Starting phenix.real_space_refine on Wed Aug 5 17:18:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xk3_38414/08_2026/8xk3_38414.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xk3_38414/08_2026/8xk3_38414.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xk3_38414/08_2026/8xk3_38414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xk3_38414/08_2026/8xk3_38414.map" model { file = "/net/cci-nas-00/data/ceres_data/8xk3_38414/08_2026/8xk3_38414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xk3_38414/08_2026/8xk3_38414.cif" } resolution = 2.76 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= 0.078 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 5719 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: 6 Type Number sf(0) Gaussians Mn 3 7.51 5 P 32 5.49 5 S 29 5.16 5 C 3910 2.51 5 N 1115 2.21 5 O 1220 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 6309 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5621 Classifications: {'peptide': 692} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 23, 'TRANS': 668} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 358 Classifications: {'DNA': 17} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 16} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {' DG:plan2': 1} Unresolved non-hydrogen planarities: 2 Chain: "C" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 179 Classifications: {'DNA': 9} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 8} Chain: "c" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 119 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 1.58, per 1000 atoms: 0.25 Number of scatterers: 6309 At special positions: 0 Unit cell: (74.037, 89.355, 107.226, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 3 24.99 S 29 16.00 P 32 15.00 O 1220 8.00 N 1115 7.00 C 3910 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: 0.52 Conformation dependent library (CDL) restraints added in 310.3 milliseconds 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1320 Finding SS restraints... Warning! O2 atom is missing from residue DC c 6 Was trying to link: DC c 6 O2 with DG B 11 N2, Saenger class: 19 Warning! O2 atom is missing from residue DC c 6 Was trying to link: DC c 6 O2 with DG B 11 N1, Saenger class: 22 Warning! O2 atom is missing from residue DC c 6 Was trying to link: DC c 6 O2 with DG B 11 N2, Saenger class: 19 Warning! O2 atom is missing from residue DC c 6 Was trying to link: DC c 6 O2 with DG B 11 N1, Saenger class: 22 Warning! O2 atom is missing from residue DC c 6 Was trying to link: DC c 6 O2 with DG B 11 N2, Saenger class: 19 Warning! O2 atom is missing from residue DC c 6 Was trying to link: DC c 6 O2 with DG B 11 N1, Saenger class: 22 Warning! N2 atom is missing from residue DG B 12 Was trying to link: DC c 5 O2 with DG B 12 N2, Saenger class: 19 Warning! N2 atom is missing from residue DG B 12 Was trying to link: DC c 5 N3 with DG B 12 N2, Saenger class: 22 Secondary structure from input PDB file: 22 helices and 8 sheets defined 36.7% alpha, 26.4% beta 11 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 36 through 48 Processing helix chain 'A' and resid 84 through 108 removed outlier: 3.699A pdb=" N HIS A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 165 removed outlier: 3.535A pdb=" N MET A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 269 removed outlier: 3.981A pdb=" N LYS A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS A 267 " --> pdb=" O ASN A 263 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 288 removed outlier: 3.520A pdb=" N TRP A 282 " --> pdb=" O CYS A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 333 removed outlier: 3.547A pdb=" N GLY A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 354 Processing helix chain 'A' and resid 358 through 373 Processing helix chain 'A' and resid 394 through 400 Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 422 through 428 Processing helix chain 'A' and resid 432 through 444 Processing helix chain 'A' and resid 453 through 468 removed outlier: 3.828A pdb=" N ILE A 457 " --> pdb=" O THR A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 488 Processing helix chain 'A' and resid 491 through 508 removed outlier: 4.077A pdb=" N THR A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 585 Processing helix chain 'A' and resid 602 through 613 removed outlier: 3.865A pdb=" N VAL A 606 " --> pdb=" O HIS A 602 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU A 607 " --> pdb=" O THR A 603 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N HIS A 612 " --> pdb=" O LYS A 608 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR A 613 " --> pdb=" O ILE A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 692 Processing helix chain 'A' and resid 693 through 695 No H-bonds generated for 'chain 'A' and resid 693 through 695' Processing helix chain 'A' and resid 706 through 721 removed outlier: 3.681A pdb=" N LEU A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 5 Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 13 removed outlier: 5.430A pdb=" N ILE A 144 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL A 127 " --> pdb=" O GLN A 122 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLN A 122 