Starting phenix.real_space_refine on Sat Jul 4 02:14:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7fho_31588/07_2026/7fho_31588.cif Found real_map, /net/cci-nas-00/data/ceres_data/7fho_31588/07_2026/7fho_31588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7fho_31588/07_2026/7fho_31588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7fho_31588/07_2026/7fho_31588.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7fho_31588/07_2026/7fho_31588.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7fho_31588/07_2026/7fho_31588.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7fho_31588/07_2026/7fho_31588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7fho_31588/07_2026/7fho_31588.map" } resolution = 2.8 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= 0.003 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 8728 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 6 9.91 5 S 44 5.16 5 C 7102 2.51 5 N 1630 2.21 5 O 1866 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10648 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5321 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 626} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 5321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5321 Classifications: {'peptide': 647} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 626} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.70, per 1000 atoms: 0.25 Number of scatterers: 10648 At special positions: 0 Unit cell: (108.498, 120.666, 100.386, 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 6 19.99 S 44 16.00 O 1866 8.00 N 1630 7.00 C 7102 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: 0.87 Conformation dependent library (CDL) restraints added in 358.9 milliseconds 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2472 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 2 sheets defined 79.3% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 29 through 43 removed outlier: 3.594A pdb=" N ASP A 43 " --> pdb=" O ASP A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 52 removed outlier: 3.661A pdb=" N ILE A 51 " --> pdb=" O PRO A 48 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A 52 " --> pdb=" O VAL A 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 48 through 52' Processing helix chain 'A' and resid 57 through 69 removed outlier: 3.738A pdb=" N TYR A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 83 Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.646A pdb=" N GLU A 88 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 95 removed outlier: 3.589A pdb=" N GLU A 94 " --> pdb=" O PRO A 90 " (cutoff:3.500A) removed outlier: 3.938A 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 146 through 149 Processing helix chain 'A' and resid 150 through 174 Processing helix chain 'A' and resid 186 through 198 Processing helix chain 'A' and resid 199 through 238 removed outlier: 4.580A pdb=" N GLY A 214 " --> pdb=" O SER A 210 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N THR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 removed outlier: 3.843A pdb=" N THR A 263 " --> pdb=" O PHE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 4.146A pdb=" N TRP A 271 " --> pdb=" O ASN A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 281 through 295 removed outlier: 3.665A pdb=" N PHE A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 335 removed outlier: 3.535A pdb=" N ALA A 313 " --> pdb=" O LYS A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 355 removed outlier: 3.770A pdb=" N PHE A 351 " --> pdb=" O CYS A 347 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 376 removed outlier: 3.703A pdb=" N LEU A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 396 removed outlier: 3.931A pdb=" N ALA A 396 " --> pdb=" O CYS A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.679A pdb=" N GLU A 409 " --> pdb=" O SER A 406 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N HIS A 410 " --> pdb=" O LEU A 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 406 through 410' Processing helix chain 'A' and resid 417 through 429 removed outlier: 3.760A pdb=" N GLN A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 453 removed outlier: 3.776A pdb=" N TYR A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 487 removed outlier: 4.183A pdb=" N TRP A 464 " --> pdb=" O ALA A 460 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TRP A 473 " --> pdb=" O PHE A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 494 removed outlier: 4.623A pdb=" N GLU A 494 " --> pdb=" O ASN A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 517 removed outlier: 3.780A pdb=" N ARG A 498 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 510 " --> pdb=" O VAL A 506 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE