Starting phenix.real_space_refine on Thu Jul 31 20:10:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7fhl_31586/07_2025/7fhl_31586.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fhl_31586/07_2025/7fhl_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7fhl_31586/07_2025/7fhl_31586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fhl_31586/07_2025/7fhl_31586.map" model { file = "/net/cci-nas-00/data/ceres_data/7fhl_31586/07_2025/7fhl_31586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fhl_31586/07_2025/7fhl_31586.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.71, per 1000 atoms: 0.61 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: 3.38 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.02 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: 3.19 Time building geometry restraints manager: 4.03 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: 0.05 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: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 27.900 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 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:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.650 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (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 TRP 0.011 0.001 TRP C 492 HIS 0.002 0.001 HIS A 134 PHE 0.016 0.001 PHE C 426 TYR 0.018 0.001 TYR C 434 ARG 0.004 0.000 ARG C 324 Details of bonding type rmsd hydrogen bonds : bond 0.19818 ( 747) hydrogen bonds : angle 6.05663 ( 2220) SS BOND : bond 0.00292 ( 2) SS BOND : angle 0.69990 ( 4) covalent geometry : bond 0.00245 (11350) covalent geometry : angle 0.54771 (15440) *********************** 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 : 1.677 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: 0.8701 (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: 0.2010 time to fit residues: 55.9026 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 : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 113 optimal weight: 6.9990 chunk 101 optimal weight: 20.0000 chunk 56 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 68 optimal weight: 20.0000 chunk 54 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- 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 = 0.3857 r_free = 0.3857 target = 0.133362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.084839 restraints weight = 19413.054| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.67 r_work: 0.2979 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 11352 Z= 0.251 Angle : 0.624 7.779 15444 Z= 0.331 Chirality : 0.041 0.177 1748 Planarity : 0.004 0.033 1914 Dihedral : 3.911 18.981 1468 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.18 % Allowed : 7.74 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.23), residues: 1318 helix: 1.49 (0.16), residues: 1036 sheet: None (None), residues: 0 loop : 0.14 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 271 HIS 0.009 0.002 HIS A 416 PHE 0.030 0.002 PHE C 408 TYR 0.024 0.002 TYR C 78 ARG 0.004 0.001 ARG A 279 Details of bonding type rmsd hydrogen bonds : bond 0.05782 ( 747) hydrogen bonds : angle 4.24962 ( 2220) SS BOND : bond 0.00264 ( 2) SS BOND : angle 0.60042 ( 4) covalent geometry : bond 0.00600 (11350) covalent geometry : angle 0.62354 (15440) *********************** 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 172 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 1.134 Fit side-chains REVERT: A 86 PHE cc_start: 0.8617 (OUTLIER) cc_final: 0.8380 (t80) REVERT: A 146 ILE cc_start: 0.9091 (mp) cc_final: 0.8768 (mm) REVERT: A 166 ASP cc_start: 0.9211 (t70) cc_final: 0.8900 (t0) REVERT: A 393 GLN cc_start: 0.8295 (mm110) cc_final: 0.7602 (tm-30) REVERT: A 434 TYR cc_start: 0.8300 (m-80) cc_final: 0.7980 (m-80) REVERT: A 597 LYS cc_start: 0.8679 (tptm) cc_final: 0.8405 (tppt) REVERT: C 146 ILE cc_start: 0.9101 (mp) cc_final: 0.8792 (mm) REVERT: C 166 ASP cc_start: 0.9228 (t70) cc_final: 0.8896 (t0) REVERT: C 434 TYR cc_start: 0.8197 (m-80) cc_final: 0.7912 (m-80) REVERT: C 539 LEU cc_start: 0.8605 (mm) cc_final: 0.8273 (mm) REVERT: C 597 LYS cc_start: 0.8771 (tptt) cc_final: 0.8564 (tppt) outliers start: 14 outliers final: 8 residues processed: 164 average