Starting phenix.real_space_refine on Thu Aug 6 01:18:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9wyk_66367/08_2026/9wyk_66367.cif Found real_map, /net/cci-nas-00/data/ceres_data/9wyk_66367/08_2026/9wyk_66367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9wyk_66367/08_2026/9wyk_66367.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9wyk_66367/08_2026/9wyk_66367.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9wyk_66367/08_2026/9wyk_66367.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9wyk_66367/08_2026/9wyk_66367.map" } resolution = 2.65 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= 0.003 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 6 7.16 5 Cu 2 5.60 5 S 46 5.16 5 C 8024 2.51 5 N 1998 2.21 5 O 2163 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12241 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5912 Classifications: {'peptide': 750} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 713} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 5912 Classifications: {'peptide': 750} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 713} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 183 Unusual residues: {' CA': 1, ' CU': 1, ' FE': 1, 'HEM': 2, 'LMT': 2, 'UQ5': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'UQ5:plan-2': 1, 'UQ5:plan-5': 1, 'UQ5:plan-6': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Unusual residues: {' CA': 1, ' CU': 1, ' FE': 1, 'HEM': 2, 'LMT': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Time building chain proxies: 2.37, per 1000 atoms: 0.19 Number of scatterers: 12241 At special positions: 0 Unit cell: (107.3, 85.1, 105.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Cu 2 28.99 Fe 6 26.01 Ca 2 19.99 S 46 16.00 O 2163 8.00 N 1998 7.00 C 8024 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.85 Conformation dependent library (CDL) restraints added in 499.9 milliseconds 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2708 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 6 sheets defined 79.3% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 4 through 33 removed outlier: 3.666A pdb=" N THR A 10 " --> pdb=" O ARG A 6 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 15 " --> pdb=" O LEU A 11 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 16 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 22 " --> pdb=" O THR A 18 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY A 23 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 82 through 105 Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 112 through 129 removed outlier: 3.956A pdb=" N ALA A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 136 Processing helix chain 'A' and resid 142 through 161 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 173 Processing helix chain 'A' and resid 182 through 202 Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 226 through 253 Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 282 through 307 removed outlier: 3.501A pdb=" N THR A 307 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 323 through 355 removed outlier: 3.545A pdb=" N ALA A 335 " --> pdb=" O HIS A 331 " (cutoff:3.500A) Proline residue: A 352 - end of helix removed outlier: 4.104A pdb=" N ASN A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 390 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 412 through 440 removed outlier: 3.700A pdb=" N GLY A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Proline residue: A 436 - end of helix Processing helix chain 'A' and resid 445 through 459 Processing helix chain 'A' and resid 462 through 468 removed outlier: 3.723A pdb=" N GLY A 465 " --> pdb=" O TYR A 462 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE A 466 " --> pdb=" O GLY A 463 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N TYR A 468 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 488 Processing helix chain 'A' and resid 491 through 508 Processing helix chain 'A' and resid 512 through 537 removed outlier: 5.072A pdb=" N ILE A 532 " --> pdb=" O MET A 528 " (cutoff:3.500A) Proline residue: A 533 - end of helix Processing helix chain 'A' and resid 545 through 555 removed outlier: 3.822A pdb=" N MET A 549 " --> pdb=" O THR A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 568 Processing helix chain 'A' and resid 571 through 576 Processing helix chain 'A' and resid 581 through 585 removed outlier: 3.746A pdb=" N GLU A 584 " --> pdb=" O PRO A 581 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN A 585 " --> pdb=" O TRP A 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 581 through 585' Processing helix chain 'A' and resid 586 through 612 removed outlier: 3.562A pdb=" N PHE A 607 " --> pdb=" O GLY A 603 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 621 removed outlier: 4.359A pdb=" N TYR A 619 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 654 removed outlier: 3.584A pdb=" N VAL A 628 " --> pdb=" O ASN A 624 " (cutoff:3.500A) removed outlier: 4.961A pdb=" N PHE A 640 " --> pdb=" O GLY A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 681 Processing helix chain 'A' and resid 