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N ILE A 129 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN A 120 " --> pdb=" O ILE A 129 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU A 131 " --> pdb=" O LEU A 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.700A pdb=" N GLU A 74 " --> pdb=" O VAL A 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 187 Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.712A pdb=" N GLU A 653 " --> pdb=" O ARG A 650 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE A 591 " --> pdb=" O ASP A 618 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N VAL A 620 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE A 593 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE A 622 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ARG A 595 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LYS A 624 " --> pdb=" O ARG A 595 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N CYS A 522 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N HIS A 594 " --> pdb=" O CYS A 522 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE A 524 " --> pdb=" O HIS A 594 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASP A 596 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ILE A 526 " --> pdb=" O ASP A 596 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY A 525 " --> pdb=" O MET A 540 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 311 removed outlier: 3.712A pdb=" N GLU A 653 " --> pdb=" O ARG A 650 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE A 591 " --> pdb=" O ASP A 618 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N VAL A 620 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE A 593 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N ILE A 622 " --> pdb=" O ILE A 593 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ARG A 595 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N LYS A 624 " --> pdb=" O ARG A 595 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N CYS A 522 " --> pdb=" O THR A 592 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N HIS A 594 " --> pdb=" O CYS A 522 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE A 524 " --> pdb=" O HIS A 594 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ASP A 596 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ILE A 526 " --> pdb=" O ASP A 596 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY A 525 " --> pdb=" O MET A 540 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N SER A 535 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 559 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA8, first strand: chain 'A' and resid 379 through 382 removed outlier: 8.752A pdb=" N THR A 416 " --> pdb=" O ASN A 340 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS A 342 " --> pdb=" O THR A 416 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N LEU A 418 " --> pdb=" O LYS A 342 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER A 344 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N PHE A 420 " --> pdb=" O SER A 344 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU A 346 " --> pdb=" O PHE A 420 " (cutoff:3.500A) 260 hydrogen bonds defined for protein. 732 hydrogen bond angles defined for protein. NA hbond rejected because one of the atoms is absent Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 1.50 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1589 1.33 - 1.45: 1367 1.45 - 1.57: 3415 1.57 - 1.69: 63 1.69 - 1.81: 51 Bond restraints: 6485 Sorted by residual: bond pdb=" P DT C 7 " pdb=" OP3 DT C 7 " ideal model delta sigma weight residual 1.480 1.601 -0.121 2.00e-02 2.50e+03 3.66e+01 bond pdb=" P DT B 1 " pdb=" OP3 DT B 1 " ideal model delta sigma weight residual 1.480 1.598 -0.118 2.00e-02 2.50e+03 3.45e+01 bond pdb=" C3' DG B 15 " pdb=" C2' DG B 15 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DT B 13 " pdb=" C2' DT B 13 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C1' DC c 5 " pdb=" N1 DC c 5 " ideal model delta sigma weight residual 1.468 1.505 -0.037 1.40e-02 5.10e+03 7.13e+00 ... (remaining 6480 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 8724 1.89 - 3.78: 166 3.78 - 5.67: 10 5.67 - 7.55: 2 7.55 - 9.44: 4 Bond angle restraints: 8906 Sorted by residual: angle pdb=" N PRO A 474 " pdb=" CA PRO A 474 " pdb=" CB PRO A 474 " ideal model delta sigma weight residual 103.25 110.99 -7.74 1.05e+00 9.07e-01 5.43e+01 angle pdb=" C ARG A 41 " pdb=" CA ARG A 41 " pdb=" CB ARG A 41 " ideal model delta sigma weight residual 110.85 118.75 -7.90 1.70e+00 3.46e-01 2.16e+01 angle pdb=" N ARG A 41 " pdb=" CA ARG A 41 " pdb=" CB ARG A 41 " ideal model delta sigma weight residual 110.16 103.75 6.41 1.48e+00 4.57e-01 1.87e+01 angle pdb=" N3 DT B 13 " pdb=" C4 DT B 13 " pdb=" O4 DT B 13 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT B 14 " pdb=" C4 DT B 14 " pdb=" O4 DT B 14 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.65e+01 ... (remaining 8901 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.90: 3617 31.90 - 63.81: 160 63.81 - 95.71: 10 95.71 - 127.62: 0 127.62 - 159.52: 2 Dihedral angle restraints: 3789 sinusoidal: 1747 harmonic: 2042 Sorted by residual: dihedral pdb=" C4' DT B 13 " pdb=" C3' DT B 13 " pdb=" O3' DT