Starting phenix.real_space_refine on Fri Jul 3 01:27:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kcm_22816/07_2026/7kcm_22816.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kcm_22816/07_2026/7kcm_22816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7kcm_22816/07_2026/7kcm_22816.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kcm_22816/07_2026/7kcm_22816.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kcm_22816/07_2026/7kcm_22816.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kcm_22816/07_2026/7kcm_22816.map" model { file = "/net/cci-nas-00/data/ceres_data/7kcm_22816/07_2026/7kcm_22816.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kcm_22816/07_2026/7kcm_22816.cif" } resolution = 3.43 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 522 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: 8 Type Number sf(0) Gaussians K 2 8.98 5 Fe 2 7.16 5 P 6 5.49 5 Mg 2 5.21 5 S 55 5.16 5 C 6845 2.51 5 N 1883 2.21 5 O 2043 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.02s 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: 10838 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 612, 4890 Classifications: {'peptide': 612} Link IDs: {'PTRANS': 18, 'TRANS': 593} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 4915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4915 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 18, 'TRANS': 595} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 963 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 113} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 1, ' MG': 1, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10324 SG CYS C 101 61.372 22.904 42.313 1.00137.29 S ATOM 10403 SG CYS C 113 61.826 21.691 38.704 1.00144.04 S ATOM 10270 SG CYS C 93 58.230 17.757 41.308 1.00147.05 S ATOM 10308 SG CYS C 98 57.052 20.959 43.032 1.00140.48 S Time building chain proxies: 2.61, per 1000 atoms: 0.24 Number of scatterers: 10838 At special positions: 0 Unit cell: (96.866, 91.982, 130.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 2 26.01 K 2 19.00 S 55 16.00 P 6 15.00 Mg 2 11.99 O 2043 8.00 N 1883 7.00 C 6845 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 262.3 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES C 201 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 98 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 113 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 101 " pdb="FE2 FES C 201 " - pdb=" SG CYS C 93 " Number of angles added : 6 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2568 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 14 sheets defined 44.2% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.632A pdb=" N LEU A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 135 removed outlier: 4.326A pdb=" N ARG A 114 " --> pdb=" O GLU A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 172 Processing helix chain 'A' and resid 178 through 186 removed outlier: 3.780A pdb=" N ALA A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 210 Processing helix chain 'A' and resid 261 through 265 removed outlier: 3.809A pdb=" N PHE A 264 " --> pdb=" O CYS A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 307 through 319 Processing helix chain 'A' and resid 382 through 386 removed outlier: 4.337A pdb=" N PHE A 386 " --> pdb=" O TRP A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 433 Processing helix chain 'A' and resid 433 through 455 removed outlier: 6.712A pdb=" N LEU A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N PHE A 447 " --> pdb=" O ASP A 443 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N MET A 448 " --> pdb=" O TYR A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 466 Processing helix chain 'A' and resid 482 through 490 removed outlier: 3.579A pdb=" N ARG A 489 " --> pdb=" O GLU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 510 Processing helix chain 'A' and resid 511 through 518 Processing helix chain 'A' and resid 531 through 540 Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'A' and resid 575 through 590 Processing helix chain 'A' and resid 614 through 628 Processing helix chain 'A' and resid 648 through 658 removed outlier: 3.743A pdb=" N LEU A 654 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ASN A 655 " --> pdb=" O ILE A 651 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLN A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 680 Processing helix chain 'A' and resid 686 through 700 removed outlier: 3.758A pdb=" N VAL A 690 " --> pdb=" O PRO A 686 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLY A 691 " --> pdb=" O ARG A 687 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ARG A 692 " --> pdb=" O ALA A 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 Processing