682 through 697 removed outlier: 3.518A pdb=" N ILE A 686 " --> pdb=" O SER A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 703 Processing helix chain 'A' and resid 704 through 709 Processing helix chain 'A' and resid 710 through 720 Processing helix chain 'A' and resid 720 through 744 Processing helix chain 'A' and resid 746 through 750 Processing helix chain 'B' and resid 4 through 33 removed outlier: 3.674A pdb=" N THR B 10 " --> pdb=" O ARG B 6 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 15 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA B 16 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLY B 23 " --> pdb=" O PHE B 19 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N PHE B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N GLY B 27 " --> pdb=" O GLY B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 64 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 82 through 105 Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 112 through 129 removed outlier: 3.953A pdb=" N ALA B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 136 Processing helix chain 'B' and resid 142 through 161 Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 166 through 173 Processing helix chain 'B' and resid 182 through 202 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 226 through 253 Processing helix chain 'B' and resid 268 through 272 Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 282 through 307 removed outlier: 3.505A pdb=" N THR B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 323 through 355 removed outlier: 3.546A pdb=" N ALA B 335 " --> pdb=" O HIS B 331 " (cutoff:3.500A) Proline residue: B 352 - end of helix removed outlier: 4.077A pdb=" N ASN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 390 Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 412 through 440 removed outlier: 3.681A pdb=" N GLY B 433 " --> pdb=" O LEU B 429 " (cutoff:3.500A) Proline residue: B 436 - end of helix Processing helix chain 'B' and resid 445 through 459 Processing helix chain 'B' and resid 462 through 468 removed outlier: 3.723A pdb=" N GLY B 465 " --> pdb=" O TYR B 462 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE B 466 " --> pdb=" O GLY B 463 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 467 " --> pdb=" O ALA B 464 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR B 468 " --> pdb=" O GLY B 465 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 462 through 468' Processing helix chain 'B' and resid 473 through 488 Processing helix chain 'B' and resid 492 through 508 Processing helix chain 'B' and resid 512 through 537 removed outlier: 5.031A pdb=" N ILE B 532 " --> pdb=" O MET B 528 " (cutoff:3.500A) Proline residue: B 533 - end of helix Processing helix chain 'B' and resid 545 through 555 removed outlier: 3.799A pdb=" N MET B 549 " --> pdb=" O THR B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 561 through 568 Processing helix chain 'B' and resid 571 through 576 Processing helix chain 'B' and resid 581 through 585 removed outlier: 3.884A pdb=" N GLU B 584 " --> pdb=" O PRO B 581 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN B 585 " --> pdb=" O TRP B 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 581 through 585' Processing helix chain 'B' and resid 586 through 612 removed outlier: 3.587A pdb=" N PHE B 607 " --> pdb=" O GLY B 603 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 621 removed outlier: 4.362A pdb=" N TYR B 619 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 654 removed outlier: 3.594A pdb=" N VAL B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N PHE B 640 " --> pdb=" O GLY B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 681 Processing helix chain 'B' and resid 682 through 697 removed outlier: 3.528A pdb=" N ILE B 686 " --> pdb=" O SER B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 698 through 703 Processing helix chain 'B' and resid 704 through 709 Processing helix chain 'B' and resid 710 through 720 Processing helix chain 'B' and resid 720 through 744 Processing helix chain 'B' and resid 746 through 750 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50 removed outlier: 6.475A pdb=" N ARG A 47 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N SER A 42 " --> pdb=" O ARG A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA3, first strand: chain 'A' and resid 312 through 313 Processing sheet with id=AA4, first strand: chain 'B' and resid 47 through 50 removed outlier: 6.475A pdb=" N ARG B 47 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N SER B 42 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA6, first strand: chain 'B' and resid 312 through 313 834 hydrogen bonds defined for protein. 