time/residue: 0.1940 time to fit residues: 47.3719 Evaluate side-chains 144 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 135 time to evaluate : 1.127 ------------------------------------------------------------------------------- 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 54 optimal weight: 0.0020 chunk 131 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 121 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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** A 585 GLN ** C 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 = 0.3896 r_free = 0.3896 target = 0.136638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.089388 restraints weight = 19402.686| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.71 r_work: 0.3068 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11352 Z= 0.117 Angle : 0.508 7.674 15444 Z= 0.268 Chirality : 0.037 0.194 1748 Planarity : 0.003 0.032 1914 Dihedral : 3.793 20.052 1468 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.09 % Allowed : 9.51 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.24), residues: 1318 helix: 1.86 (0.16), residues: 1036 sheet: None (None), residues: 0 loop : 0.24 (0.41), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 271 HIS 0.006 0.001 HIS A 416 PHE 0.028 0.001 PHE C 408 TYR 0.014 0.001 TYR C 78 ARG 0.002 0.000 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.04341 ( 747) hydrogen bonds : angle 3.87580 ( 2220) SS BOND : bond 0.00294 ( 2) SS BOND : angle 0.75151 ( 4) covalent geometry : bond 0.00251 (11350) covalent geometry : angle 0.50787 (15440) *********************** 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 170 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 1.278 Fit side-chains REVERT: A 142 GLU cc_start: 0.8309 (tm-30) cc_final: 0.8087 (tm-30) REVERT: A 162 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9116 (mp) REVERT: A 166 ASP cc_start: 0.9164 (t70) cc_final: 0.8878 (t0) REVERT: A 294 TYR cc_start: 0.8911 (m-10) cc_final: 0.8353 (m-10) REVERT: A 322 MET cc_start: 0.8690 (tmm) cc_final: 0.8457 (tmm) REVERT: A 393 GLN cc_start: 0.8259 (mm110) cc_final: 0.7667 (tm-30) REVERT: A 434 TYR cc_start: 0.8265 (m-80) cc_final: 0.7930 (m-80) REVERT: A 597 LYS cc_start: 0.8591 (tptm) cc_final: 0.8293 (tppt) REVERT: A 673 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8594 (mm-30) REVERT: C 146 ILE cc_start: 0.9098 (mp) cc_final: 0.8753 (mm) REVERT: C 166 ASP cc_start: 0.9176 (t70) cc_final: 0.8846 (t0) REVERT: C 408 PHE cc_start: 0.8281 (t80) cc_final: 0.7833 (t80) REVERT: C 434 TYR cc_start: 0.8177 (m-80) cc_final: 0.7871 (m-80) REVERT: C 597 LYS cc_start: 0.8676 (tptt) cc_final: 0.8408 (tppt) REVERT: C 678 GLU cc_start: 0.8860 (tm-30) cc_final: 0.8501 (tm-30) outliers start: 13 outliers final: 8 residues processed: 164 average time/residue: 0.1989 time to fit residues: 49.2228 Evaluate side-chains 158 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 149 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 LYS Chi-restraints excluded: chain A residue 162 ILE 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 220 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 502 LEU Chi-restraints excluded: chain C residue 636 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 51 optimal weight: 0.2980 chunk 111 optimal weight: 0.1980 chunk 82 optimal weight: 0.0570 chunk 69 optimal weight: 3.9990 chunk 117 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 overall best weight: 0.4098 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.138220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.091003 restraints weight = 19125.684| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.69 r_work: 0.3099 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 11352 Z= 0.108 Angle : 0.493 7.448 15444 Z= 0.258 Chirality : 0.037 0.210 1748 Planarity : 0.003 0.032 1914 Dihedral : 3.643 18.861 1468 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.52 % Allowed : 10.77 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.41 (0.24), residues: 1318 helix: 2.02 (0.16), residues: 1026 sheet: None (None), residues: 0 loop : 0.14 (0.40), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 632 HIS 0.008 0.001 HIS A 416 PHE 0.033 0.001 PHE A 