helix chain 'B' and resid 110 through 134 removed outlier: 4.129A pdb=" N ARG B 114 " --> pdb=" O GLU B 110 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP B 134 " --> pdb=" O LYS B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 172 Processing helix chain 'B' and resid 178 through 186 removed outlier: 4.032A pdb=" N ALA B 182 " --> pdb=" O SER B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 266 through 278 Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.520A pdb=" N VAL B 306 " --> pdb=" O PRO B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 Processing helix chain 'B' and resid 381 through 387 removed outlier: 4.344A pdb=" N PHE B 386 " --> pdb=" O TRP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 433 Processing helix chain 'B' and resid 434 through 455 removed outlier: 6.858A pdb=" N LEU B 446 " --> pdb=" O GLU B 442 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N PHE B 447 " --> pdb=" O ASP B 443 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N MET B 448 " --> pdb=" O TYR B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 466 Processing helix chain 'B' and resid 483 through 490 Processing helix chain 'B' and resid 504 through 510 Processing helix chain 'B' and resid 511 through 518 Processing helix chain 'B' and resid 532 through 540 Processing helix chain 'B' and resid 550 through 557 Processing helix chain 'B' and resid 575 through 590 Processing helix chain 'B' and resid 614 through 623 removed outlier: 3.584A pdb=" N HIS B 620 " --> pdb=" O GLY B 616 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG B 623 " --> pdb=" O ARG B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 639 Processing helix chain 'B' and resid 648 through 661 removed outlier: 3.721A pdb=" N GLN B 656 " --> pdb=" O LYS B 652 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ALA B 659 " --> pdb=" O ASN B 655 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 660 " --> pdb=" O GLN B 656 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 680 Processing helix chain 'B' and resid 688 through 701 removed outlier: 4.488A pdb=" N ARG B 692 " --> pdb=" O ALA B 688 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 704 No H-bonds generated for 'chain 'B' and resid 702 through 704' Processing helix chain 'C' and resid 66 through 68 No H-bonds generated for 'chain 'C' and resid 66 through 68' Processing helix chain 'C' and resid 71 through 82 removed outlier: 3.857A pdb=" N ALA C 75 " --> pdb=" O MET C 71 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 140 removed outlier: 4.418A pdb=" N VAL C 140 " --> pdb=" O ILE C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 152 removed outlier: 3.791A pdb=" N GLN C 149 " --> pdb=" O ASN C 145 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 80 through 81 Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 81 removed outlier: 4.005A pdb=" N ARG B 214 " --> pdb=" O HIS B 256 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 92 removed outlier: 7.228A pdb=" N GLN A 91 " --> pdb=" O ILE B 175 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 291 removed outlier: 4.233A pdb=" N ARG A 214 " --> pdb=" O HIS A 256 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 290 through 291 removed outlier: 4.233A pdb=" N ARG A 214 " --> pdb=" O HIS A 256 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 174 through 175 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 333 removed outlier: 3.840A pdb=" N TYR A 327 " --> pdb=" O VAL A 345 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 471 through 472 removed outlier: 3.706A pdb=" N GLU A 471 " --> pdb=" O PHE A 526 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR A 499 " --> pdb=" O ILE A 548 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 596 through 599 removed outlier: 6.290A pdb=" N ASN A 596 " --> pdb=" O LEU A 642 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ILE A 644 " --> pdb=" O ASN A 596 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LYS A 598 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 325 through 333 removed outlier: 3.589A pdb=" N TYR B 327 " --> pdb=" O VAL B 345 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER B 393 " --> pdb=" O TYR B 366 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 469 through 470 Processing sheet with id=AB3, first strand: chain 'B' and resid 524 through 527 removed outlier: 8.950A pdb=" N LEU B 525 " --> pdb=" O ASN B 496 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N TYR B 498 " --> pdb=" O LEU B 525 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N CYS B 527 " --> pdb=" O TYR B 498 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU B 500 " --> pdb=" O CYS B 527 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE B 497 " --> pdb=" O