=" OG SER C 265 " pdb=" OE1 GLN C 633 " model vdw 2.150 3.040 nonbonded pdb=" OG SER A 265 " pdb=" OE1 GLN A 633 " model vdw 2.151 3.040 nonbonded pdb=" O TYR C 107 " pdb=" ND2 ASN C 614 " model vdw 2.186 3.120 nonbonded pdb=" O TYR A 107 " pdb=" ND2 ASN A 614 " model vdw 2.196 3.120 nonbonded pdb=" O PHE C 426 " pdb=" OG SER C 429 " model vdw 2.222 3.040 ... (remaining 87042 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.050 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 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 : 0.002 0.035 11352 Z= 0.125 Angle : 0.548 7.463 15444 Z= 0.304 Chirality : 0.035 0.145 1748 Planarity : 0.004 0.030 1914 Dihedral : 12.500 88.221 3982 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.23), residues: 1318 helix: 1.14 (0.16), residues: 970 sheet: None (None), residues: 0 loop : -0.17 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 324 TYR 0.018 0.001 TYR C 434 PHE 0.016 0.001 PHE C 426 TRP 0.011 0.001 TRP C 492 HIS 0.002 0.001 HIS A 134 Details of bonding type rmsd covalent geometry : bond 0.00245 (11350) covalent geometry : angle 0.54771 (15440) SS BOND : bond 0.00292 ( 2) SS BOND : angle 0.69990 ( 4) hydrogen bonds : bond 0.19818 ( 747) hydrogen bonds : angle 6.05663 ( 2220) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.315 Fit side-chains REVERT: A 146 ILE cc_start: 0.8886 (mp) cc_final: 0.8550 (mm) REVERT: A 166 ASP cc_start: 0.9032 (t70) cc_final: 0.8795 (t0) REVERT: A 294 TYR cc_start: 0.8296 (m-10) cc_final: 0.7625 (m-10) REVERT: A 322 MET cc_start: 0.8782 (tmm) cc_final: 0.8554 (tmm) REVERT: A 393 GLN cc_start: 0.8548 (mm110) cc_final: 0.7764 (tm-30) REVERT: A 434 TYR cc_start: 0.8349 (m-80) cc_final: 0.7969 (m-80) REVERT: A 486 TYR cc_start: 0.8702 (m-80) cc_final: 0.8431 (m-10) REVERT: A 597 LYS cc_start: 0.8649 (tptm) cc_final: 0.8404 (tppt) REVERT: A 602 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7599 (mt-10) REVERT: A 664 LEU cc_start: 0.8786 (mm) cc_final: 0.8156 (mm) REVERT: C 98 LYS cc_start: 0.7997 (mmtt) cc_final: 0.7736 (mppt) REVERT: C 146 ILE cc_start: 0.8922 (mp) cc_final: 0.8595 (mm) REVERT: C 166 ASP cc_start: 0.9036 (t70) cc_final: 0.8780 (t0) REVERT: C 294 TYR cc_start: 0.8326 (m-10) cc_final: 0.7911 (m-10) REVERT: C 434 TYR cc_start: 0.8207 (m-80) cc_final: 0.7819 (m-80) REVERT: C 597 LYS cc_start: 0.8750 (tptt) cc_final: 0.8482 (tppt) REVERT: C 637 GLU cc_start: 0.7785 (pt0) cc_final: 0.6790 (pt0) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.0869 time to fit residues: 24.5306 Evaluate side-chains 153 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 443 ASN ** C 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 521 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.137424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.089575 restraints weight = 19331.060| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.69 r_work: 0.3066 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11352 Z= 0.144 Angle : 0.550 7.696 15444 Z= 0.291 Chirality : 0.038 0.183 1748 Planarity : 0.004 0.032 1914 Dihedral : 3.770 18.098 1468 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.76 % Allowed : 7.15 % Favored : 92.09 % 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 are not related in a simple way. whole: 2.01 (0.24), residues: 1318 helix: 1.72 (0.16), residues: 1034 sheet: None (None), residues: 0 loop : 0.02 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 537 TYR 0.021 0.002 TYR C 78 PHE 0.032 0.001 PHE C 408 TRP 0.010 0.001 TRP C 632 HIS 0.009 0.002 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00317 (11350) covalent geometry : angle 0.55023 (15440) SS BOND : bond 0.00193 ( 2) SS BOND : angle 0.63400 ( 4) hydrogen bonds : bond 0.05151 ( 747) hydrogen bonds : angle 4.05633 ( 2220) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 176 time to evaluate : 0.432 Fit side-chains REVERT: A 146 ILE cc_start: 0.9035 (mp) cc_final: 0.8719 (mm) REVERT: A 166 ASP cc_start: 0.9183 (t70) cc_final: 0.8887 (t0) REVERT: A 294 TYR cc_start: 0.8822 (m-10) cc_final: 0.8236 (m-10) REVERT: A 322 MET cc_start: 0.8689 (tmm) cc_final: 0.8431 (tmm) REVERT: A 393 GLN cc_start: 0.8268 (mm110) cc_final: 0.7600 (tm-30) REVERT: A 434 TYR cc_start: 0.8277 (m-80) cc_final: 0.7930 (m-80) REVERT: A 602 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7985 (mt-10) REVERT: A 673 GLU cc_start: 0.8840 (mm-30) cc_final: 0.8554 (mm-30) REVERT: C 146 ILE cc_start: 0.9052 (mp) cc_final: 0.8750 (mm) REVERT: C 166 ASP cc_start: 0.9197 (t70) cc_final: 0.8873 (t0) REVERT: C 294 TYR cc_start: 0.8752 (m-10) cc_final: 0.8305 (m-10) REVERT: C 434 TYR cc_start: 0.8153 (m-80) cc_final: 0.7829 (m-80) REVERT: C 492 TRP cc_start: 0.8513 (t-100) cc_final: 0.8276 (t-100) REVERT: C 539 LEU cc_start: 0.8539 (mm) cc_final: 0.8241 (mm) REVERT: C 597 LYS cc_start: 0.8704 (tptt) cc_final: 0.8460 (tppt) REVERT: C 637 GLU cc_start: 0.8316 (pt0) cc_final: 0.8081 (pt0) outliers start: 9 outliers final: 6 residues processed: 179 average time/residue: 0.0824 time to fit residues: 22.4759 Evaluate side-chains 156 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 150 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 502 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 128 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.134052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.086382 restraints weight = 19489.139| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.67 r_work: 0.3015 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11352 Z= 0.181 Angle : 0.556 7.666 15444 Z= 0.292 Chirality : 0.039 0.162 1748 Planarity : 0.003 0.032 1914 Dihedral : 3.795 17.239 1468 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.52 % Allowed : 8.92 % Favored : 89.56 % 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 are not related in a simple way. whole: 2.12 (0.24), residues: 1318 helix: 1.79 (0.16), residues: 1038 sheet: None (None), residues: 0 loop : 0.09 (0.40), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 279 TYR 0.023 0.002 TYR A 78 PHE 0.015 0.001 PHE A 501 TRP 0.014 0.001 TRP C 271 HIS 0.006 0.001 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00430 (11350) covalent geometry : angle 0.55609 (15440) SS BOND : bond 0.00286 ( 2) SS BOND : angle 0.69509 ( 4) hydrogen bonds : bond 0.04879 ( 747) hydrogen bonds : angle 3.98615 ( 2220) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.329 Fit side-chains REVERT: A 86 PHE cc_start: 0.8497 (OUTLIER) cc_final: 0.8159 (t80) REVERT: A 166 ASP cc_start: 0.9185 (t70) cc_final: 0.8870 (t0) REVERT: A 322 MET cc_start: 0.8688 (tmm) cc_final: 0.8393 (tmm) REVERT: A 393 GLN cc_start: 0.8264 (mm110) cc_final: 0.7662 (tm-30) REVERT: A 434 TYR cc_start: 0.8307 (m-80) cc_final: 0.7990 (m-80) REVERT: A 597 LYS cc_start: 0.8691 (tppt) cc_final: 0.8392 (tppt) REVERT: A 602 GLU cc_start: 0.8393 (mt-10) cc_final: 0.7993 (mt-10) REVERT: A 673 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8625 (mm-30) REVERT: C 146 ILE cc_start: 0.9144 (mp) cc_final: 0.8801 (mm) REVERT: C 166 ASP cc_start: 0.9202 (t70) cc_final: 0.8871 (t0) REVERT: C 393 GLN cc_start: 0.8009 (mm110) cc_final: 0.7306 (tm-30) REVERT: C 434 TYR cc_start: 0.8182 (m-80) cc_final: 0.7872 (m-80) REVERT: C 539 LEU cc_start: 0.8639 (mm) cc_final: 0.8269 (mm) REVERT: C 597 LYS cc_start: 0.8718 (tptt) cc_final: 0.8500 (tppt) outliers start: 18 outliers final: 10 residues processed: 165 average time/residue: 0.0848 time to fit residues: 21.1837 Evaluate side-chains 157 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 146 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 658 ILE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 542 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 34 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 114 optimal weight: 0.0020 chunk 28 optimal weight: 1.