408 TYR 0.013 0.001 TYR C 491 ARG 0.002 0.000 ARG A 324 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 747) hydrogen bonds : angle 3.69641 ( 2220) SS BOND : bond 0.00257 ( 2) SS BOND : angle 0.83165 ( 4) covalent geometry : bond 0.00232 (11350) covalent geometry : angle 0.49337 (15440) *********************** 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 179 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 1.097 Fit side-chains REVERT: A 98 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8096 (mptt) REVERT: A 160 VAL cc_start: 0.9014 (OUTLIER) cc_final: 0.8803 (p) REVERT: A 166 ASP cc_start: 0.9214 (t70) cc_final: 0.8977 (t0) REVERT: A 294 TYR cc_start: 0.8818 (m-10) cc_final: 0.8221 (m-10) REVERT: A 322 MET cc_start: 0.8683 (tmm) cc_final: 0.8436 (tmm) REVERT: A 393 GLN cc_start: 0.8273 (mm110) cc_final: 0.7801 (tm-30) REVERT: A 434 TYR cc_start: 0.8243 (m-80) cc_final: 0.7946 (m-80) REVERT: A 597 LYS cc_start: 0.8550 (tptm) cc_final: 0.8232 (tppt) REVERT: A 673 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8584 (mm-30) REVERT: C 98 LYS cc_start: 0.8502 (pttp) cc_final: 0.8217 (mptt) REVERT: C 166 ASP cc_start: 0.9165 (t70) cc_final: 0.8863 (t0) REVERT: C 310 GLU cc_start: 0.8559 (tp30) cc_final: 0.8305 (tp30) REVERT: C 434 TYR cc_start: 0.8178 (m-80) cc_final: 0.7870 (m-80) REVERT: C 597 LYS cc_start: 0.8624 (tptt) cc_final: 0.8343 (tppt) outliers start: 18 outliers final: 10 residues processed: 170 average time/residue: 0.1880 time to fit residues: 48.4652 Evaluate side-chains 159 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 162 ILE Chi-restraints excluded: chain A residue 355 THR 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 220 LEU Chi-restraints excluded: chain C residue 328 GLU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 502 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 72 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 75 optimal weight: 0.0470 chunk 58 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 chunk 74 optimal weight: 0.0970 chunk 82 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 56 optimal weight: 0.1980 overall best weight: 0.4478 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.138606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.091306 restraints weight = 19169.010| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.69 r_work: 0.3102 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11352 Z= 0.109 Angle : 0.501 8.262 15444 Z= 0.260 Chirality : 0.037 0.213 1748 Planarity : 0.003 0.031 1914 Dihedral : 3.589 18.307 1468 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.60 % Allowed : 12.54 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.24), residues: 1318 helix: 2.01 (0.16), residues: 1038 sheet: None (None), residues: 0 loop : 0.14 (0.42), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 271 HIS 0.015 0.002 HIS A 416 PHE 0.014 0.001 PHE A 501 TYR 0.011 0.001 TYR C 491 ARG 0.002 0.000 ARG A 145 Details of bonding type rmsd hydrogen bonds : bond 0.03500 ( 747) hydrogen bonds : angle 3.63776 ( 2220) SS BOND : bond 0.00225 ( 2) SS BOND : angle 0.77048 ( 4) covalent geometry : bond 0.00239 (11350) covalent geometry : angle 0.50088 (15440) *********************** 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 175 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 1.233 Fit side-chains REVERT: A 98 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8083 (mptt) REVERT: A 160 VAL cc_start: 0.8995 (OUTLIER) cc_final: 0.8784 (p) REVERT: A 162 ILE cc_start: 0.9298 (OUTLIER) cc_final: 0.9082 (mp) REVERT: A 166 ASP cc_start: 0.9218 (t70) cc_final: 0.8975 (t0) REVERT: A 212 MET cc_start: 0.8857 (mmm) cc_final: 0.8234 (mtt) REVERT: A 294 TYR cc_start: 0.8827 (m-10) cc_final: 0.8286 (m-10) REVERT: A 320 ASP cc_start: 0.8666 (t70) cc_final: 0.8322 (t0) REVERT: A 322 MET cc_start: 0.8684 (tmm) cc_final: 0.8421 (tmm) REVERT: A 393 GLN cc_start: 0.8257 (mm110) cc_final: 0.7824 (tm-30) REVERT: A 434 TYR cc_start: 0.8240 (m-80) cc_final: 0.7925 (m-80) REVERT: A 597 LYS cc_start: 0.8521 (tptm) cc_final: 0.8199 (tppt) REVERT: A 673 GLU cc_start: 0.8877 (mm-30) cc_final: 0.8576 (mm-30) REVERT: C 98 LYS cc_start: 0.8454 (pttp) cc_final: 0.8203 (mptt) REVERT: C 166 