ILE B 548 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 597 through 599 removed outlier: 6.518A pdb=" N LYS B 598 " --> pdb=" O ILE B 644 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR B 641 " --> pdb=" O THR B 611 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 57 through 64 removed outlier: 4.306A pdb=" N HIS C 57 " --> pdb=" O ARG C 46 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG C 46 " --> pdb=" O HIS C 57 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN C 59 " --> pdb=" O ILE C 44 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N SER C 125 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LYS C 41 " --> pdb=" O SER C 125 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N ILE C 127 " --> pdb=" O LYS C 41 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ALA C 43 " --> pdb=" O ILE C 127 " (cutoff:3.500A) 537 hydrogen bonds defined for protein. 1488 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: 1.67 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.42: 4537 1.42 - 1.62: 6393 1.62 - 1.81: 96 1.81 - 2.01: 1 2.01 - 2.20: 4 Bond restraints: 11031 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.556 0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.73e+01 bond pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.71e+01 bond pdb=" O5' ANP A 801 " pdb=" PA ANP A 801 " ideal model delta sigma weight residual 1.655 1.579 0.076 2.00e-02 2.50e+03 1.44e+01 ... (remaining 11026 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.37: 14812 3.37 - 6.73: 61 6.73 - 10.10: 9 10.10 - 13.46: 2 13.46 - 16.83: 2 Bond angle restraints: 14886 Sorted by residual: angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 110.12 16.83 3.00e+00 1.11e-01 3.15e+01 angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 110.27 16.68 3.00e+00 1.11e-01 3.09e+01 angle pdb=" O1B ANP B 801 " pdb=" PB ANP B 801 " pdb=" O2B ANP B 801 " ideal model delta sigma weight residual 120.08 108.91 11.17 3.00e+00 1.11e-01 1.39e+01 angle pdb=" O1B ANP A 801 " pdb=" PB ANP A 801 " pdb=" O2B ANP A 801 " ideal model delta sigma weight residual 120.08 108.95 11.13 3.00e+00 1.11e-01 1.38e+01 angle pdb=" CA ARG C 94 " pdb=" CB ARG C 94 " pdb=" CG ARG C 94 " ideal model delta sigma weight residual 114.10 120.88 -6.78 2.00e+00 2.50e-01 1.15e+01 ... (remaining 14881 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 5956 17.88 - 35.75: 611 35.75 - 53.62: 121 53.62 - 71.50: 34 71.50 - 89.37: 16 Dihedral angle restraints: 6738 sinusoidal: 2783 harmonic: 3955 Sorted by residual: dihedral pdb=" CA LEU C 130 " pdb=" C LEU C 130 " pdb=" N PRO C 131 " pdb=" CA PRO C 131 " ideal model delta harmonic sigma weight residual -180.00 -156.16 -23.84 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA TYR B 277 " pdb=" C TYR B 277 " pdb=" N SER B 278 " pdb=" CA SER B 278 " ideal model delta harmonic sigma weight residual -180.00 -162.36 -17.64 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ASP B 158 " pdb=" CB ASP B 158 " pdb=" CG ASP B 158 " pdb=" OD1 ASP B 158 " ideal model delta sinusoidal sigma weight residual -30.00 -88.78 58.78 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 6735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1432 0.055 - 0.109: 207 0.109 - 0.164: 32 0.164 - 0.219: 1 0.219 - 0.273: 2 Chirality restraints: 1674 Sorted by residual: chirality pdb=" C3' ANP B 801 " pdb=" C2' ANP B 801 " pdb=" C4' ANP B 801 " pdb=" O3' ANP B 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C3' ANP A 801 " pdb=" C2' ANP A 801 " pdb=" C4' ANP A 801 " pdb=" O3' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA GLU C 154 " pdb=" N GLU C 154 " pdb=" C GLU C 154 " pdb=" CB GLU C 154 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.81e-01 ... (remaining 1671 not shown) Planarity restraints: 1889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 661 " 0.068 5.00e-02 4.00e+02 1.03e-01 1.69e+01 pdb=" N PRO A 662 " -0.178 5.00e-02 4.00e+02 pdb=" CA PRO A 662 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 662 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 585 " -0.012 2.00e-02 2.50e+03 1.20e-02 3.62e+00 pdb=" CG TRP B 585 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP B 585 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP B 585 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 585 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 585 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 585 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 585 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 585 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 585 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 585 " 0.011 2.00e-02 2.50e+03 9.12e-03 2.08e+00 pdb=" CG TRP A 585 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 