2421 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.71 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 4567 1.38 - 1.55: 7852 1.55 - 1.72: 13 1.72 - 1.89: 88 1.89 - 2.05: 16 Bond restraints: 12536 Sorted by residual: bond pdb=" N LEU A 558 " pdb=" CA LEU A 558 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.30e-02 5.92e+03 8.12e+00 bond pdb=" C1B LMT A 806 " pdb=" O1B LMT A 806 " ideal model delta sigma weight residual 1.395 1.446 -0.051 2.00e-02 2.50e+03 6.55e+00 bond pdb=" N GLU B 559 " pdb=" CA GLU B 559 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.33e-02 5.65e+03 6.54e+00 bond pdb=" C GLU B 494 " pdb=" N VAL B 495 " ideal model delta sigma weight residual 1.334 1.304 0.030 1.25e-02 6.40e+03 5.82e+00 bond pdb=" N GLU A 559 " pdb=" CA GLU A 559 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.29e-02 6.01e+03 5.50e+00 ... (remaining 12531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.42: 16878 2.42 - 4.85: 228 4.85 - 7.27: 41 7.27 - 9.70: 6 9.70 - 12.12: 4 Bond angle restraints: 17157 Sorted by residual: angle pdb=" N LEU A 529 " pdb=" CA LEU A 529 " pdb=" C LEU A 529 " ideal model delta sigma weight residual 112.23 106.66 5.57 1.26e+00 6.30e-01 1.96e+01 angle pdb=" N GLU B 494 " pdb=" CA GLU B 494 " pdb=" CB GLU B 494 " ideal model delta sigma weight residual 110.28 104.11 6.17 1.55e+00 4.16e-01 1.59e+01 angle pdb=" CB MET B 477 " pdb=" CG MET B 477 " pdb=" SD MET B 477 " ideal model delta sigma weight residual 112.70 124.14 -11.44 3.00e+00 1.11e-01 1.45e+01 angle pdb=" CB MET A 477 " pdb=" CG MET A 477 " pdb=" SD MET A 477 " ideal model delta sigma weight residual 112.70 124.07 -11.37 3.00e+00 1.11e-01 1.44e+01 angle pdb=" N PHE B 492 " pdb=" CA PHE B 492 " pdb=" C PHE B 492 " ideal model delta sigma weight residual 114.56 110.09 4.47 1.27e+00 6.20e-01 1.24e+01 ... (remaining 17152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.48: 6727 26.48 - 52.96: 307 52.96 - 79.44: 46 79.44 - 105.93: 13 105.93 - 132.41: 6 Dihedral angle restraints: 7099 sinusoidal: 2837 harmonic: 4262 Sorted by residual: dihedral pdb=" O1B LMT A 806 " pdb=" C1B LMT A 806 " pdb=" C2B LMT A 806 " pdb=" O2B LMT A 806 " ideal model delta sinusoidal sigma weight residual 53.26 -79.15 132.41 1 3.00e+01 1.11e-03 1.79e+01 dihedral pdb=" O2B LMT A 806 " pdb=" C1B LMT A 806 " pdb=" C2B LMT A 806 " pdb=" O5B LMT A 806 " ideal model delta sinusoidal sigma weight residual -176.42 -45.76 -130.66 1 3.00e+01 1.11e-03 1.76e+01 dihedral pdb=" C3B LMT A 806 " pdb=" C1B LMT A 806 " pdb=" C2B LMT A 806 " pdb=" O1B LMT A 806 " ideal model delta sinusoidal sigma weight residual 70.08 -160.66 -129.26 1 3.00e+01 1.11e-03 1.74e+01 ... (remaining 7096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1546 0.059 - 0.118: 264 0.118 - 0.176: 13 0.176 - 0.235: 1 0.235 - 0.294: 2 Chirality restraints: 1826 Sorted by residual: chirality pdb=" CG LEU B 529 " pdb=" CB LEU B 529 " pdb=" CD1 LEU B 529 " pdb=" CD2 LEU B 529 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.16e+00 chirality pdb=" CA GLU B 494 " pdb=" N GLU B 494 " pdb=" C GLU B 494 " pdb=" CB GLU B 494 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CG LEU A 590 " pdb=" CB LEU A 590 " pdb=" CD1 LEU A 590 " pdb=" CD2 LEU A 590 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.74e-01 ... (remaining 1823 not shown) Planarity restraints: 2119 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 488 " -0.018 2.00e-02 2.50e+03 1.97e-02 9.67e+00 pdb=" CG TRP A 488 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP A 488 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 488 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 488 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 488 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 488 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 488 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 488 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 488 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 488 " 0.017 2.00e-02 2.50e+03 1.90e-02 9.05e+00 pdb=" CG TRP B 488 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP B 488 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP B 488 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 488 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 488 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 488 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 488 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 488 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 488 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 488 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.26e+00 pdb=" C TRP A 488 " -0.050 2.00e-02 2.50e+03 pdb=" O TRP A 488 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 489 " 0.017 2.00e-02 2.50e+03 ... (remaining 2116 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.33: 33 2.33 - 2.97: 6235 2.97 - 3.62: 19370 3.62 - 4.26: 29425 4.26 - 4.90: 49694 Nonbonded interactions: 104757 Sorted by model distance: nonbonded pdb="FE FE B 804 " pdb=" O HOH B 906 " model vdw 1.688 2.260 nonbonded pdb="FE FE A 802 " pdb=" O HOH A 904 " model vdw 1.703 2.260 nonbonded pdb=" NE2 HIS A 486 " pdb="FE FE A 802 " model vdw 1.821 2.340 nonbonded pdb=" NE2 HIS B 486 " pdb="FE FE B 804 " model vdw 1.995 2.340 nonbonded pdb=" ND1 HIS A 224 " pdb="CU CU A 807 " model vdw 2.120 2.320 ... (remaining 104752 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 801 or resid 803 or (resid 805 and (name C1 or n \ ame C1' or name C1B or name C2 or name C2' or name C2B or name C3 or name C3' or \ name C3B or name C4 or name C4' or name C4B or name C5 or name C5' or name C5B \ or name C6 or name C6' or name C6B or name C7 or name C8 or name O1' or name O1B \ or name O2' or name O2B or name O3' or name O3B or name O4' or name O5' or name \ O5B or name O6' or name O6B)))) selection = (chain 'B' and (resid 1 through 801 or resid 803 or resid 805)) } 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: 3.