ASP cc_start: 0.9161 (t70) cc_final: 0.8858 (t0) REVERT: C 434 TYR cc_start: 0.8181 (m-80) cc_final: 0.7850 (m-80) REVERT: C 597 LYS cc_start: 0.8617 (tptt) cc_final: 0.8333 (tppt) outliers start: 19 outliers final: 11 residues processed: 166 average time/residue: 0.1919 time to fit residues: 48.5855 Evaluate side-chains 159 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 1.244 ------------------------------------------------------------------------------- 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 162 ILE 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 196 ILE Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 634 VAL Chi-restraints excluded: chain C residue 659 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 41 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 3 optimal weight: 0.0670 chunk 2 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.138043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.090547 restraints weight = 19322.627| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.70 r_work: 0.3095 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11352 Z= 0.110 Angle : 0.498 8.517 15444 Z= 0.258 Chirality : 0.037 0.216 1748 Planarity : 0.003 0.032 1914 Dihedral : 3.537 17.023 1468 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.94 % Allowed : 12.96 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.42 (0.24), residues: 1318 helix: 2.01 (0.16), residues: 1038 sheet: None (None), residues: 0 loop : 0.14 (0.42), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 271 HIS 0.004 0.001 HIS A 416 PHE 0.032 0.001 PHE A 408 TYR 0.017 0.001 TYR A 491 ARG 0.002 0.000 ARG C 324 Details of bonding type rmsd hydrogen bonds : bond 0.03486 ( 747) hydrogen bonds : angle 3.63750 ( 2220) SS BOND : bond 0.00244 ( 2) SS BOND : angle 0.79096 ( 4) covalent geometry : bond 0.00252 (11350) covalent geometry : angle 0.49836 (15440) *********************** 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: 23 poor density : 152 time to evaluate : 1.158 Fit side-chains REVERT: A 86 PHE cc_start: 0.8362 (OUTLIER) cc_final: 0.7822 (t80) REVERT: A 98 LYS cc_start: 0.8441 (OUTLIER) cc_final: 0.8035 (mptt) REVERT: A 162 ILE cc_start: 0.9295 (OUTLIER) cc_final: 0.9075 (mp) REVERT: A 166 ASP cc_start: 0.9227 (t70) cc_final: 0.8977 (t0) REVERT: A 212 MET cc_start: 0.8727 (mmm) cc_final: 0.8288 (mtt) REVERT: A 320 ASP cc_start: 0.8662 (t70) cc_final: 0.8323 (t0) REVERT: A 322 MET cc_start: 0.8664 (tmm) cc_final: 0.8414 (tmm) REVERT: A 393 GLN cc_start: 0.8242 (mm110) cc_final: 0.7819 (tm-30) REVERT: A 408 PHE cc_start: 0.8264 (t80) cc_final: 0.7813 (t80) REVERT: A 414 ILE cc_start: 0.8710 (mm) cc_final: 0.8510 (mm) REVERT: A 434 TYR cc_start: 0.8205 (m-80) cc_final: 0.7902 (m-80) REVERT: A 597 LYS cc_start: 0.8509 (tptm) cc_final: 0.8116 (tppt) REVERT: A 673 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8574 (mm-30) REVERT: C 98 LYS cc_start: 0.8467 (pttp) cc_final: 0.8167 (mptt) REVERT: C 166 ASP cc_start: 0.9158 (t70) cc_final: 0.8861 (t0) REVERT: C 434 TYR cc_start: 0.8189 (m-80) cc_final: 0.7844 (m-80) REVERT: C 597 LYS cc_start: 0.8618 (tptt) cc_final: 0.8322 (tppt) outliers start: 23 outliers final: 13 residues processed: 162 average time/residue: 0.1869 time to fit residues: 46.2628 Evaluate side-chains 161 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 162 ILE 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 18 optimal weight: 2.9990 chunk 133 optimal weight: 20.0000 chunk 66 optimal weight: 20.0000 chunk 74 optimal weight: 0.6980 chunk 130 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 8.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.136717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.088877 restraints weight = 19389.400| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.68 r_work: 0.3058 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11352 Z= 0.131 Angle : 0.512 9.138 15444 Z= 0.265 Chirality : 0.038 0.219 1748 Planarity : 0.003 0.032 1914 Dihedral : 3.535 16.801 1468 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.94 % Allowed : 13.55 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.24), residues: 1318 helix: 1.99 (0.16), residues: 1040 sheet: None (None), residues: 0 loop : -0.01 (0.41), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 271 HIS 0.006 0.001 HIS A 416 PHE 0.025 0.001 PHE A 408 TYR 0.023 0.001 TYR A 491 ARG 0.002 0.000 ARG C 324 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 747) hydrogen bonds : angle 3.71085 ( 2220) SS BOND : bond 0.00250 ( 2) SS BOND : angle 0.80948 ( 4) covalent geometry : bond 0.00314 (11350) covalent geometry : angle 0.51164 (15440) *********************** 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 171 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 1.135 Fit side-chains REVERT: A 86 PHE cc_start: 0.8361 (OUTLIER) cc_final: 0.7942 (t80) REVERT: A 98 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8073 (mptt) REVERT: A 162 ILE cc_start: 0.9293 (OUTLIER) cc_final: 0.9070 (mp) REVERT: A 166 ASP cc_start: 0.9236 (t70) cc_final: 0.8980 (t0) REVERT: A 212 MET cc_start: 0.8750 (mmm) cc_final: 0.8373 (mtt) REVERT: A 320 ASP cc_start: 0.8726 (t70) cc_final: 0.8416 (t0) REVERT: A 322 MET cc_start: 0.8694 (tmm) cc_final: 0.8466 (tmm) REVERT: A 393 GLN cc_start: 0.8211 (mm110) cc_final: 0.7842 (tm-30) REVERT: A 408 PHE cc_start: 0.8335 (t80) cc_final: 0.7823 (t80) REVERT: A 434 TYR cc_start: 0.8207 (m-80) cc_final: 0.7915 (m-80) REVERT: A 597 LYS cc_start: 0.8531 (tptm) cc_final: 0.8164 (tppt) REVERT: A 673 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8590 (mm-30) REVERT: C 86 PHE cc_start: 0.8394 (OUTLIER) cc_final: 0.7861 (t80) REVERT: C 98 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.8141 (mptt) REVERT: C 166 ASP cc_start: 0.9156 (t70) cc_final: 0.8859 (t0) REVERT: C 434 TYR cc_start: 0.8214 (m-80) cc_final: 0.7848 (m-80) REVERT: C 597 LYS cc_start: 0.8668 (tptt) cc_final: 0.8385 (tppt) outliers start: 23 outliers final: 15 residues processed: 158 average time/residue: 0.1793 time to fit residues: 43.0955 Evaluate side-chains 163 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 1.169 ------------------------------------------------------------------------------- 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 162 ILE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 355 THR 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 196 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 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 38 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 416 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.133844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.085288 restraints weight = 19465.394| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.67 r_work: 0.3003 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 11352 Z= 0.211 Angle : 0.577 8.790 15444 Z= 0.301 Chirality : 0.040 0.202 1748 Planarity : 0.003 0.033 1914 Dihedral : 3.672 17.800 1468 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.10 % Allowed : 13.55 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.19 (0.24), residues: 1318 helix: 1.86 (0.16), residues: 1040 sheet: None (None), residues: 0 loop : 0.03 (0.42), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 271 HIS 0.004 0.001 HIS A 416 PHE 0.021 0.001 PHE A 408 TYR 0.018 0.002 TYR A 491 ARG 0.003 0.000 ARG A 203 Details of bonding type rmsd hydrogen bonds : bond 0.04461 ( 747) hydrogen bonds : angle 3.90150 ( 2220) SS BOND : bond 0.00262 ( 2) SS BOND : angle 0.86392 ( 4) covalent geometry : bond 0.00511 (11350) covalent geometry : angle 0.57719 (15440) *********************** 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 168 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 1.232 Fit side-chains REVERT: A 86 PHE cc_start: 0.8548 (OUTLIER) cc_final: 0.8262 (t80) REVERT: A 98 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.7916 (mppt) REVERT: A 162 ILE cc_start: 0.9312 (mt) cc_final: 0.9089 (mp) REVERT: A 166 ASP cc_start: 0.9253 (t70) cc_final: 0.8946 (t0) REVERT: A 212 MET cc_start: 0.8809 (mmm) cc_final: 0.8508 (mtt) REVERT: A 320 ASP cc_start: 0.8777 (t70) cc_final: 0.8462 (t0) REVERT: A 322 MET cc_start: 0.8733 (tmm) cc_final: 0.8511 (tmm) REVERT: A 393 GLN cc_start: 0.8214 (mm110) cc_final: 0.7806 (tm-30) REVERT: A 408 PHE cc_start: 0.8456 (t80) cc_final: 0.7833 (t80) REVERT: A 414 ILE cc_start: 0.8766 (mm) cc_final: 0.8545 (mm) REVERT: A 434 TYR cc_start: 