A 515 " --> pdb=" O GLU A 511 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 517 " --> pdb=" O ALA A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 542 removed outlier: 3.566A pdb=" N ILE A 542 " --> pdb=" O MET A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 547 Processing helix chain 'A' and resid 548 through 587 removed outlier: 4.244A pdb=" N PHE A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 562 " --> pdb=" O PHE A 558 " (cutoff:3.500A) Proline residue: A 563 - end of helix Proline residue: A 567 - end of helix Processing helix chain 'A' and resid 601 through 606 Processing helix chain 'A' and resid 615 through 628 removed outlier: 3.668A pdb=" N PHE A 624 " --> pdb=" O MET A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 644 removed outlier: 3.876A pdb=" N MET A 636 " --> pdb=" O TRP A 632 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP A 641 " --> pdb=" O GLU A 637 " (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: 4.195A pdb=" N PHE A 652 " --> pdb=" O SER A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 684 removed outlier: 3.937A pdb=" N GLU A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU A 683 " --> pdb=" O LEU A 679 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 684 " --> pdb=" O ASP A 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 43 removed outlier: 3.599A pdb=" N ASP C 43 " --> pdb=" O ASP C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 52 removed outlier: 3.630A pdb=" N ILE C 51 " --> pdb=" O PRO C 48 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU C 52 " --> pdb=" O VAL C 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 48 through 52' Processing helix chain 'C' and resid 57 through 69 removed outlier: 3.734A pdb=" N TYR C 63 " --> pdb=" O GLU C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 70 through 83 Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.634A pdb=" N GLU C 88 " --> pdb=" O ASN C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 95 removed outlier: 3.577A pdb=" N GLU C 94 " --> pdb=" O PRO C 90 " (cutoff:3.500A) removed outlier: 3.878A 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 146 through 149 Processing helix chain 'C' and resid 150 through 174 Processing helix chain 'C' and resid 186 through 198 Processing helix chain 'C' and resid 199 through 238 removed outlier: 4.779A pdb=" N GLY C 214 " --> pdb=" O SER C 210 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N THR C 215 " --> pdb=" O GLY C 211 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU C 222 " --> pdb=" O ASN C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 Processing helix chain 'C' and resid 266 through 271 removed outlier: 4.199A pdb=" N TRP C 271 " --> pdb=" O ASN C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 278 Processing helix chain 'C' and resid 280 through 335 removed outlier: 4.412A pdb=" N PHE C 284 " --> pdb=" O TRP C 280 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 355 removed outlier: 3.613A pdb=" N CYS C 347 " --> pdb=" O ASP C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 376 removed outlier: 3.513A pdb=" N PHE C 368 " --> pdb=" O SER C 364 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY C 369 " --> pdb=" O LYS C 365 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP C 376 " --> pdb=" O PHE C 372 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 390 through 396 removed outlier: 3.546A pdb=" N ALA C 394 " --> pdb=" O ASP C 390 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA C 396 " --> pdb=" O CYS C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.710A pdb=" N GLU C 409 " --> pdb=" O SER C 406 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N HIS C 410 " --> pdb=" O LEU C 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 406 through 410' Processing helix chain 'C' and resid 417 through 429 Processing helix chain 'C' and resid 430 through 453 removed outlier: 3.756A pdb=" N TYR C 434 " --> pdb=" O PRO C 430 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 453 " --> pdb=" O VAL C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 460 through 487 removed outlier: 4.484A pdb=" N TRP C 464 " --> pdb=" O ALA C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 494 removed outlier: 4.669A pdb=" N GLU C 494 " --> pdb=" O ASN C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 516 removed outlier: 3.714A pdb=" N ARG C 498 " --> pdb=" O GLU C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 526 through 541 Processing helix chain 'C' and resid 542 through 547 Processing helix chain 'C' and resid 548 through 565 removed outlier: 3.700A pdb=" N PHE C 554 " --> pdb=" O ARG C 550 " (cutoff:3.500A) Proline residue: C 563 - end of helix Processing helix chain 'C' and resid 565 through 