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.190 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 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 : 0.006 0.371 12540 Z= 0.171 Angle : 0.672 12.122 17157 Z= 0.329 Chirality : 0.041 0.294 1826 Planarity : 0.004 0.056 2119 Dihedral : 16.071 132.408 4391 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.54 % Favored : 96.12 % Rotamer: Outliers : 1.11 % Allowed : 13.57 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 2.22 (0.23), residues: 1496 helix: 2.30 (0.17), residues: 1068 sheet: None (None), residues: 0 loop : -0.72 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 255 TYR 0.019 0.001 TYR A 462 PHE 0.009 0.001 PHE A 635 TRP 0.053 0.001 TRP A 488 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.17 (12536) covalent geometry : angle 0.67225 / 0.33 (17157) hydrogen bonds : bond 0.11910 / 7.82 ( 834) hydrogen bonds : angle 4.89937 / 3.67 ( 2421) Misc. bond : bond 0.26532 / 13.27 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6571 (tpt) cc_final: 0.6300 (tpp) REVERT: A 430 MET cc_start: 0.9540 (tpt) cc_final: 0.9322 (mmt) REVERT: A 515 MET cc_start: 0.9012 (tpp) cc_final: 0.8547 (tmm) REVERT: A 527 PHE cc_start: 0.8128 (m-80) cc_final: 0.7106 (m-80) REVERT: A 528 MET cc_start: 0.7700 (mmp) cc_final: 0.7366 (tpp) REVERT: A 583 MET cc_start: 0.8712 (pmm) cc_final: 0.8374 (pmm) REVERT: B 1 MET cc_start: 0.6427 (tpt) cc_final: 0.5912 (tpp) REVERT: B 19 PHE cc_start: 0.8017 (t80) cc_final: 0.7777 (t80) REVERT: B 477 MET cc_start: 0.9247 (tmm) cc_final: 0.9021 (tmm) REVERT: B 515 MET cc_start: 0.9069 (tpp) cc_final: 0.8613 (tmm) REVERT: B 527 PHE cc_start: 0.7314 (m-80) cc_final: 0.7099 (m-80) REVERT: B 583 MET cc_start: 0.8719 (pmm) cc_final: 0.8434 (pmm) outliers start: 13 outliers final: 8 residues processed: 93 average time/residue: 0.5211 time to fit residues: 53.9905 Evaluate side-chains 86 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 461 PHE Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 673 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN A 147 GLN A 213 ASN B 147 GLN B 213 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.069348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.049284 restraints weight = 38730.061| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 3.19 r_work: 0.2531 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8911 moved from start: 0.0927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.306 12540 Z= 0.278 Angle : 0.715 15.353 17157 Z= 0.331 Chirality : 0.044 0.299 1826 Planarity : 0.004 0.044 2119 Dihedral : 10.449 109.002 1867 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.54 % Favored : 96.19 % Rotamer: Outliers : 3.16 % Allowed : 11.35 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 2.15 (0.23), residues: 1496 helix: 2.20 (0.16), residues: 1082 sheet: None (None), residues: 0 loop : -0.72 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 255 TYR 0.013 0.001 TYR A 324 PHE 0.012 0.001 PHE A 194 TRP 0.020 0.001 TRP A 488 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00668 / 0.28 (12536) covalent geometry : angle 0.71514 / 0.33 (17157) hydrogen bonds : bond 0.05074 / 3.43 ( 834) hydrogen bonds : angle 4.64564 / 3.49 ( 2421) Misc. bond : bond 0.23068 / 11.57 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 76 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6548 (tpt) cc_final: 0.6319 (tpp) REVERT: A 515 MET cc_start: 0.9030 (tpp) cc_final: 0.8552 (tmm) REVERT: A 527 PHE cc_start: 0.7205 (m-80) cc_final: 0.6963 (m-80) REVERT: A 528 MET cc_start: 0.7827 (mmp) cc_final: 0.7605 (tpp) REVERT: B 1 MET cc_start: 0.6663 (tpt) cc_final: 0.6175 (tpp) REVERT: B 19 PHE cc_start: 0.8179 (t80) cc_final: 0.7914 (t80) REVERT: B 515 MET cc_start: 0.9072 (tpp) cc_final: 0.8598 (tmm) outliers start: 37 outliers final: 10 residues processed: 104 average time/residue: 0.4165 time to fit residues: 48.9699 Evaluate side-chains 82 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 461 PHE Chi-restraints excluded: chain B residue 563 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 28 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 58 optimal weight: 0.0670 chunk 63 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN B 147 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.072026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.052109 restraints weight = 38670.616| |-----------------------------------------------------------------------------| r_work (start): 0.2765 rms_B_bonded: 3.26 r_work: 0.2617 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 12540 Z= 0.118 Angle : 0.590 11.207 17157 Z= 0.278 Chirality : 0.040 0.264 