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 HIS ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 GLN C 443 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.134448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.086721 restraints weight = 19510.946| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.68 r_work: 0.3023 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11352 Z= 0.153 Angle : 0.535 8.467 15444 Z= 0.280 Chirality : 0.038 0.200 1748 Planarity : 0.003 0.032 1914 Dihedral : 3.776 19.816 1468 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.02 % Allowed : 9.93 % Favored : 88.05 % 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 are not related in a simple way. whole: 2.20 (0.24), residues: 1318 helix: 1.86 (0.16), residues: 1040 sheet: None (None), residues: 0 loop : 0.03 (0.41), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 279 TYR 0.015 0.002 TYR A 78 PHE 0.035 0.001 PHE C 408 TRP 0.011 0.001 TRP C 271 HIS 0.006 0.001 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00363 (11350) covalent geometry : angle 0.53510 (15440) SS BOND : bond 0.00306 ( 2) SS BOND : angle 0.79060 ( 4) hydrogen bonds : bond 0.04364 ( 747) hydrogen bonds : angle 3.87436 ( 2220) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.358 Fit side-chains REVERT: A 86 PHE cc_start: 0.8471 (OUTLIER) cc_final: 0.8132 (t80) REVERT: A 166 ASP cc_start: 0.9177 (t70) cc_final: 0.8863 (t0) REVERT: A 322 MET cc_start: 0.8696 (tmm) cc_final: 0.8417 (tmm) REVERT: A 393 GLN cc_start: 0.8255 (mm110) cc_final: 0.7733 (tm-30) REVERT: A 434 TYR cc_start: 0.8287 (m-80) cc_final: 0.7972 (m-80) REVERT: A 597 LYS cc_start: 0.8577 (tppt) cc_final: 0.8219 (tppt) REVERT: A 602 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7942 (mt-10) REVERT: A 673 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8617 (mm-30) REVERT: C 86 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.7999 (t80) REVERT: C 146 ILE cc_start: 0.9150 (mp) cc_final: 0.8775 (mm) REVERT: C 166 ASP cc_start: 0.9184 (t70) cc_final: 0.8839 (t0) REVERT: C 393 GLN cc_start: 0.8076 (mm110) cc_final: 0.7348 (tm-30) REVERT: C 434 TYR cc_start: 0.8191 (m-80) cc_final: 0.7864 (m-80) REVERT: C 597 LYS cc_start: 0.8727 (tptt) cc_final: 0.8450 (tppt) outliers start: 24 outliers final: 16 residues processed: 163 average time/residue: 0.0826 time to fit residues: 20.6837 Evaluate side-chains 157 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 126 ILE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 659 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 73 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 132 optimal weight: 0.0870 chunk 89 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 67 optimal weight: 10.0000 chunk 92 optimal weight: 0.6980 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 HIS ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.135693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.087790 restraints weight = 19266.311| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.67 r_work: 0.3048 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11352 Z= 0.127 Angle : 0.511 8.312 15444 Z= 0.268 Chirality : 0.037 0.202 1748 Planarity : 0.003 0.032 1914 Dihedral : 3.703 20.126 1468 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.52 % Allowed : 12.21 % Favored : 86.28 % 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 are not related in a simple way. whole: 2.25 (0.24), residues: 1318 helix: 1.93 (0.16), residues: 1040 sheet: None (None), residues: 0 loop : -0.08 (0.40), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 324 TYR 0.012 0.001 TYR C 305 PHE 0.014 0.001 PHE A 501 TRP 0.010 0.001 TRP C 271 HIS 0.005 0.001 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00299 (11350) covalent geometry : angle 0.51138 (15440) SS BOND : bond 0.00280 ( 2) SS BOND : angle 0.83387 ( 4) hydrogen bonds : bond 0.03987 ( 747) hydrogen bonds : angle 3.76975 ( 2220) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.378 Fit side-chains REVERT: A 86 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.8042 (t80) REVERT: A 166 ASP cc_start: 0.9216 (t70) cc_final: 0.8908 (t0) REVERT: A 322 MET cc_start: 0.8675 (tmm) cc_final: 0.8417 (tmm) REVERT: A 393 GLN cc_start: 0.8242 (mm110) cc_final: 0.7809 (tm-30) REVERT: A 434 TYR cc_start: 0.8264 (m-80) cc_final: 0.7972 (m-80) REVERT: A 597 LYS cc_start: 0.8517 (tppt) cc_final: 0.8097 (tppt) REVERT: A 602 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7937 (mt-10) REVERT: A 673 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8601 (mm-30) REVERT: C 86 PHE cc_start: 0.8400 (OUTLIER) cc_final: 0.7953 (t80) REVERT: C 166 ASP cc_start: 0.9173 (t70) cc_final: 0.8824 (t0) REVERT: C 434 TYR cc_start: 0.8204 (m-80) cc_final: 0.7845 (m-80) REVERT: C 597 LYS cc_start: 0.8686 (tptt) cc_final: 0.8395 (tppt) outliers start: 18 outliers final: 13 residues processed: 163 average time/residue: 0.0861 time to fit residues: 21.2089 Evaluate side-chains 155 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 634 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 82 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 76 optimal weight: 0.0470 chunk 12 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 5 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN A 416 HIS ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.136256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.088280 restraints weight = 19429.607| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.69 r_work: 0.3052 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 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 : 0.003 0.058 11352 Z= 0.120 Angle : 0.523 8.085 15444 Z= 0.274 Chirality : 0.038 0.213 1748 Planarity : 0.003 0.032 1914 Dihedral : 3.681 19.303 1468 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.19 % Allowed : 12.12 % Favored : 85.69 % 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 are not related in a simple way. whole: 2.26 (0.24), residues: 1318 helix: 1.93 (0.16), residues: 1040 sheet: None (None), residues: 0 loop : -0.06 (0.40), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 537 TYR 0.012 0.001 TYR A 415 PHE 0.031 0.001 PHE A 408 TRP 0.010 0.001 TRP C 271 HIS 0.005 0.001 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00278 (11350) covalent geometry : angle 0.52250 (15440) SS BOND : bond 0.00249 ( 2) SS BOND : angle 0.78206 ( 4) hydrogen bonds : bond 0.03841 ( 747) hydrogen bonds : angle 3.74519 ( 2220) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 0.431 Fit side-chains REVERT: A 86 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.7960 (t80) REVERT: A 98 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.7940 (mppt) REVERT: A 166 ASP cc_start: 0.9220 (t70) cc_final: 0.8910 (t0) REVERT: A 212 MET cc_start: 0.8913 (mmm) cc_final: 0.8242 (mtt) REVERT: A 322 MET cc_start: 