587 Processing helix chain 'C' and resid 601 through 606 Processing helix chain 'C' and resid 615 through 628 removed outlier: 3.562A pdb=" N PHE C 624 " --> pdb=" O MET C 620 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 644 removed outlier: 3.890A pdb=" N MET C 636 " --> pdb=" O TRP C 632 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS C 640 " --> pdb=" O MET C 636 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP C 641 " --> pdb=" O GLU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 647 No H-bonds generated for 'chain 'C' and resid 645 through 647' Processing helix chain 'C' and resid 648 through 659 removed outlier: 4.119A pdb=" N PHE C 652 " --> pdb=" O SER C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 683 Processing sheet with id=AA1, first strand: chain 'A' and resid 341 through 342 removed outlier: 3.532A pdb=" N ILE A 383 " --> pdb=" O ILE A 342 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 341 through 342 686 hydrogen bonds defined for protein. 2025 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: 1.53 Time building geometry restraints manager: 1.12 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: 3192 1.34 - 1.46: 2416 1.46 - 1.58: 5254 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 10934 Sorted by residual: bond pdb=" C ALA A 187 " pdb=" N PRO A 188 " ideal model delta sigma weight residual 1.334 1.365 -0.031 1.51e-02 4.39e+03 4.08e+00 bond pdb=" C ALA C 187 " pdb=" N PRO C 188 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.38e-02 5.25e+03 3.48e+00 bond pdb=" CG GLU C 352 " pdb=" CD GLU C 352 " ideal model delta sigma weight residual 1.516 1.486 0.030 2.50e-02 1.60e+03 1.41e+00 bond pdb=" C PHE A 137 " pdb=" N PRO A 138 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.25e+00 bond pdb=" C PHE C 137 " pdb=" N PRO C 138 " ideal model delta sigma weight residual 1.334 1.360 -0.026 2.34e-02 1.83e+03 1.24e+00 ... (remaining 10929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 14600 1.76 - 3.51: 233 3.51 - 5.27: 34 5.27 - 7.02: 5 7.02 - 8.78: 4 Bond angle restraints: 14876 Sorted by residual: angle pdb=" C GLU C 111 " pdb=" N LEU C 112 " pdb=" CA LEU C 112 " ideal model delta sigma weight residual 122.21 113.43 8.78 2.87e+00 1.21e-01 9.35e+00 angle pdb=" C GLU A 111 " pdb=" N LEU A 112 " pdb=" CA LEU A 112 " ideal model delta sigma weight residual 122.21 113.51 8.70 2.87e+00 1.21e-01 9.19e+00 angle pdb=" N GLY A 110 " pdb=" CA GLY A 110 " pdb=" C GLY A 110 " ideal model delta sigma weight residual 113.18 120.35 -7.17 2.37e+00 1.78e-01 9.16e+00 angle pdb=" N GLY C 110 " pdb=" CA GLY C 110 " pdb=" C GLY C 110 " ideal model delta sigma weight residual 113.18 120.34 -7.16 2.37e+00 1.78e-01 9.12e+00 angle pdb=" C ILE C 186 " pdb=" N ALA C 187 " pdb=" CA ALA C 187 " ideal model delta sigma weight residual 120.58 124.36 -3.78 1.32e+00 5.74e-01 8.19e+00 ... (remaining 14871 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 5691 16.90 - 33.79: 518 33.79 - 50.69: 79 50.69 - 67.58: 21 67.58 - 84.48: 3 Dihedral angle restraints: 6312 sinusoidal: 2484 harmonic: 3828 Sorted by residual: dihedral pdb=" CB CYS C 93 " pdb=" SG CYS C 93 " pdb=" SG CYS C 101 " pdb=" CB CYS C 101 " ideal model delta sinusoidal sigma weight residual 93.00 148.41 -55.41 1 1.00e+01 1.00e-02 4.15e+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 93.00 147.57 -54.57 1 1.00e+01 1.00e-02 4.04e+01 dihedral pdb=" CA GLY A 110 " pdb=" C GLY A 110 " pdb=" N GLU A 111 " pdb=" CA GLU A 111 " ideal model delta harmonic sigma weight residual 180.00 158.54 21.46 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 6309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1107 0.032 - 0.064: 443 0.064 - 0.096: 105 0.096 - 0.128: 28 0.128 - 0.159: 3 Chirality restraints: 1686 Sorted by residual: chirality pdb=" CA GLU C 111 " pdb=" N GLU C 111 " pdb=" C GLU C 111 " pdb=" CB GLU C 111 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.35e-01 chirality pdb=" CA GLU A 111 " pdb=" N GLU A 111 " pdb=" C GLU A 111 " pdb=" CB GLU A 111 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.34e-01 chirality pdb=" CA ILE C 542 " pdb=" N ILE C 542 " pdb=" C ILE C 542 " pdb=" CB ILE C 542 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 ... (remaining 1683 not shown) Planarity restraints: 1832 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 562 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.81e+00 pdb=" N PRO A 563 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 563 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 563 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 562 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO C 563 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 563 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 