1826 Planarity : 0.004 0.045 2119 Dihedral : 9.594 101.215 1859 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.27 % Favored : 97.46 % Rotamer: Outliers : 2.82 % Allowed : 12.46 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.23), residues: 1496 helix: 2.40 (0.16), residues: 1068 sheet: None (None), residues: 0 loop : -0.63 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 255 TYR 0.009 0.001 TYR A 156 PHE 0.008 0.001 PHE A 194 TRP 0.028 0.001 TRP A 488 HIS 0.006 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (12536) covalent geometry : angle 0.58957 / 0.28 (17157) hydrogen bonds : bond 0.03972 / 2.69 ( 834) hydrogen bonds : angle 4.32249 / 3.24 ( 2421) Misc. bond : bond 0.08705 / 4.37 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 81 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6471 (tpt) cc_final: 0.6264 (tpp) REVERT: A 515 MET cc_start: 0.8947 (tpp) cc_final: 0.8481 (tmm) REVERT: A 528 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7510 (tpp) REVERT: B 1 MET cc_start: 0.6688 (tpt) cc_final: 0.6233 (tpp) REVERT: B 19 PHE cc_start: 0.8061 (t80) cc_final: 0.7819 (t80) REVERT: B 515 MET cc_start: 0.9018 (tpp) cc_final: 0.8546 (tmm) outliers start: 33 outliers final: 12 residues processed: 106 average time/residue: 0.4315 time to fit residues: 51.8659 Evaluate side-chains 86 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 461 PHE Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 566 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 28 optimal weight: 4.9990 chunk 135 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 120 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 139 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 118 optimal weight: 0.0570 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 GLN A 213 ASN B 147 GLN B 213 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.072531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.052523 restraints weight = 37998.288| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 3.20 r_work: 0.2615 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.147 12540 Z= 0.130 Angle : 0.607 10.314 17157 Z= 0.279 Chirality : 0.041 0.258 1826 Planarity : 0.004 0.047 2119 Dihedral : 9.306 99.760 1857 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.41 % Favored : 97.33 % Rotamer: Outliers : 2.56 % Allowed : 13.48 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 2.32 (0.23), residues: 1496 helix: 2.38 (0.16), residues: 1082 sheet: None (None), residues: 0 loop : -0.82 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 186 TYR 0.008 0.001 TYR A 324 PHE 0.022 0.001 PHE A 527 TRP 0.023 0.001 TRP A 488 HIS 0.006 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (12536) covalent geometry : angle 0.60742 / 0.28 (17157) hydrogen bonds : bond 0.03989 / 2.70 ( 834) hydrogen bonds : angle 4.30381 / 3.23 ( 2421) Misc. bond : bond 0.10933 / 5.49 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 430 MET cc_start: 0.9490 (tpp) cc_final: 0.9261 (tpt) REVERT: A 515 MET cc_start: 0.8964 (tpp) cc_final: 0.8530 (tmm) REVERT: A 528 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7425 (tpp) REVERT: A 529 LEU cc_start: 0.7114 (OUTLIER) cc_final: 0.6892 (mm) REVERT: B 1 MET cc_start: 0.6710 (tpt) cc_final: 0.6491 (tpp) REVERT: B 19 PHE cc_start: 0.8114 (t80) cc_final: 0.7860 (t80) REVERT: B 515 MET cc_start: 0.9008 (tpp) cc_final: 0.8552 (tmm) REVERT: B 528 MET cc_start: 0.7604 (mmp) cc_final: 0.7290 (tpp) REVERT: B 558 LEU cc_start: 0.9308 (mt) cc_final: 0.8838 (pp) REVERT: B 583 MET cc_start: 0.8692 (pmm) cc_final: 0.8273 (pmm) outliers start: 30 outliers final: 12 residues processed: 102 average time/residue: 0.4054 time to fit residues: 46.3748 Evaluate side-chains 86 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 461 PHE Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 566 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 43 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 1 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 39 optimal weight: 0.0980 chunk 53 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 82 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 213 ASN B 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.072315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.052716 restraints weight = 38589.746| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 3.23 r_work: 0.2631 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 12540 Z= 0.114 Angle : 0.603 10.856 17157 Z= 0.276 Chirality : 0.040 0.276 1826 Planarity : 0.004 0.046 2119 Dihedral : 9.037 96.293 1855 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.21 % Favored : 97.53 % Rotamer: Outliers : 2.30 % Allowed : 13.48 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 2.37 (0.23), residues: 1496 helix: 2.41 (0.16), residues: 1084 sheet: None (None), residues: 0 loop : -0.79 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 255 TYR 0.008 0.001 TYR B 156 PHE 0.012 0.001 PHE A 527 TRP 0.028 0.001 TRP A 488 HIS 0.006 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 (12536) covalent geometry : angle 0.60334 / 0.28 (17157) hydrogen bonds : bond 0.03756 / 2.54 ( 834) hydrogen bonds : angle 4.22642 / 3.16 ( 2421) Misc. bond : bond 0.08108 / 4.07 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6713 (tpp) cc_final: 0.6359 (tpp) REVERT: A 430 MET cc_start: 0.9388 (tpp) cc_final: 0.9141 (tpt) REVERT: A 492 PHE cc_start: 0.8264 (m-80) cc_final: 0.8049 (m-80) REVERT: A 515 MET cc_start: 0.8966 (tpp) cc_final: 0.8570 (tmm) REVERT: A 528 MET cc_start: 0.7563 (OUTLIER) cc_final: 0.7338 (tpp) REVERT: A 558 LEU cc_start: 0.9176 (mt) cc_final: 0.8810 (pp) REVERT: A 734 MET cc_start: 0.9534 (OUTLIER) cc_final: 0.8866 (tpp) REVERT: B 1 MET cc_start: 0.6803 (tpt) cc_final: 0.6582 (tpp) REVERT: B 19 PHE cc_start: 0.8052 (t80) cc_final: 0.7828 (t80) REVERT: B 515 MET cc_start: 0.9010 (tpp) cc_final: 0.8583 (tmm) REVERT: B 527 PHE cc_start: 0.7662 (m-80) cc_final: 0.7389 (m-80) REVERT: B 528 MET cc_start: 0.7602 (mmp) cc_final: 0.7393 (tpp) REVERT: B 558 LEU cc_start: 0.9283 (mt) cc_final: 0.8827 (pp) REVERT: B 559 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8781 (mp0) REVERT: B 583 MET cc_start: 0.8723 (pmm) cc_final: 0.8256 (pmm) REVERT: B 734 MET cc_start: 0.9539 (OUTLIER) cc_final: 0.8865 (tpp) outliers start: 27 outliers final: 11 residues processed: 102 average time/residue: 0.4050 time to fit residues: 46.3909 Evaluate side-chains 90 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 461 PHE Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 734 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 76 optimal weight: 7.9990 chunk 107 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 26 optimal weight: 7.9990 chunk 60 optimal weight: 0.5980 chunk 139 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 0.0270 chunk 64 optimal weight: 3.9990 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 62 GLN B 213 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.072542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.052981 restraints weight = 38646.505| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 3.25 r_work: 0.2640 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 12540 Z= 0.114 Angle : 0.600 11.134 17157 Z= 0.273 Chirality : 0.040 0.270 1826 Planarity : 0.004 0.044 2119 Dihedral : 8.859 92.465 1855 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.27 % Favored : 97.46 % Rotamer: Outliers : 2.73 % Allowed : 13.57 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.23), residues: 1496 helix: 2.43 (0.16), residues: 1084 sheet: None (None), residues: 0 loop : -0.79 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 186 TYR 0.014 0.001 TYR B 462 PHE 0.029 0.001 PHE A 19 TRP 0.029 0.001 TRP A 488 HIS 0.006 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (12536) covalent geometry : angle 0.60043 / 0.27 (17157) hydrogen bonds : bond 0.03676 / 2.48 ( 834) hydrogen bonds : angle 4.18549 / 3.13 ( 2421) Misc. bond : bond 0.08060 / 4.05 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 77 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6841 (tpp) cc_final: 0.6534 (tpp) REVERT: A 430 MET cc_start: 0.9385 (tpp) cc_final: 0.9047 (tpt) REVERT: A 515 MET cc_start: 0.8962 (tpp) cc_final: 0.8590 (tmm) REVERT: A 558 LEU cc_start: 0.9133 (mt) cc_final: 0.8831 (pp) REVERT: A 734 MET cc_start: 0.9530 (OUTLIER) cc_final: 0.8850 (tpp) REVERT: B 1 MET cc_start: 0.6816 (tpt) cc_final: 0.6602 (tpp) REVERT: B 19 PHE cc_start: 0.8050 (t80) cc_final: 0.7819 (t80) REVERT: B 515 MET cc_start: 0.9008 (tpp) cc_final: 0.8599 (tmm) REVERT: B 527 PHE cc_start: 0.7764 (m-80) cc_final: 0.7415 (m-80) REVERT: B 558 LEU cc_start: 0.9269 (mt) cc_final: 0.8832 (pp) REVERT: B 559 GLU cc_start: 0.9254 (OUTLIER) cc_final: 0.8859 (mp0) REVERT: B 583 MET cc_start: 0.8694 (pmm) cc_final: 0.8239 (pmm) REVERT: B 734 MET cc_start: 0.9533 (OUTLIER) cc_final: 0.8845 (tpp) outliers start: 32 outliers final: 15 residues processed: 104 average time/residue: 0.4278 time to fit residues: 50.1804 Evaluate side-chains 91 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 458 ILE Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 510 LEU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 566 LEU Chi-restraints excluded: chain A residue 734 MET Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 461 PHE Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 510 LEU Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 734 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 15 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 56 optimal weight: 0.0270 chunk 6 optimal weight: 6.9990 chunk 85 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 overall best weight: 1.8044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 213 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.071947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.051944 restraints weight = 38381.381| |-----------------------------------------------------------------------------| r_work (start): 0.2753 rms_B_bonded: 3.26 r_work: 0.2604 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 12540 Z= 0.155 Angle : 0.652 13.597 17157 Z= 0.293 Chirality : 0.041 0.301 1826 Planarity : 0.004 0.041 2119 