0.8675 (tmm) cc_final: 0.8416 (tmm) REVERT: A 393 GLN cc_start: 0.8248 (mm110) cc_final: 0.7831 (tm-30) REVERT: A 408 PHE cc_start: 0.8212 (t80) cc_final: 0.7804 (t80) REVERT: A 434 TYR cc_start: 0.8252 (m-80) cc_final: 0.7957 (m-80) REVERT: A 597 LYS cc_start: 0.8434 (tppt) cc_final: 0.7993 (tppt) REVERT: A 602 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7930 (mt-10) REVERT: A 673 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8583 (mm-30) REVERT: C 86 PHE cc_start: 0.8370 (OUTLIER) cc_final: 0.7881 (t80) REVERT: C 119 GLU cc_start: 0.5266 (tp30) cc_final: 0.5051 (tp30) REVERT: C 166 ASP cc_start: 0.9143 (t70) cc_final: 0.8842 (t0) REVERT: C 310 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8218 (tp30) REVERT: C 434 TYR cc_start: 0.8212 (m-80) cc_final: 0.7885 (m-80) REVERT: C 597 LYS cc_start: 0.8660 (tptt) cc_final: 0.8384 (tppt) outliers start: 26 outliers final: 16 residues processed: 161 average time/residue: 0.0792 time to fit residues: 19.6079 Evaluate side-chains 163 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 546 MET Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 659 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 133 optimal weight: 20.0000 chunk 125 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 8 optimal weight: 0.0060 chunk 86 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 47 optimal weight: 0.0070 overall best weight: 1.4020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 HIS ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.134698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.086426 restraints weight = 19384.635| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.67 r_work: 0.3020 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11352 Z= 0.153 Angle : 0.540 9.244 15444 Z= 0.281 Chirality : 0.039 0.210 1748 Planarity : 0.003 0.032 1914 Dihedral : 3.663 19.302 1468 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.44 % Allowed : 12.63 % Favored : 84.93 % 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 are not related in a simple way. whole: 2.23 (0.24), residues: 1318 helix: 1.90 (0.16), residues: 1040 sheet: None (None), residues: 0 loop : -0.03 (0.41), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 537 TYR 0.013 0.001 TYR A 305 PHE 0.025 0.001 PHE A 408 TRP 0.012 0.001 TRP C 271 HIS 0.006 0.001 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00367 (11350) covalent geometry : angle 0.53962 (15440) SS BOND : bond 0.00265 ( 2) SS BOND : angle 0.84887 ( 4) hydrogen bonds : bond 0.04080 ( 747) hydrogen bonds : angle 3.82491 ( 2220) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.333 Fit side-chains REVERT: A 86 PHE cc_start: 0.8483 (OUTLIER) cc_final: 0.8143 (t80) REVERT: A 98 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7936 (mppt) REVERT: A 166 ASP cc_start: 0.9209 (t70) cc_final: 0.8885 (t0) REVERT: A 212 MET cc_start: 0.8818 (mmm) cc_final: 0.8375 (mtt) REVERT: A 320 ASP cc_start: 0.8753 (t70) cc_final: 0.8444 (t0) REVERT: A 322 MET cc_start: 0.8696 (tmm) cc_final: 0.8481 (tmm) REVERT: A 387 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8913 (pt0) REVERT: A 393 GLN cc_start: 0.8243 (mm110) cc_final: 0.7887 (tm-30) REVERT: A 408 PHE cc_start: 0.8387 (t80) cc_final: 0.7833 (t80) REVERT: A 434 TYR cc_start: 0.8211 (m-80) cc_final: 0.7914 (m-80) REVERT: A 597 LYS cc_start: 0.8480 (tppt) cc_final: 0.8191 (tppt) REVERT: A 602 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8111 (mt-10) REVERT: A 673 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8598 (mm-30) REVERT: C 86 PHE cc_start: 0.8492 (OUTLIER) cc_final: 0.8128 (t80) REVERT: C 166 ASP cc_start: 0.9155 (t70) cc_final: 0.8847 (t0) REVERT: C 434 TYR cc_start: 0.8221 (m-80) cc_final: 0.7881 (m-80) REVERT: C 597 LYS cc_start: 0.8656 (tptt) cc_final: 0.8410 (tppt) outliers start: 29 outliers final: 19 residues processed: 159 average time/residue: 0.0813 time to fit residues: 19.7866 Evaluate side-chains 161 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 138 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 196 ILE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 350 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 546 MET Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 659 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 7.9990 chunk 81 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 HIS ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.135333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.087310 restraints weight = 19332.200| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.68 r_work: 0.3033 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 11352 Z= 0.133 Angle : 0.533 8.233 15444 Z= 0.277 Chirality : 0.039 0.220 1748 Planarity : 0.003 0.032 1914 Dihedral : 3.649 19.272 1468 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.19 % Allowed : 13.38 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.24), residues: 1318 helix: 1.93 (0.16), residues: 1040 sheet: None (None), residues: 0 loop : -0.03 (0.41), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 537 TYR 0.012 0.001 TYR A 305 PHE 0.022 0.001 PHE A 408 TRP 0.011 0.001 TRP C 271 HIS 0.002 0.000 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00319 (11350) covalent geometry : angle 0.53327 (15440) SS BOND : bond 0.00257 ( 2) SS BOND : angle 0.80617 ( 4) hydrogen bonds : bond 0.03947 ( 747) hydrogen bonds : angle 3.80826 ( 2220) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.526 Fit side-chains revert: symmetry clash REVERT: A 86 PHE cc_start: 0.8461 (OUTLIER) cc_final: 0.8072 (t80) REVERT: A 98 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.7916 (mppt) REVERT: A 166 ASP cc_start: 0.9200 (t70) cc_final: 0.8883 (t0) REVERT: A 320 ASP cc_start: 0.8753 (t70) cc_final: 0.8446 (t0) REVERT: A 322 MET cc_start: 0.8696 (tmm) cc_final: 0.8482 (tmm) REVERT: A 387 GLU cc_start: 0.9119 (OUTLIER) cc_final: 0.8913 (pt0) REVERT: A 393 GLN cc_start: 0.8234 (mm110) cc_final: 0.7887 (tm-30) REVERT: A 408 PHE cc_start: 0.8415 (t80) cc_final: 0.7853 (t80) REVERT: A 434 TYR cc_start: 0.8185 (m-80) cc_final: 0.7893 (m-80) REVERT: A 597 LYS cc_start: 0.8447 (tppt) cc_final: 0.8144 (tppt) REVERT: A 602 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8097 (mt-10) REVERT: A 673 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8588 (mm-30) REVERT: C 86 PHE cc_start: 0.8473 (OUTLIER) cc_final: 0.8065 (t80) REVERT: C 166 ASP cc_start: 0.9155 (t70) cc_final: 0.8847 (t0) REVERT: C 310 GLU cc_start: 0.8460 (tm-30) cc_final: 0.8242 (tp30) REVERT: C 434 TYR cc_start: 0.8218 (m-80) cc_final: 0.7871 (m-80) REVERT: C 597 LYS cc_start: 0.8698 (tptt) cc_final: 0.8427 (tppt) outliers start: 26 outliers final: 16 residues processed: 158 average time/residue: 0.0897 time to fit residues: 21.3280 Evaluate side-chains 160 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 546 MET Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 659 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 4 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 71 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 HIS ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 585 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.136133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.087950 restraints weight = 19187.328| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.68 