0.8211 (m-80) cc_final: 0.7911 (m-80) REVERT: A 597 LYS cc_start: 0.8603 (tptm) cc_final: 0.8246 (tppt) REVERT: A 673 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8633 (mm-30) REVERT: C 86 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.8236 (t80) REVERT: C 166 ASP cc_start: 0.9177 (t70) cc_final: 0.8829 (t0) REVERT: C 434 TYR cc_start: 0.8290 (m-80) cc_final: 0.7945 (m-80) REVERT: C 597 LYS cc_start: 0.8683 (tptt) cc_final: 0.8433 (tppt) outliers start: 25 outliers final: 18 residues processed: 156 average time/residue: 0.1874 time to fit residues: 44.7088 Evaluate side-chains 160 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 350 LEU Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 415 TYR Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 542 ILE Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain A residue 659 THR Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 154 LEU 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 636 MET 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 57 optimal weight: 0.1980 chunk 87 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 117 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 100 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.136189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.087874 restraints weight = 19244.019| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.69 r_work: 0.3044 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11352 Z= 0.127 Angle : 0.538 9.407 15444 Z= 0.277 Chirality : 0.038 0.216 1748 Planarity : 0.003 0.032 1914 Dihedral : 3.610 18.940 1468 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.60 % Allowed : 14.39 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.31 (0.24), residues: 1318 helix: 1.95 (0.16), residues: 1040 sheet: None (None), residues: 0 loop : 0.00 (0.42), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 271 HIS 0.006 0.001 HIS A 416 PHE 0.021 0.001 PHE A 408 TYR 0.015 0.001 TYR A 491 ARG 0.003 0.000 ARG C 200 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 747) hydrogen bonds : angle 3.77330 ( 2220) SS BOND : bond 0.00266 ( 2) SS BOND : angle 0.74492 ( 4) covalent geometry : bond 0.00301 (11350) covalent geometry : angle 0.53827 (15440) *********************** 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 164 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 1.262 Fit side-chains REVERT: A 86 PHE cc_start: 0.8437 (OUTLIER) cc_final: 0.8090 (t80) REVERT: A 98 LYS cc_start: 0.8505 (OUTLIER) cc_final: 0.7861 (mppt) REVERT: A 162 ILE cc_start: 0.9293 (mt) cc_final: 0.9069 (mp) REVERT: A 166 ASP cc_start: 0.9215 (t70) cc_final: 0.8965 (t0) REVERT: A 212 MET cc_start: 0.8833 (mmm) cc_final: 0.8394 (mtt) REVERT: A 320 ASP cc_start: 0.8714 (t70) cc_final: 0.8414 (t0) REVERT: A 322 MET cc_start: 0.8701 (tmm) cc_final: 0.8484 (tmm) REVERT: A 393 GLN cc_start: 0.8220 (mm110) cc_final: 0.7895 (tm-30) REVERT: A 408 PHE cc_start: 0.8412 (t80) cc_final: 0.7752 (t80) REVERT: A 414 ILE cc_start: 0.8685 (mm) cc_final: 0.8436 (mm) REVERT: A 434 TYR cc_start: 0.8135 (m-80) cc_final: 0.7862 (m-80) REVERT: A 597 LYS cc_start: 0.8513 (tptm) cc_final: 0.8146 (tppt) REVERT: A 673 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8579 (mm-30) REVERT: C 86 PHE cc_start: 0.8475 (OUTLIER) cc_final: 0.8035 (t80) REVERT: C 166 ASP cc_start: 0.9156 (t70) cc_final: 0.8859 (t0) REVERT: C 434 TYR cc_start: 0.8190 (m-80) cc_final: 0.7801 (m-80) REVERT: C 597 LYS cc_start: 0.8664 (tptt) cc_final: 0.8391 (tppt) outliers start: 19 outliers final: 13 residues processed: 155 average time/residue: 0.1889 time to fit residues: 44.7809 Evaluate side-chains 151 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 355 THR Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain A residue 628 VAL Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 154 LEU 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 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 29 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 37 optimal weight: 0.0670 chunk 53 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 35 optimal weight: 6.