Dihedral : 8.851 90.183 1855 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.41 % Favored : 97.33 % Rotamer: Outliers : 2.56 % Allowed : 14.25 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 2.43 (0.23), residues: 1496 helix: 2.45 (0.17), residues: 1084 sheet: None (None), residues: 0 loop : -0.77 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 186 TYR 0.013 0.001 TYR B 462 PHE 0.015 0.001 PHE A 527 TRP 0.032 0.001 TRP A 488 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.15 (12536) covalent geometry : angle 0.65170 / 0.29 (17157) hydrogen bonds : bond 0.04021 / 2.72 ( 834) hydrogen bonds : angle 4.25605 / 3.18 ( 2421) Misc. bond : bond 0.13372 / 6.71 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 74 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6886 (tpp) cc_final: 0.6563 (tpp) REVERT: A 515 MET cc_start: 0.8980 (tpp) cc_final: 0.8613 (tmm) REVERT: A 558 LEU cc_start: 0.9124 (mt) cc_final: 0.8783 (pp) REVERT: A 583 MET cc_start: 0.8644 (pmm) cc_final: 0.8380 (pmm) REVERT: B 1 MET cc_start: 0.6903 (tpt) cc_final: 0.6702 (tpp) REVERT: B 19 PHE cc_start: 0.8085 (t80) cc_final: 0.7849 (t80) REVERT: B 430 MET cc_start: 0.9607 (tpt) cc_final: 0.9399 (mmt) REVERT: B 515 MET cc_start: 0.9012 (tpp) cc_final: 0.8609 (tmm) REVERT: B 558 LEU cc_start: 0.9267 (mt) cc_final: 0.8847 (pp) REVERT: B 559 GLU cc_start: 0.9248 (OUTLIER) cc_final: 0.8884 (mp0) REVERT: B 734 MET cc_start: 0.9543 (OUTLIER) cc_final: 0.8886 (tpp) outliers start: 30 outliers final: 14 residues processed: 101 average time/residue: 0.4558 time to fit residues: 52.0427 Evaluate side-chains 89 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 564 ILE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 461 PHE Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 734 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 112 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 75 optimal weight: 40.0000 chunk 123 optimal weight: 0.6980 chunk 27 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 = 0.3298 r_free = 0.3298 target = 0.071281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.051446 restraints weight = 38481.814| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 3.23 r_work: 0.2601 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.172 12540 Z= 0.150 Angle : 0.649 13.775 17157 Z= 0.291 Chirality : 0.041 0.299 1826 Planarity : 0.004 0.040 2119 Dihedral : 8.760 89.632 1855 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.67 % Favored : 97.06 % Rotamer: Outliers : 1.88 % Allowed : 15.02 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 2.58 (0.23), residues: 1496 helix: 2.61 (0.17), residues: 1056 sheet: None (None), residues: 0 loop : -0.62 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 579 TYR 0.013 0.001 TYR B 462 PHE 0.031 0.001 PHE A 19 TRP 0.033 0.001 TRP A 488 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (12536) covalent geometry : angle 0.64853 / 0.29 (17157) hydrogen bonds : bond 0.04059 / 2.74 ( 834) hydrogen bonds : angle 4.26625 / 3.19 ( 2421) Misc. bond : bond 0.12811 / 6.43 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7008 (tpp) cc_final: 0.6579 (tpp) REVERT: A 515 MET cc_start: 0.8983 (tpp) cc_final: 0.8626 (tmm) REVERT: A 558 LEU cc_start: 0.9118 (mt) cc_final: 0.8793 (pp) REVERT: B 1 MET cc_start: 0.6960 (tpt) cc_final: 0.6742 (tpp) REVERT: B 19 PHE cc_start: 0.8134 (t80) cc_final: 0.7898 (t80) REVERT: B 515 MET cc_start: 0.9024 (tpp) cc_final: 0.8633 (tmm) REVERT: B 558 LEU cc_start: 0.9266 (mt) cc_final: 0.8830 (pp) REVERT: B 559 GLU cc_start: 0.9261 (OUTLIER) cc_final: 0.8740 (mp0) REVERT: B 583 MET cc_start: 0.8575 (pmm) cc_final: 0.8219 (pmm) outliers start: 22 outliers final: 12 residues processed: 92 average time/residue: 0.4402 time to fit residues: 45.4879 Evaluate side-chains 84 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 461 PHE Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 566 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 87 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 84 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 1 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 91 optimal weight: 0.9980 chunk 137 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3330 r_free = 0.3330 target = 0.073700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.053621 restraints weight = 37959.353| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 3.27 r_work: 0.2641 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.105 12540 Z= 0.114 Angle : 0.632 13.222 17157 Z= 0.285 Chirality : 0.041 0.318 1826 Planarity : 0.004 0.040 2119 Dihedral : 8.501 87.995 1855 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.47 % Favored : 97.26 % Rotamer: Outliers : 1.45 % Allowed : 15.44 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 2.56 (0.23), residues: 1496 helix: 2.60 (0.16), residues: 1056 sheet: None (None), residues: 0 loop : -0.61 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 186 TYR 0.012 0.001 TYR B 462 PHE 0.049 0.001 PHE A 527 TRP 0.035 0.001 TRP A 488 HIS 0.006 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.11 (12536) covalent geometry : angle 0.63239 / 0.28 (17157) hydrogen bonds : bond 0.03700 / 2.50 ( 834) hydrogen bonds : angle 4.19606 / 3.13 ( 2421) Misc. bond : bond 0.07475 / 3.76 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7069 (tpp) cc_final: 0.6644 (tpp) REVERT: A 515 MET cc_start: 0.8976 (tpp) cc_final: 0.8618 (tmm) REVERT: A 558 LEU cc_start: 0.9074 (mt) cc_final: 0.8785 (pp) REVERT: B 1 MET cc_start: 0.6896 (tpt) cc_final: 0.6470 (tpp) REVERT: B 19 PHE cc_start: 0.8056 (t80) cc_final: 0.7828 (t80) REVERT: B 515 MET cc_start: 0.9002 (tpp) cc_final: 0.8649 (tmm) REVERT: B 558 LEU cc_start: 0.9227 (mt) cc_final: 0.8808 (pp) REVERT: B 559 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8725 (mp0) REVERT: B 583 MET cc_start: 0.8556 (pmm) cc_final: 0.8207 (pmm) outliers start: 17 outliers final: 12 residues processed: 91 average time/residue: 0.4882 time to fit residues: 49.6437 Evaluate side-chains 88 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 461 PHE Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 561 VAL Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 566 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 51 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 46 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 133 optimal weight: 4.9990 chunk 61 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 chunk 23 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.3302 r_free = 0.3302 target = 0.071579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.051744 restraints weight = 38804.988| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 3.24 r_work: 0.2599 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.192 12540 Z= 0.160 Angle : 0.680 13.854 17157 Z= 0.302 Chirality : 0.042 0.310 1826 Planarity : 0.004 0.039 2119 Dihedral : 8.457 89.872 1855 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.54 % Favored : 97.19 % Rotamer: Outliers : 1.28 % Allowed : 15.70 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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: 2.53 (0.23), residues: 1496 helix: 2.58 (0.17), residues: 1068 sheet: None (None), residues: 0 loop : -0.72 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 186 TYR 0.011 0.001 TYR B 462 PHE 0.039 0.001 PHE B 527 TRP 0.036 0.001 TRP A 488 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (12536) covalent geometry : angle 0.67970 / 0.30 (17157) hydrogen bonds : bond 0.04123 / 2.78 ( 834) hydrogen bonds : angle 4.29204 / 3.20 ( 2421) Misc. bond : bond 0.14468 / 7.26 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2992 Ramachandran restraints generated. 1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7164 (tpp) cc_final: 0.6758 (tpp) REVERT: A 515 MET cc_start: 0.9002 (tpp) cc_final: 0.8636 (tmm) REVERT: A 558 LEU cc_start: 0.9105 (mt) cc_final: 0.8782 (pp) REVERT: A 583 MET cc_start: 0.8657 (pmm) cc_final: 0.8267 (pmm) REVERT: B 1 MET cc_start: 0.6940 (tpt) cc_final: 0.6512 (tpp) REVERT: B 19 PHE cc_start: 0.8160 (t80) cc_final: 0.7914 (t80) REVERT: B 515 MET cc_start: 0.9012 (tpp) cc_final: 0.8652 (tmm) REVERT: B 558 LEU cc_start: 0.9253 (mt) cc_final: 0.8809 (pp) REVERT: B 559 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.8641 (mp0) REVERT: B 583 MET cc_start: 0.8582 (pmm) cc_final: 0.8219 (pmm) outliers start: 15 outliers final: 7 residues processed: 92 average time/residue: 0.4914 time to fit residues: 50.8086 Evaluate side-chains 84 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 461 PHE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain B residue 123 LEU Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 559 GLU Chi-restraints excluded: chain B residue 561 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 137 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 140 optimal weight: 0.8980 chunk 71 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3337 r_free = 0.3337 target = 0.073964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.053870 restraints weight = 38036.411| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 3.27 r_work: 0.2640 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 12540 Z= 0.115 Angle : 0.648 14.069 17157 Z= 0.289 Chirality : 0.041 0.328 1826 Planarity : 0.003 0.040 2119 Dihedral : 7.959 88.609 1853 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.27 % Allowed : 2.67 % Favored : 97.06 % Rotamer: Outliers : 1.19 % Allowed : 16.30 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.78 % 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 (0.23), residues: 1496 helix: 2.66 (0.16), residues: 1052 sheet: None (None), residues: 0 loop : -0.64 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 186 TYR 0.013 0.001 TYR B 462 PHE 0.009 0.001 PHE A 527 TRP 0.035 0.001 TRP A 488 HIS 0.007 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.11 (12536) covalent geometry : angle 0.64818 / 0.29 (17157) hydrogen bonds : bond 0.03673 / 2.48 ( 834) hydrogen bonds : angle 4.18207 / 3.12 ( 2421) Misc. bond : bond 0.07611 / 3.83 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3244.99 seconds wall clock time: 56 minutes 15.51 seconds (3375.51 seconds total)