r_work: 0.3044 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 11352 Z= 0.123 Angle : 0.535 9.115 15444 Z= 0.276 Chirality : 0.038 0.221 1748 Planarity : 0.003 0.032 1914 Dihedral : 3.621 18.941 1468 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.85 % Allowed : 14.23 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.24), residues: 1318 helix: 1.95 (0.16), residues: 1040 sheet: None (None), residues: 0 loop : -0.04 (0.42), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 537 TYR 0.012 0.001 TYR A 415 PHE 0.021 0.001 PHE A 408 TRP 0.010 0.001 TRP C 271 HIS 0.003 0.000 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00290 (11350) covalent geometry : angle 0.53464 (15440) SS BOND : bond 0.00252 ( 2) SS BOND : angle 0.79621 ( 4) hydrogen bonds : bond 0.03807 ( 747) hydrogen bonds : angle 3.77144 ( 2220) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.349 Fit side-chains REVERT: A 86 PHE cc_start: 0.8456 (OUTLIER) cc_final: 0.8070 (t80) REVERT: A 98 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7923 (mppt) REVERT: A 166 ASP cc_start: 0.9194 (t70) cc_final: 0.8874 (t0) REVERT: A 212 MET cc_start: 0.8851 (mmm) cc_final: 0.8644 (mtp) REVERT: A 320 ASP cc_start: 0.8720 (t70) cc_final: 0.8404 (t0) REVERT: A 322 MET cc_start: 0.8692 (tmm) cc_final: 0.8482 (tmm) REVERT: A 387 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8908 (pt0) REVERT: A 393 GLN cc_start: 0.8227 (mm110) cc_final: 0.7887 (tm-30) REVERT: A 408 PHE cc_start: 0.8420 (t80) cc_final: 0.7911 (t80) REVERT: A 434 TYR cc_start: 0.8148 (m-80) cc_final: 0.7872 (m-80) REVERT: A 597 LYS cc_start: 0.8434 (tppt) cc_final: 0.8121 (tppt) REVERT: A 602 GLU cc_start: 0.8248 (mt-10) cc_final: 0.8047 (mt-10) REVERT: A 673 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8574 (mm-30) REVERT: C 86 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.7985 (t80) REVERT: C 119 GLU cc_start: 0.5277 (tp30) cc_final: 0.5046 (tp30) REVERT: C 166 ASP cc_start: 0.9205 (t70) cc_final: 0.8914 (t0) REVERT: C 310 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8227 (tp30) REVERT: C 434 TYR cc_start: 0.8207 (m-80) cc_final: 0.7830 (m-80) REVERT: C 597 LYS cc_start: 0.8682 (tptt) cc_final: 0.8398 (tppt) outliers start: 22 outliers final: 16 residues processed: 157 average time/residue: 0.0850 time to fit residues: 20.2094 Evaluate side-chains 158 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 387 GLU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 194 ILE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 542 ILE Chi-restraints excluded: chain C residue 546 MET Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 659 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 116 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 102 optimal weight: 0.0470 chunk 89 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 overall best weight: 0.5280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.137980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.089908 restraints weight = 19320.996| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.72 r_work: 0.3079 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 11352 Z= 0.110 Angle : 0.538 10.915 15444 Z= 0.273 Chirality : 0.038 0.228 1748 Planarity : 0.003 0.032 1914 Dihedral : 3.558 17.953 1468 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.43 % Allowed : 14.31 % Favored : 84.26 % 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 are not related in a simple way. whole: 2.40 (0.24), residues: 1318 helix: 2.06 (0.16), residues: 1028 sheet: None (None), residues: 0 loop : -0.05 (0.41), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 537 TYR 0.014 0.001 TYR A 415 PHE 0.020 0.001 PHE A 408 TRP 0.009 0.001 TRP C 464 HIS 0.007 0.001 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00252 (11350) covalent geometry : angle 0.53837 (15440) SS BOND : bond 0.00254 ( 2) SS BOND : angle 0.80314 ( 4) hydrogen bonds : bond 0.03441 ( 747) hydrogen bonds : angle 3.67200 ( 2220) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2636 Ramachandran restraints generated. 