563 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 293 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.06e+00 pdb=" C VAL C 293 " -0.030 2.00e-02 2.50e+03 pdb=" O VAL C 293 " 0.011 2.00e-02 2.50e+03 pdb=" N TYR C 294 " 0.010 2.00e-02 2.50e+03 ... (remaining 1829 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 366 2.72 - 3.27: 11324 3.27 - 3.81: 17529 3.81 - 4.36: 21125 4.36 - 4.90: 35713 Nonbonded interactions: 86057 Sorted by model distance: nonbonded pdb=" OG SER C 265 " pdb=" OE1 GLN C 633 " model vdw 2.179 3.040 nonbonded pdb=" OG SER A 265 " pdb=" OE1 GLN A 633 " model vdw 2.181 3.040 nonbonded pdb=" OH TYR C 114 " pdb=" OD1 ASP C 615 " model vdw 2.198 3.040 nonbonded pdb=" OH TYR A 114 " pdb=" OD1 ASP A 615 " model vdw 2.211 3.040 nonbonded pdb=" OH TYR C 216 " pdb=" O VAL C 657 " model vdw 2.236 3.040 ... (remaining 86052 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.970 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 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 0.031 10936 Z= 0.124 Angle : 0.572 8.776 14880 Z= 0.329 Chirality : 0.036 0.159 1686 Planarity : 0.004 0.049 1832 Dihedral : 12.957 84.477 3834 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.17 % Allowed : 0.52 % Favored : 99.31 % 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: 1.34 (0.24), residues: 1282 helix: 1.43 (0.17), residues: 948 sheet: None (None), residues: 0 loop : -0.59 (0.37), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 185 TYR 0.012 0.001 TYR A 294 PHE 0.023 0.001 PHE A 331 TRP 0.011 0.001 TRP C 271 HIS 0.001 0.000 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 (10934) covalent geometry : angle 0.57229 / 0.33 (14876) SS BOND : bond 0.00215 / 0.13 ( 2) SS BOND : angle 0.93929 / 0.47 ( 4) hydrogen bonds : bond 0.18333 / 12.01 ( 686) hydrogen bonds : angle 5.58980 / 3.92 ( 2025) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 0.395 Fit side-chains REVERT: A 543 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.6714 (mmp-170) REVERT: A 670 PHE cc_start: 0.7673 (m-10) cc_final: 0.7312 (t80) REVERT: C 258 MET cc_start: 0.8705 (mmm) cc_final: 0.8455 (mmp) REVERT: C 469 PHE cc_start: 0.6942 (t80) cc_final: 0.6621 (t80) outliers start: 2 outliers final: 1 residues processed: 161 average time/residue: 0.4898 time to fit residues: 85.3581 Evaluate side-chains 103 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 101 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 543 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.0980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0040 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 ASN ** C 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 547 ASN C 585 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.170098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.113227 restraints weight = 13103.859| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.93 r_work: 0.3193 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10936 Z= 0.127 Angle : 0.526 6.959 14880 Z= 0.275 Chirality : 0.038 0.169 1686 Planarity : 0.004 0.045 1832 Dihedral : 3.785 22.956 1412 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.13 % Allowed : 8.75 % Favored : 90.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.14 (0.24), residues: 1282 helix: 1.99 (0.17), residues: 938 sheet: None (None), residues: 0 loop : -0.12 (0.37), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 379 TYR 0.013 0.001 TYR A 294 PHE 0.022 0.001 PHE C 331 TRP 0.011 0.001 TRP A 271 HIS 0.001 0.000 HIS C 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (10934) covalent geometry : angle 0.52591 / 0.27 (14876) SS BOND : bond 0.00417 / 0.25 ( 2) SS BOND : angle 1.52977 / 0.74 ( 4) hydrogen bonds : bond 0.04698 / 3.02 ( 686) hydrogen bonds : angle 3.93897 / 2.81 ( 2025) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.351 Fit side-chains REVERT: A 390 ASP cc_start: 0.7787 (t70) cc_final: 0.7296 (t0) REVERT: C 390 ASP cc_start: 0.7893 (t70) cc_final: 0.7300 (t0) REVERT: C 537 ARG cc_start: 0.7441 (mtm-85) cc_final: 0.7236 (mtm-85) REVERT: C 566 MET cc_start: 0.9239 (OUTLIER) cc_final: 0.9025 (mmm) outliers start: 13 outliers final: 2 residues processed: 133 average time/residue: 0.4769 time to fit residues: 69.4960 Evaluate side-chains 102 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 479 MET Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain C residue 566 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 90 optimal weight: 1.9990 chunk 127 optimal weight: 3.9990 chunk 122 optimal weight: 0.7980 chunk 93 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 101 optimal weight: 20.0000 chunk 62 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 218 ASN A 497 ASN C 585 