585 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP A 585 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 585 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 585 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 585 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 585 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 585 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 585 " 0.002 2.00e-02 2.50e+03 ... (remaining 1886 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.62: 148 2.62 - 3.25: 10854 3.25 - 3.88: 22134 3.88 - 4.51: 29363 4.51 - 5.14: 46205 Nonbonded interactions: 108704 Sorted by model distance: nonbonded pdb=" O3G ANP A 801 " pdb="MG MG A 802 " model vdw 1.994 2.170 nonbonded pdb=" OD1 ASN A 119 " pdb="MG MG A 802 " model vdw 2.010 2.170 nonbonded pdb=" O3G ANP B 801 " pdb="MG MG B 802 " model vdw 2.042 2.170 nonbonded pdb=" OD1 ASN B 119 " pdb="MG MG B 802 " model vdw 2.048 2.170 nonbonded pdb=" O1B ANP B 801 " pdb="MG MG B 802 " model vdw 2.068 2.170 ... (remaining 108699 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 70 through 355 or resid 361 through 626 or resid 631 throu \ gh 803)) selection = (chain 'B' and (resid 70 through 355 or resid 361 through 625 or resid 631 or re \ sid 636 through 803)) } 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: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 11.540 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 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 : 0.004 0.144 11035 Z= 0.188 Angle : 0.650 16.828 14892 Z= 0.322 Chirality : 0.041 0.273 1674 Planarity : 0.003 0.103 1889 Dihedral : 15.766 89.374 4170 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % 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: 0.75 (0.25), residues: 1329 helix: 1.26 (0.24), residues: 543 sheet: 1.47 (0.40), residues: 200 loop : -0.55 (0.28), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 540 TYR 0.014 0.001 TYR C 150 PHE 0.012 0.001 PHE A 112 TRP 0.033 0.002 TRP B 585 HIS 0.007 0.001 HIS A 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.19 (11031) covalent geometry : angle 0.64298 / 0.32 (14886) hydrogen bonds : bond 0.16567 / 11.51 ( 502) hydrogen bonds : angle 6.53142 / 4.76 ( 1488) metal coordination : bond 0.00579 / 0.40 ( 4) metal coordination : angle 4.84622 / 2.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 586 MET cc_start: 0.8787 (mpp) cc_final: 0.7777 (mpp) REVERT: B 292 MET cc_start: 0.7199 (ppp) cc_final: 0.6933 (ppp) REVERT: B 517 MET cc_start: 0.6882 (tmm) cc_final: 0.6580 (tmm) REVERT: B 576 GLU cc_start: 0.7480 (tp30) cc_final: 0.7231 (tp30) REVERT: C 44 ILE cc_start: 0.8049 (mt) cc_final: 0.7838 (mm) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.0896 time to fit residues: 18.4926 Evaluate side-chains 112 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 112 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.0670 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.3720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 506 HIS A 620 HIS A 704 HIS B 288 ASN B 510 HIS B 671 GLN C 132 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.115784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.091138 restraints weight = 20877.240| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 2.99 r_work: 0.3065 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11035 Z= 0.155 Angle : 0.574 11.421 14892 Z= 0.287 Chirality : 0.042 0.162 1674 Planarity : 0.004 0.071 1889 Dihedral : 4.874 58.587 1484 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.51 % Allowed : 9.08 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.24), residues: 1329 helix: 1.23 (0.23), residues: 538 sheet: 1.11 (0.39), residues: 200 loop : -0.49 (0.28), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 495 TYR 0.014 0.001 TYR A 437 PHE 0.018 0.001 PHE C 146 TRP 0.015 0.002 TRP B 585 HIS 0.012 0.001 HIS B 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (11031) covalent geometry : angle 0.55678 / 0.29 (14886) hydrogen bonds : bond 0.03643 / 2.42 ( 502) hydrogen bonds : angle 4.87541 / 3.54 ( 1488) metal coordination : bond 0.01206 / 0.76 ( 4) metal coordination : angle 6.96271 / 3.94 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 118 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 583 MET cc_start: 0.7703 (mtm) cc_final: 0.7450 (mtm) REVERT: B 517 MET cc_start: 0.7654 (tmm) cc_final: 0.7279 (tmm) REVERT: B 624 MET cc_start: 0.7366 (ppp) cc_final: 0.7161 (ppp) outliers start: 6 outliers final: 3 residues processed: 120 average time/residue: 0.1005 time to fit residues: 17.1845 Evaluate side-chains 114 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 111 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 390 