1318 Oldfield, 0 Emsley, 1318 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.300 Fit side-chains REVERT: A 86 PHE cc_start: 0.8365 (OUTLIER) cc_final: 0.7923 (t80) REVERT: A 98 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8161 (mptt) REVERT: A 166 ASP cc_start: 0.9184 (t70) cc_final: 0.8905 (t0) REVERT: A 212 MET cc_start: 0.8803 (mmm) cc_final: 0.8546 (mtp) REVERT: A 320 ASP cc_start: 0.8745 (t70) cc_final: 0.8462 (t0) REVERT: A 326 MET cc_start: 0.7814 (tmm) cc_final: 0.7422 (tmm) REVERT: A 393 GLN cc_start: 0.8209 (mm110) cc_final: 0.7881 (tm-30) REVERT: A 408 PHE cc_start: 0.8347 (t80) cc_final: 0.7795 (t80) REVERT: A 434 TYR cc_start: 0.8129 (m-80) cc_final: 0.7826 (m-80) REVERT: A 597 LYS cc_start: 0.8389 (tppt) cc_final: 0.8067 (tppt) REVERT: A 673 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8554 (mm-30) REVERT: C 83 PHE cc_start: 0.8037 (m-10) cc_final: 0.7597 (m-80) REVERT: C 86 PHE cc_start: 0.8387 (OUTLIER) cc_final: 0.7818 (t80) REVERT: C 119 GLU cc_start: 0.5243 (tp30) cc_final: 0.5013 (tp30) REVERT: C 166 ASP cc_start: 0.9203 (t70) cc_final: 0.8919 (t0) REVERT: C 310 GLU cc_start: 0.8443 (tm-30) cc_final: 0.8221 (tp30) REVERT: C 434 TYR cc_start: 0.8169 (m-80) cc_final: 0.7767 (m-80) REVERT: C 597 LYS cc_start: 0.8631 (tptt) cc_final: 0.8329 (tppt) outliers start: 17 outliers final: 13 residues processed: 163 average time/residue: 0.0854 time to fit residues: 21.3132 Evaluate side-chains 156 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 140 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 PHE Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 98 LYS Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 160 VAL Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 546 MET Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 659 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 7 optimal weight: 0.0670 chunk 128 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 127 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 267 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.137549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.089343 restraints weight = 19316.809| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.73 r_work: 0.3070 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 11352 Z= 0.120 Angle : 0.559 10.968 15444 Z= 0.283 Chirality : 0.039 0.240 1748 Planarity : 0.003 0.032 1914 Dihedral : 3.532 17.355 1468 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.52 % Allowed : 14.73 % Favored : 83.75 % 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 are not related in a simple way. whole: 2.39 (0.24), residues: 1318 helix: 2.05 (0.16), residues: 1028 sheet: None (None), residues: 0 loop : -0.05 (0.41), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 537 TYR 0.014 0.001 TYR C 532 PHE 0.020 0.001 PHE A 408 TRP 0.009 0.001 TRP C 271 HIS 0.003 0.001 HIS A 416 Details of bonding type rmsd covalent geometry : bond 0.00287 (11350) covalent geometry : angle 0.55848 (15440) SS BOND : bond 0.00242 ( 2) SS BOND : angle 0.84677 ( 4) hydrogen bonds : bond 0.03519 ( 747) hydrogen bonds : angle 3.67945 ( 2220) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2670.57 seconds wall clock time: 46 minutes 12.96 seconds (2772.96 seconds total)