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.168935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.111791 restraints weight = 13179.249| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.94 r_work: 0.3159 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10936 Z= 0.136 Angle : 0.524 7.031 14880 Z= 0.269 Chirality : 0.038 0.215 1686 Planarity : 0.004 0.044 1832 Dihedral : 3.621 22.462 1406 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.21 % Allowed : 10.49 % Favored : 88.30 % 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: 2.21 (0.24), residues: 1282 helix: 2.09 (0.17), residues: 938 sheet: None (None), residues: 0 loop : -0.25 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 325 TYR 0.014 0.001 TYR C 256 PHE 0.016 0.001 PHE A 164 TRP 0.012 0.001 TRP A 271 HIS 0.001 0.000 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (10934) covalent geometry : angle 0.52401 / 0.27 (14876) SS BOND : bond 0.00250 / 0.15 ( 2) SS BOND : angle 0.81122 / 0.39 ( 4) hydrogen bonds : bond 0.04602 / 2.92 ( 686) hydrogen bonds : angle 3.80764 / 2.71 ( 2025) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 121 time to evaluate : 0.368 Fit side-chains REVERT: A 351 PHE cc_start: 0.8087 (m-80) cc_final: 0.7777 (m-80) REVERT: A 390 ASP cc_start: 0.7842 (t70) cc_final: 0.7328 (t0) REVERT: A 499 PHE cc_start: 0.7652 (t80) cc_final: 0.7328 (t80) REVERT: C 331 PHE cc_start: 0.7808 (t80) cc_final: 0.7561 (t80) REVERT: C 390 ASP cc_start: 0.7954 (t70) cc_final: 0.7313 (t0) REVERT: C 469 PHE cc_start: 0.7084 (t80) cc_final: 0.6793 (t80) outliers start: 14 outliers final: 2 residues processed: 130 average time/residue: 0.4244 time to fit residues: 60.8322 Evaluate side-chains 100 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 98 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain C residue 483 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 22 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 98 optimal weight: 0.0980 chunk 62 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 585 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.169846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.112638 restraints weight = 13342.069| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.96 r_work: 0.3170 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10936 Z= 0.116 Angle : 0.495 7.518 14880 Z= 0.255 Chirality : 0.037 0.242 1686 Planarity : 0.004 0.046 1832 Dihedral : 3.560 21.657 1406 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.13 % Allowed : 12.65 % Favored : 86.22 % 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: 1282 helix: 2.19 (0.17), residues: 940 sheet: None (None), residues: 0 loop : -0.05 (0.36), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 537 TYR 0.014 0.001 TYR C 256 PHE 0.014 0.001 PHE A 501 TRP 0.011 0.001 TRP A 271 HIS 0.001 0.000 HIS C 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 (10934) covalent geometry : angle 0.49481 / 0.25 (14876) SS BOND : bond 0.00177 / 0.11 ( 2) SS BOND : angle 0.58003 / 0.30 ( 4) hydrogen bonds : bond 0.04186 / 2.65 ( 686) hydrogen bonds : angle 3.68459 / 2.63 ( 2025) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.326 Fit side-chains REVERT: A 351 PHE cc_start: 0.8073 (m-80) cc_final: 0.7803 (m-80) REVERT: A 390 ASP cc_start: 0.7832 (t70) cc_final: 0.7281 (t0) REVERT: A 499 PHE cc_start: 0.7619 (t80) cc_final: 0.7301 (t80) REVERT: C 331 PHE cc_start: 0.7833 (t80) cc_final: 0.7583 (t80) REVERT: C 352 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8371 (pp20) REVERT: C 390 ASP cc_start: 0.7984 (t70) cc_final: 0.7339 (t0) outliers start: 13 outliers final: 2 residues processed: 125 average time/residue: 0.3758 time to fit residues: 51.8497 Evaluate side-chains 107 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 170 ASP Chi-restraints excluded: chain C residue 352 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 114 optimal weight: 0.8980 chunk 119 optimal weight: 3.9990 chunk 75 optimal weight: 0.0570 chunk 127 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 298 ASN C 384 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.170438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.113153 restraints weight = 13034.878| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.93 r_work: 0.3184 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10936 Z= 0.112 Angle : 0.484 7.761 14880 Z= 0.249 Chirality : 0.037 0.261 1686 Planarity : 0.004 0.045 1832 Dihedral : 3.488 20.662 1406 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.52 % Allowed : 13.60 % Favored : 85.88 % 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: 2.61 (0.24), residues: 1282 helix: 2.33 (0.17), residues: 940 sheet: None (None), residues: 0 loop : 0.06 (0.36), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 