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 89 optimal weight: 9.9990 chunk 67 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 114 optimal weight: 9.9990 chunk 104 optimal weight: 0.5980 chunk 106 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 510 HIS B 620 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.115493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.091115 restraints weight = 21089.118| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.87 r_work: 0.3059 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11035 Z= 0.129 Angle : 0.532 13.291 14892 Z= 0.265 Chirality : 0.041 0.156 1674 Planarity : 0.003 0.060 1889 Dihedral : 4.728 55.537 1484 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.85 % Allowed : 11.12 % Favored : 88.03 % 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: 0.60 (0.24), residues: 1329 helix: 1.26 (0.23), residues: 539 sheet: 0.98 (0.40), residues: 183 loop : -0.54 (0.27), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 495 TYR 0.012 0.001 TYR A 437 PHE 0.007 0.001 PHE C 146 TRP 0.018 0.002 TRP B 585 HIS 0.005 0.001 HIS B 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (11031) covalent geometry : angle 0.51602 / 0.27 (14886) hydrogen bonds : bond 0.03311 / 2.20 ( 502) hydrogen bonds : angle 4.62863 / 3.35 ( 1488) metal coordination : bond 0.00866 / 0.59 ( 4) metal coordination : angle 6.44484 / 3.54 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 586 MET cc_start: 0.8968 (mpp) cc_final: 0.8400 (mpp) REVERT: B 292 MET cc_start: 0.8105 (ppp) cc_final: 0.7732 (ppp) REVERT: B 517 MET cc_start: 0.7731 (tmm) cc_final: 0.7386 (tmm) REVERT: B 576 GLU cc_start: 0.7732 (tp30) cc_final: 0.7458 (tp30) REVERT: B 692 ARG cc_start: 0.8488 (mtm180) cc_final: 0.8271 (mtt90) REVERT: C 44 ILE cc_start: 0.8218 (mm) cc_final: 0.8012 (mp) outliers start: 10 outliers final: 5 residues processed: 131 average time/residue: 0.1057 time to fit residues: 20.1649 Evaluate side-chains 121 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 116 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain C residue 146 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 99 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 88 optimal weight: 0.7980 chunk 52 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 70 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 330 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.112496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.087807 restraints weight = 21122.097| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.80 r_work: 0.2989 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11035 Z= 0.192 Angle : 0.582 14.609 14892 Z= 0.288 Chirality : 0.042 0.162 1674 Planarity : 0.004 0.053 1889 Dihedral : 4.831 54.263 1484 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.53 % Allowed : 13.75 % Favored : 84.72 % 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: 0.49 (0.24), residues: 1329 helix: 1.21 (0.23), residues: 539 sheet: 0.81 (0.38), residues: 190 loop : -0.61 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 495 TYR 0.020 0.002 TYR A 315 PHE 0.011 0.001 PHE B 264 TRP 0.024 0.002 TRP A 585 HIS 0.004 0.001 HIS A 330 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.19 (11031) covalent geometry : angle 0.56594 / 0.29 (14886) hydrogen bonds : bond 0.03422 / 2.28 ( 502) hydrogen bonds : angle 4.65965 / 3.36 ( 1488) metal coordination : bond 0.01428 / 0.87 ( 4) metal coordination : angle 6.75332 / 3.72 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 117 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: A 586 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8434 (mpp) REVERT: B 576 GLU cc_start: 0.7833 (tp30) cc_final: 0.7548 (tp30) REVERT: B 692 ARG cc_start: 0.8553 (mtm180) cc_final: 0.8110 (mtt90) outliers start: 18 outliers final: 11 residues processed: 129 average time/residue: 0.0931 time to fit residues: 17.6598 Evaluate side-chains 120 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain C residue 146 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 7 optimal weight: 3.9990 chunk 97 optimal weight: 0.7980 chunk 118 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 116 optimal weight: 7.9990 chunk 16 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 190 GLN B 279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.111988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.087444 restraints weight = 21005.598| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.77 r_work: 0.2987 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 11035 Z= 0.203 Angle : 0.583 13.608 14892 Z= 0.290 Chirality : 0.042 0.164 1674 Planarity : 0.003 0.051 1889 Dihedral : 4.884 53.747 1484 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.04 % Allowed : 14.52 % Favored : 83.45 % 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: 0.33 (0.24), residues: 1329 helix: 1.11 (0.23), residues: 540 sheet: 0.63 (0.38), residues: 191 loop : -0.72 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 469 TYR 0.032 0.002 TYR C 147 PHE 0.012 0.001 PHE C 146 TRP 0.026 0.002 TRP A 585 HIS 0.003 0.001 HIS B 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.20 (11031) covalent geometry : angle 0.56585 / 0.29 (14886) hydrogen bonds : bond 0.03382 / 2.24 ( 502) hydrogen bonds : angle 4.69139 / 3.37 ( 1488) metal coordination : bond 0.01510 / 0.91 ( 4) metal coordination : angle 6.93832 / 4.