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- 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** 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 = 0.137187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.089082 restraints weight = 19150.250| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.69 r_work: 0.3063 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11352 Z= 0.115 Angle : 0.527 8.438 15444 Z= 0.271 Chirality : 0.038 0.227 1748 Planarity : 0.003 0.032 1914 Dihedral : 3.564 19.344 1468 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.24), residues: 1318 helix: 1.98 (0.16), residues: 1040 sheet: None (None), residues: 0 loop : -0.05 (0.42), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 271 HIS 0.008 0.001 HIS A 416 PHE 0.020 0.001 PHE A 408 TYR 0.019 0.001 TYR A 415 ARG 0.002 0.000 ARG C 324 Details of bonding type rmsd hydrogen bonds : bond 0.03663 ( 747) hydrogen bonds : angle 3.71456 ( 2220) SS BOND : bond 0.00256 ( 2) SS BOND : angle 0.75671 ( 4) covalent geometry : bond 0.00263 (11350) covalent geometry : angle 0.52716 (15440) ********************** 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 157 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 1.253 Fit side-chains REVERT: A 86 PHE cc_start: 0.8406 (OUTLIER) cc_final: 0.7967 (t80) REVERT: A 98 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8103 (mptt) REVERT: A 119 GLU cc_start: 0.5212 (tp30) cc_final: 0.4989 (tp30) REVERT: A 162 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.9059 (mp) REVERT: A 166 ASP cc_start: 0.9210 (t70) cc_final: 0.8957 (t0) REVERT: A 212 MET cc_start: 0.8807 (mmm) cc_final: 0.8312 (mtt) REVERT: A 320 ASP cc_start: 0.8708 (t70) cc_final: 0.8408 (t0) REVERT: A 322 MET cc_start: 0.8675 (tmm) cc_final: 0.8465 (tmm) REVERT: A 393 GLN cc_start: 0.8188 (mm110) cc_final: 0.7866 (tm-30) REVERT: A 434 TYR cc_start: 0.8098 (m-80) cc_final: 0.7807 (m-80) REVERT: A 492 TRP cc_start: 0.8618 (t-100) cc_final: 0.8392 (t-100) REVERT: A 597 LYS cc_start: 0.8498 (tptm) cc_final: 0.8127 (tppt) REVERT: A 673 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8556 (mm-30) REVERT: C 86 PHE cc_start: 0.8429 (OUTLIER) cc_final: 0.7888 (t80) REVERT: C 166 ASP cc_start: 0.9215 (t70) cc_final: 0.8930 (t0) REVERT: C 434 TYR cc_start: 0.8165 (m-80) cc_final: 0.7780 (m-80) REVERT: C 597 LYS cc_start: 0.8640 (tptt) cc_final: 0.8349 (tppt) outliers start: 17 outliers final: 13 residues processed: 149 average time/residue: 0.2141 time to fit residues: 48.6683 Evaluate side-chains 153 residues out of total 1192 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 136 time to evaluate : 1.108 ------------------------------------------------------------------------------- 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 162 ILE Chi-restraints excluded: chain A residue 355 THR Chi-restraints excluded: chain A residue 416 HIS Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 546 MET Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 154 LEU 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 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 50 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 71 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.137097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.088782 restraints weight = 19156.025| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.69 r_work: 0.3059 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 11352 Z= 0.122 Angle : 0.536 9.333 15444 Z= 0.274 Chirality : 0.038 0.220 1748 Planarity : 0.003 0.032 1914 Dihedral : 3.551 20.115 1468 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.60 % Allowed : 14.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.33 (0.24), residues: 1318 helix: 1.99 (0.16), residues: 1038 sheet: None (None), residues: 0 loop : -0.04 (0.41), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 271 HIS 0.006 0.001 HIS A 416 PHE 0.015 0.001 PHE A 426 TYR 0.017 0.001 TYR A 415 ARG 0.002 0.000 ARG C 324 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 747) hydrogen bonds : angle 3.70476 ( 2220) SS BOND : bond 0.00254 ( 2) SS BOND : angle 0.79262 ( 4) covalent geometry : bond 0.00286 (11350) covalent geometry : angle 0.53561 (15440) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5875.16 seconds wall clock time: 102 minutes 36.05 seconds (6156.05 seconds total)