537 TYR 0.014 0.001 TYR C 256 PHE 0.014 0.001 PHE A 164 TRP 0.011 0.001 TRP A 271 HIS 0.000 0.000 HIS C 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (10934) covalent geometry : angle 0.48373 / 0.25 (14876) SS BOND : bond 0.00082 / 0.05 ( 2) SS BOND : angle 0.23947 / 0.13 ( 4) hydrogen bonds : bond 0.03940 / 2.49 ( 686) hydrogen bonds : angle 3.61750 / 2.59 ( 2025) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 121 time to evaluate : 0.431 Fit side-chains REVERT: A 351 PHE cc_start: 0.8181 (m-80) cc_final: 0.7908 (m-80) REVERT: A 390 ASP cc_start: 0.7876 (t70) cc_final: 0.7292 (t0) REVERT: A 499 PHE cc_start: 0.7578 (t80) cc_final: 0.7279 (t80) REVERT: A 585 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.7659 (tm-30) REVERT: C 331 PHE cc_start: 0.7820 (t80) cc_final: 0.7565 (t80) REVERT: C 352 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8373 (pp20) REVERT: C 390 ASP cc_start: 0.7971 (t70) cc_final: 0.7278 (t0) REVERT: C 469 PHE cc_start: 0.7057 (t80) cc_final: 0.6737 (t80) outliers start: 6 outliers final: 0 residues processed: 126 average time/residue: 0.4586 time to fit residues: 63.9654 Evaluate side-chains 111 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain C residue 352 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 28 optimal weight: 3.9990 chunk 101 optimal weight: 20.0000 chunk 14 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 119 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 48 optimal weight: 8.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.164797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.104739 restraints weight = 13071.213| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.90 r_work: 0.3054 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10936 Z= 0.189 Angle : 0.561 8.169 14880 Z= 0.287 Chirality : 0.040 0.279 1686 Planarity : 0.004 0.044 1832 Dihedral : 3.749 21.476 1406 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.39 % Allowed : 14.12 % Favored : 84.49 % 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: 2.36 (0.24), residues: 1282 helix: 2.13 (0.16), residues: 954 sheet: None (None), residues: 0 loop : -0.07 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 279 TYR 0.020 0.002 TYR C 294 PHE 0.015 0.002 PHE A 308 TRP 0.014 0.001 TRP C 271 HIS 0.002 0.001 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.19 (10934) covalent geometry : angle 0.56141 / 0.29 (14876) SS BOND : bond 0.00224 / 0.14 ( 2) SS BOND : angle 0.73182 / 0.34 ( 4) hydrogen bonds : bond 0.04833 / 3.03 ( 686) hydrogen bonds : angle 3.80039 / 2.71 ( 2025) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.444 Fit side-chains REVERT: A 331 PHE cc_start: 0.7612 (t80) cc_final: 0.7329 (t80) REVERT: A 390 ASP cc_start: 0.7933 (t70) cc_final: 0.7320 (t0) REVERT: A 499 PHE cc_start: 0.7549 (t80) cc_final: 0.7226 (t80) REVERT: A 585 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7586 (tm-30) REVERT: C 331 PHE cc_start: 0.7757 (t80) cc_final: 0.7529 (t80) REVERT: C 352 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8389 (pm20) REVERT: C 390 ASP cc_start: 0.7926 (t70) cc_final: 0.7264 (t0) REVERT: C 585 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7529 (tm-30) outliers start: 16 outliers final: 5 residues processed: 122 average time/residue: 0.4971 time to fit residues: 66.6079 Evaluate side-chains 110 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 102 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 585 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 25 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 75 optimal weight: 0.0970 chunk 101 optimal weight: 20.0000 chunk 98 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 115 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 218 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.166529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.107131 restraints weight = 13118.978| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.91 r_work: 0.3095 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10936 Z= 0.139 Angle : 0.524 8.596 14880 Z= 0.268 Chirality : 0.038 0.285 1686 Planarity : 0.004 0.047 1832 Dihedral : 3.704 22.175 1406 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.95 % Allowed : 14.99 % Favored : 84.06 % 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: 2.47 (0.24), residues: 1282 helix: 2.19 (0.16), residues: 954 sheet: None (None), residues: 0 loop : 0.02 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 537 TYR 0.017 0.001 TYR C 294 PHE 0.014 0.001 PHE A 164 TRP 0.011 0.001 TRP C 271 HIS 0.001 0.000 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (10934) covalent geometry : angle 0.52367 / 0.27 (14876) SS BOND : bond 0.00096 / 0.06 ( 2) SS BOND : angle 0.51280 / 0.25 ( 4) hydrogen bonds : bond 0.04406 / 2.77 ( 686) hydrogen bonds : angle 3.72778 / 2.66 ( 2025) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.435 Fit side-chains REVERT: A 331 PHE cc_start: 0.7605 (t80) cc_final: 0.7286 (t80) REVERT: A 390 ASP cc_start: 0.7942 (t70) cc_final: 0.7307 (t0) REVERT: A 499 PHE cc_start: 0.7565 (t80) cc_final: 0.7231 (t80) REVERT: A 585 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7558 (tm-30) REVERT: C 331 PHE cc_start: 0.7756 (t80) cc_final: 0.7515 (t80) REVERT: C 352 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8340 (pp20) REVERT: C 390 ASP cc_start: 0.7907 (t70) cc_final: 0.7237 (t0) REVERT: C 511 GLU cc_start: 0.6792 (tp30) cc_final: 0.6326 (tm-30) REVERT: C 637 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.7765 (mp0) outliers start: 11 outliers final: 5 residues processed: 124 average time/residue: 0.4972 time to fit residues: 67.6576 Evaluate side-chains 117 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 109 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 483 ILE Chi-restraints excluded: chain A residue 585 GLN Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain C residue 637 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 69 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 122 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 ASN A 153 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.167923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.109909 restraints weight = 13065.400| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.88 r_work: 0.3117 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10936 Z= 0.119 Angle : 0.509 9.075 14880 Z= 0.259 Chirality : 0.038 0.298 1686 Planarity : 0.004 0.049 1832 Dihedral : 3.580 21.073 1406 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.04 % Allowed : 15.16 % Favored : 83.80 % 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: 2.62 (0.24), residues: 1282 helix: 2.29 (0.17), residues: 954 sheet: None (None), residues: 0 loop : 0.10 (0.37), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 537 TYR 0.015 0.001 TYR C 256 PHE 0.015 0.001 PHE A 164 TRP 0.011 0.001 TRP C 271 HIS 0.000 0.000 HIS C 416 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (10934) covalent geometry : angle 0.50869 / 0.26 (14876) SS BOND : bond 0.00155 / 0.09 ( 2) SS BOND : angle 0.45347 / 0.22 ( 4) hydrogen bonds : bond 0.04046 / 2.55 ( 686) hydrogen bonds : angle 3.64160 / 2.60 ( 2025) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.426 Fit side-chains REVERT: A 331 PHE cc_start: 0.7680 (t80) cc_final: 0.7440 (t80) REVERT: A 358 ARG cc_start: 0.7125 (mtm180) cc_final: 0.6849 (mmp80) REVERT: A 390 ASP cc_start: 0.7878 (t70) cc_final: 0.7261 (t0) REVERT: A 499 PHE cc_start: 0.7551 (t80) cc_final: 0.7249 (t80) REVERT: C 256 TYR cc_start: 0.8860 (t80) cc_final: 0.8572 (t80) REVERT: C 331 PHE cc_start: 0.7662 (t80) cc_final: 0.7412 (t80) REVERT: C 352 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8381 (pm20) REVERT: C 390 ASP cc_start: 0.7913 (t70) cc_final: 0.7215 (t0) REVERT: C 511 GLU cc_start: 0.6764 (tp30) cc_final: 0.6289 (tm-30) REVERT: C 637 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.7538 (mp0) outliers start: 12 outliers final: 1 residues processed: 119 average time/residue: 0.4848 time to fit residues: 63.3897 Evaluate side-chains 109 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 106 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain C residue 352 GLU Chi-restraints excluded: chain C residue 637 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 85 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 41 optimal weight: 0.0870 chunk 4 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 48 optimal weight: 0.0020 chunk 60 optimal weight: 2.9990 overall best weight: 0.5566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 96 ASN A 497 ASN A 585 GLN C 497 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.170250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.113709 restraints weight = 13186.772| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.91 r_work: 0.3183 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 10936 Z= 0.109 Angle : 0.511 11.704 14880 Z= 0.256 Chirality : 0.038 0.303 1686 Planarity : 0.004 0.049 1832 Dihedral : 3.490 19.871 1406 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.95 % Allowed : 15.25 % Favored : 83.80 % 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: 2.85 (0.24), residues: 1282 helix: 2.45 (0.17), residues: 938 sheet: None (None), residues: 0 loop : 0.35 (0.37), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 537 TYR 0.018 0.001 TYR A 256 PHE 0.016 0.001 PHE A 164 TRP 0.012 0.001 TRP C 492 HIS 0.000 0.000 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (10934) covalent