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7556 (mp0) REVERT: A 582 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.7723 (tp) REVERT: A 586 MET cc_start: 0.9036 (OUTLIER) cc_final: 0.8472 (mpp) REVERT: B 517 MET cc_start: 0.7854 (tmm) cc_final: 0.7632 (tmm) REVERT: B 670 ASP cc_start: 0.8756 (t70) cc_final: 0.8510 (m-30) REVERT: B 692 ARG cc_start: 0.8608 (mtm180) cc_final: 0.8306 (mtt90) outliers start: 24 outliers final: 14 residues processed: 137 average time/residue: 0.0987 time to fit residues: 19.9198 Evaluate side-chains 130 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 446 LEU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain C residue 146 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 80 optimal weight: 0.8980 chunk 15 optimal weight: 10.0000 chunk 85 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 279 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.114064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.089312 restraints weight = 21084.081| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.97 r_work: 0.3012 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11035 Z= 0.120 Angle : 0.554 13.709 14892 Z= 0.271 Chirality : 0.041 0.168 1674 Planarity : 0.003 0.050 1889 Dihedral : 4.674 50.351 1484 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.38 % Allowed : 14.77 % Favored : 82.85 % 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: 0.38 (0.24), residues: 1329 helix: 1.17 (0.23), residues: 541 sheet: 0.49 (0.38), residues: 193 loop : -0.65 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 469 TYR 0.037 0.001 TYR C 147 PHE 0.012 0.001 PHE C 146 TRP 0.029 0.002 TRP A 585 HIS 0.004 0.001 HIS A 311 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (11031) covalent geometry : angle 0.54012 / 0.27 (14886) hydrogen bonds : bond 0.03068 / 2.04 ( 502) hydrogen bonds : angle 4.55066 / 3.27 ( 1488) metal coordination : bond 0.00955 / 0.61 ( 4) metal coordination : angle 6.05806 / 3.79 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7513 (mp0) REVERT: A 586 MET cc_start: 0.8972 (OUTLIER) cc_final: 0.8429 (mpp) REVERT: B 292 MET cc_start: 0.8132 (ppp) cc_final: 0.7646 (ppp) REVERT: B 517 MET cc_start: 0.7944 (tmm) cc_final: 0.7665 (tmm) REVERT: B 586 MET cc_start: 0.8708 (mtm) cc_final: 0.8410 (mtt) REVERT: B 624 MET cc_start: 0.7571 (ppp) cc_final: 0.7326 (mmm) REVERT: B 670 ASP cc_start: 0.8742 (t70) cc_final: 0.8532 (m-30) REVERT: B 692 ARG cc_start: 0.8597 (mtm180) cc_final: 0.8278 (mtt90) REVERT: C 151 LYS cc_start: 0.8368 (mmtt) cc_final: 0.8095 (mmtp) outliers start: 28 outliers final: 13 residues processed: 140 average time/residue: 0.0989 time to fit residues: 20.5813 Evaluate side-chains 128 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain C residue 146 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 90 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 132 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 279 ASN B 429 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.111965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.087645 restraints weight = 20972.373| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.78 r_work: 0.2978 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11035 Z= 0.190 Angle : 0.602 14.177 14892 Z= 0.295 Chirality : 0.042 0.177 1674 Planarity : 0.004 0.049 1889 Dihedral : 4.780 50.752 1484 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 2.21 % Allowed : 15.28 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.29 (0.24), residues: 1329 helix: 1.12 (0.23), residues: 541 sheet: 0.43 (0.38), residues: 193 loop : -0.72 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 469 TYR 0.031 0.002 TYR C 147 PHE 0.014 0.001 PHE C 146 TRP 0.032 0.002 TRP A 585 HIS 0.006 0.001 HIS B 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (11031) covalent geometry : angle 0.58673 / 0.29 (14886) hydrogen bonds : bond 0.03266 / 2.17 ( 502) hydrogen bonds : angle 4.63333 / 3.33 ( 1488) metal coordination : bond 0.01888 / 1.06 ( 4) metal coordination : angle 6.72474 / 4.51 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7491 (mp0) REVERT: A 586 MET cc_start: 0.9015 (OUTLIER) cc_final: 0.8446 (mpp) REVERT: B 292 MET cc_start: 0.8274 (ppp) cc_final: 0.7732 (ppp) REVERT: B 490 MET cc_start: 0.8339 (ptt) cc_final: 0.8134 (ptt) REVERT: B 586 MET cc_start: 0.8692 (mtm) cc_final: 0.8381 (mtt) REVERT: B 670 ASP cc_start: 0.8768 (t70) cc_final: 0.8547 (m-30) REVERT: B 692 ARG cc_start: 0.8615 (mtm180) cc_final: 0.8360 (mtt90) outliers start: 26 outliers final: 19 residues processed: 134 average time/residue: 0.0963 time to fit residues: 19.1905 Evaluate side-chains 130 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain C residue 146 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 60 optimal weight: 8.9990 chunk 30 optimal weight: 0.1980 chunk 23 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 75 optimal weight: 0.0570 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS B 279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.114307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.090320 restraints weight = 21045.970| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.80 r_work: 0.3031 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11035 Z= 0.115 Angle : 0.553 13.860 14892 Z= 0.273 Chirality : 0.041 0.184 1674 Planarity : 0.003 0.051 1889 Dihedral : 4.576 46.991 1484 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.04 % Allowed : 15.79 % Favored : 82.17 % 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: 0.40 (0.24), residues: 1329 helix: 1.24 (0.23), residues: 537 sheet: 0.49 (0.39), residues: 194 loop : -0.68 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 469 TYR 0.031 0.001 TYR C 147 PHE 0.013 0.001 PHE C 146 TRP 0.032 0.002 TRP A 585 HIS 0.005 0.001 HIS B 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (11031) covalent geometry : angle 0.53989 / 0.27 (14886) hydrogen bonds : bond 0.02959 / 1.96 ( 502) hydrogen bonds : angle 4.48756 / 3.23 ( 1488) metal coordination : bond 0.00940 / 0.58 ( 4) metal coordination : angle 6.01478 / 4.32 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: A 582 LEU cc_start: 0.8734 (OUTLIER) cc_final: 0.7646 (tp) REVERT: A 586 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8453 (mpp) REVERT: B 353 PHE cc_start: 0.7531 (t80) cc_final: 0.7311 (t80) REVERT: B 586 MET cc_start: 0.8725 (mtm) cc_final: 0.8430 (mtt) REVERT: B 692 ARG cc_start: 0.8593 (mtm180) cc_final: 0.8337 (mtt90) REVERT: C 71 MET cc_start: 0.6476 (ttt) cc_final: 0.5882 (ptp) outliers start: 24 outliers final: 17 residues processed: 135 average time/residue: 0.0997 time to fit residues: 19.9104 Evaluate side-chains 129 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain C residue 146 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 34 optimal weight: 3.9990 chunk 121 optimal weight: 0.6980 chunk 127 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 73 optimal weight: 0.1980 chunk 14 optimal weight: 2.9990 chunk 45 optimal weight: 0.0870 chunk 131 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS A 406 GLN B 279 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.113469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.089672 restraints weight = 20925.183| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.78 r_work: 0.3017 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11035 Z= 0.125 Angle : 0.571 13.749 14892 Z= 0.280 Chirality : 0.041 0.190 1674 Planarity : 0.003 0.049 1889 Dihedral : 4.522 45.253 1484 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.04 % Allowed : 16.04 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.24), residues: 1329 helix: 1.28 (0.23), residues: 536 sheet: 0.44 (0.38), residues: 194 loop : -0.70 (0.27), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.017 0.001 TYR A 315 PHE 0.013 0.001 PHE C 146 TRP 0.032 0.002 TRP A 585 HIS 0.007 0.001 HIS B 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (11031) covalent geometry : angle 0.55893 / 0.28 (14886) hydrogen bonds : bond 0.02997 / 1.99 ( 502) hydrogen bonds : angle 4.43388 / 3.18 ( 1488) metal coordination : bond 0.01006 / 0.62 ( 4) metal coordination : angle 5.74960 / 3.96 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7459 (mp0) REVERT: A 582 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.7615 (tp) REVERT: A 586 MET cc_start: 0.8960 (OUTLIER) cc_final: 0.8449 (mpp) REVERT: A 609 MET cc_start: 0.8447 (ttm) cc_final: 0.8224 (ttm) REVERT: B 292 MET cc_start: 0.8042 (ppp) cc_final: 0.7684 (ppp) REVERT: B 353 PHE cc_start: 0.7545 (t80) cc_final: 0.7304 (t80) REVERT: B 586 MET cc_start: 0.8753 (mtm) cc_final: 0.8457 (mtt) REVERT: B 692 ARG cc_start: 0.8560 (mtm180) cc_final: 0.8186 (mtt90) REVERT: C 71 MET cc_start: 0.6470 (ttt) cc_final: 0.5911 (ptp) outliers start: 24 outliers final: 19 residues processed: 132 average time/residue: 0.1006 time to fit residues: 19.4470 Evaluate side-chains 130 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 156 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 72 HIS Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 672 ILE Chi-restraints excluded: chain B residue 683 VAL Chi-restraints excluded: chain C residue 146 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 23 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 0.0870 chunk 123 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 67 optimal weight: 0.3980 chunk 105 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS B 279 ASN B 704 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.114740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.090813 restraints weight = 21010.465| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.58 r_work: 0.3062 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11035 Z= 0.111 Angle : 0.571 15.491 14892 Z= 0.280 Chirality : 0.041 0.187 1674 Planarity : 0.003 0.055 1889 Dihedral : 4.481 43.968 1484 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.61 % Allowed : 16.64 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.24), residues: 1329 helix: 1.29 (0.23), residues: 536 sheet: 0.46 (0.38), residues: 193 loop : -0.71 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 128 TYR 0.020 0.001 TYR A 317 PHE 0.014 0.001 PHE B 280 TRP 0.033 0.002 TRP A 585 HIS 0.007 0.001 HIS B 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (11031) covalent geometry : angle 0.55961 / 0.28 (14886) hydrogen bonds : bond 0.02938 / 1.94 ( 502) hydrogen bonds : angle 4.39385 / 3.15 ( 1488) metal coordination : bond 0.00775 / 0.49 ( 4) metal coordination : angle 5.60514 / 3.86 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2658 Ramachandran restraints generated. 1329 Oldfield, 0 Emsley, 1329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 462 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: A 582 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.7618 (tp) REVERT: A 586 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8445 (mpp) REVERT: A 609 MET cc_start: 0.8349 (ttm) cc_final: 0.8128 (ttm) REVERT: A 703 ARG cc_start: 0.7325 (tpp-160) cc_final: 0.7032 (mmt-90) REVERT: B 353 PHE cc_start: 0.7475 (t80) cc_final: 0.7233 (t80) REVERT: B 586 MET cc_start: 0.8685 (mtm) cc_final: 0.8381 (mtt) REVERT: B 692 ARG cc_start: 0.8523 (mtm180) cc_final: 0.8146 (mtt90) REVERT: C 71 MET cc_start: 0.6359 (ttt) cc_final: 0.5847 (ptp) REVERT: C 151 LYS cc_start: 0.8024 (mmtm) cc_final: 0.7795 (mmtm) outliers start: 19 outliers final: 14 residues processed: 127 average time/residue: 0.0998 time to fit residues: 18.5413 Evaluate side-chains 125 residues out of total 1182 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 442 GLU Chi-restraints excluded: chain A residue 462 GLU Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 586 MET Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain B residue 110 GLU Chi-restraints excluded: chain B residue 279 ASN Chi-restraints excluded: chain B residue 306 VAL Chi-restraints excluded: chain B residue 390 VAL Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain C residue 146 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 2 optimal weight: 0.0000 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 91 optimal weight: 0.0020 chunk 130 optimal weight: 0.1980 chunk 30 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 102 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 144 HIS B 279 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.112608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.088901 restraints weight = 21096.486| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.77 r_work: 0.3004 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11035 Z= 0.155 Angle : 0.588 15.563 14892 Z= 0.289 Chirality : 0.042 0.189 1674 Planarity : 0.003 0.050 1889 Dihedral : 4.548 45.547 1484 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 1.95 % Allowed : 16.72 % Favored : 81.32 % 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: 0.37 (0.24), residues: 1329 helix: 1.26 (0.23), residues: 536 sheet: 0.47 (0.39), residues: 194 loop : -0.74 (0.26), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 290 TYR 0.024 0.002 TYR A 317 PHE 0.014 0.001 PHE C 146 TRP 0.033 0.002 TRP A 585 HIS 0.007 0.001 HIS B 620 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (11031) covalent geometry : angle 0.57575 / 0.29 (14886) hydrogen bonds : bond 0.03074 / 2.04 ( 502) hydrogen bonds : angle 4.48955 / 3.22 ( 1488) metal coordination : bond 0.01008 / 0.66 ( 4) metal coordination : angle 5.90323 / 4.35 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2122.94 seconds wall clock time: 37 minutes 29.34 seconds (2249.34 seconds total)