geometry : angle 0.51069 / 0.26 (14876) SS BOND : bond 0.00149 / 0.09 ( 2) SS BOND : angle 0.29670 / 0.14 ( 4) hydrogen bonds : bond 0.03774 / 2.39 ( 686) hydrogen bonds : angle 3.56466 / 2.54 ( 2025) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 114 time to evaluate : 0.347 Fit side-chains REVERT: A 331 PHE cc_start: 0.7860 (t80) cc_final: 0.7629 (t80) REVERT: A 358 ARG cc_start: 0.7207 (mtm180) cc_final: 0.6956 (mmp80) REVERT: A 390 ASP cc_start: 0.7865 (t70) cc_final: 0.7248 (t0) REVERT: A 499 PHE cc_start: 0.7578 (t80) cc_final: 0.7261 (t80) REVERT: C 331 PHE cc_start: 0.7892 (t80) cc_final: 0.7646 (t80) REVERT: C 390 ASP cc_start: 0.7894 (t70) cc_final: 0.7244 (t0) REVERT: C 511 GLU cc_start: 0.6785 (tp30) cc_final: 0.6344 (tm-30) REVERT: C 602 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8043 (mt-10) REVERT: C 637 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7698 (mp0) outliers start: 11 outliers final: 4 residues processed: 123 average time/residue: 0.4858 time to fit residues: 65.5790 Evaluate side-chains 109 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 104 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain C residue 637 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 120 optimal weight: 1.9990 chunk 41 optimal weight: 0.0570 chunk 98 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 60 optimal weight: 0.3980 chunk 76 optimal weight: 0.0070 chunk 20 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 497 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.170969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.114573 restraints weight = 13130.914| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.91 r_work: 0.3195 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10936 Z= 0.106 Angle : 0.517 10.011 14880 Z= 0.258 Chirality : 0.038 0.303 1686 Planarity : 0.004 0.060 1832 Dihedral : 3.460 18.855 1406 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.61 % Allowed : 15.86 % Favored : 83.54 % 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: 2.92 (0.24), residues: 1282 helix: 2.49 (0.17), residues: 938 sheet: None (None), residues: 0 loop : 0.42 (0.37), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 379 TYR 0.014 0.001 TYR C 256 PHE 0.018 0.001 PHE A 501 TRP 0.016 0.001 TRP C 492 HIS 0.000 0.000 HIS C 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (10934) covalent geometry : angle 0.51687 / 0.26 (14876) SS BOND : bond 0.00143 / 0.08 ( 2) SS BOND : angle 0.23358 / 0.11 ( 4) hydrogen bonds : bond 0.03673 / 2.33 ( 686) hydrogen bonds : angle 3.54474 / 2.53 ( 2025) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 109 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 331 PHE cc_start: 0.7832 (t80) cc_final: 0.7589 (t80) REVERT: A 390 ASP cc_start: 0.7874 (t70) cc_final: 0.7244 (t0) REVERT: A 499 PHE cc_start: 0.7569 (t80) cc_final: 0.7266 (t80) REVERT: C 331 PHE cc_start: 0.7853 (t80) cc_final: 0.7634 (t80) REVERT: C 390 ASP cc_start: 0.7906 (t70) cc_final: 0.7241 (t0) REVERT: C 511 GLU cc_start: 0.6752 (tp30) cc_final: 0.6348 (tm-30) REVERT: C 602 GLU cc_start: 0.8382 (mt-10) cc_final: 0.8124 (mt-10) outliers start: 7 outliers final: 3 residues processed: 115 average time/residue: 0.4487 time to fit residues: 56.6400 Evaluate side-chains 108 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 105 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ARG Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain C residue 637 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 497 ASN C 497 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.167114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.109046 restraints weight = 13157.374| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.88 r_work: 0.3121 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10936 Z= 0.138 Angle : 0.547 9.518 14880 Z= 0.274 Chirality : 0.039 0.297 1686 Planarity : 0.004 0.054 1832 Dihedral : 3.594 18.902 1406 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.43 % Allowed : 16.03 % Favored : 83.54 % 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: 2.73 (0.24), residues: 1282 helix: 2.35 (0.16), residues: 952 sheet: None (None), residues: 0 loop : 0.26 (0.37), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 379 TYR 0.024 0.001 TYR C 256 PHE 0.015 0.001 PHE A 164 TRP 0.019 0.001 TRP C 492 HIS 0.001 0.000 HIS A 134 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (10934) covalent geometry : angle 0.54722 / 0.27 (14876) SS BOND : bond 0.00167 / 0.10 ( 2) SS BOND : angle 0.49669 / 0.24 ( 4) hydrogen bonds : bond 0.04177 / 2.63 ( 686) hydrogen bonds : angle 3.61923 / 2.58 ( 2025) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4027.92 seconds wall clock time: 69 minutes 10.79 seconds (4150.79 seconds total)