B 13 " pdb=" P DT B 14 " ideal model delta sinusoidal sigma weight residual 220.00 60.48 159.52 1 3.50e+01 8.16e-04 1.52e+01 dihedral pdb=" CA VAL A 157 " pdb=" C VAL A 157 " pdb=" N TYR A 158 " pdb=" CA TYR A 158 " ideal model delta harmonic sigma weight residual 180.00 161.54 18.46 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" C4' DT B 16 " pdb=" C3' DT B 16 " pdb=" O3' DT B 16 " pdb=" P DA B 17 " ideal model delta sinusoidal sigma weight residual 220.00 84.98 135.02 1 3.50e+01 8.16e-04 1.34e+01 ... (remaining 3786 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 928 0.094 - 0.188: 63 0.188 - 0.281: 1 0.281 - 0.375: 1 0.375 - 0.469: 1 Chirality restraints: 994 Sorted by residual: chirality pdb=" P DT C 7 " pdb=" OP1 DT C 7 " pdb=" OP2 DT C 7 " pdb=" O5' DT C 7 " both_signs ideal model delta sigma weight residual True 2.34 2.80 -0.47 2.00e-01 2.50e+01 5.50e+00 chirality pdb=" P DT B 1 " pdb=" OP1 DT B 1 " pdb=" OP2 DT B 1 " pdb=" O5' DT B 1 " both_signs ideal model delta sigma weight residual True 2.34 2.66 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CA PRO A 474 " pdb=" N PRO A 474 " pdb=" C PRO A 474 " pdb=" CB PRO A 474 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.35e-01 ... (remaining 991 not shown) Planarity restraints: 1020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT B 1 " 0.025 2.00e-02 2.50e+03 1.30e-02 4.26e+00 pdb=" N1 DT B 1 " -0.029 2.00e-02 2.50e+03 pdb=" C2 DT B 1 " 0.009 2.00e-02 2.50e+03 pdb=" O2 DT B 1 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DT B 1 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT B 1 " 0.001 2.00e-02 2.50e+03 pdb=" O4 DT B 1 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DT B 1 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT B 1 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT B 1 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 41 " -0.148 9.50e-02 1.11e+02 6.62e-02 2.74e+00 pdb=" NE ARG A 41 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 41 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG A 41 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 41 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT C 7 " 0.017 2.00e-02 2.50e+03 9.52e-03 2.27e+00 pdb=" N1 DT C 7 " -0.023 2.00e-02 2.50e+03 pdb=" C2 DT C 7 " 0.006 2.00e-02 2.50e+03 pdb=" O2 DT C 7 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DT C 7 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT C 7 " 0.001 2.00e-02 2.50e+03 pdb=" O4 DT C 7 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DT C 7 " -0.001 2.00e-02 2.50e+03 pdb=" C7 DT C 7 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DT C 7 " -0.001 2.00e-02 2.50e+03 ... (remaining 1017 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 9 2.39 - 3.01: 3197 3.01 - 3.64: 8881 3.64 - 4.27: 14645 4.27 - 4.90: 24375 Nonbonded interactions: 51107 Sorted by model distance: nonbonded pdb=" OD1 ASP A 713 " pdb="MN MN A 802 " model vdw 1.758 2.320 nonbonded pdb=" OP2 DT C 7 " pdb="MN MN A 802 " model vdw 2.085 2.320 nonbonded pdb=" OP1 DA B 3 " pdb="MN MN B 101 " model vdw 2.232 2.320 nonbonded pdb=" O GLN A 669 " pdb=" O HOH A 901 " model vdw 2.250 3.040 nonbonded pdb=" OD1 ASP A 618 " pdb=" OG1 THR A 677 " model vdw 2.291 3.040 ... (remaining 51102 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.290 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 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 0.121 6485 Z= 0.286 Angle : 0.607 9.442 8906 Z= 0.419 Chirality : 0.049 0.469 994 Planarity : 0.004 0.066 1020 Dihedral : 16.629 159.524 2469 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.29 % Allowed : 4.23 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: -0.17 (0.31), residues: 686 helix: 0.55 (0.34), residues: 239 sheet: 1.25 (0.41), residues: 151 loop : -1.42 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 41 TYR 0.011 0.001 TYR A 37 PHE 0.019 0.002 PHE A 101 TRP 0.007 0.001 TRP A 282 HIS 0.005 0.001 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.29 ( 6485) covalent geometry : angle 0.60723 / 0.42 ( 8906) hydrogen bonds : bond 0.16319 / 10.37 ( 260) hydrogen bonds : angle 6.82605 / 4.96 ( 780) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.245 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.6012 time to fit residues: 71.5810 Evaluate side-chains 81 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 GLN ** A 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 ASN ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 638 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.173943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.135514 restraints weight = 6275.426| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.50 r_work: 0.3251 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6485 Z= 0.152 Angle : 0.558 6.035 8906 Z= 0.321 Chirality : 0.045 0.227 994 Planarity : 0.004 0.034 1020 Dihedral : 16.125 163.064 1106 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.63 % Allowed : 10.84 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.32), residues: 686 helix: 0.77 (0.35), residues: 240 sheet: 1.33 (0.40), residues: 156 loop : -1.46 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 11 TYR 0.014 0.001 TYR A 158 PHE 0.011 0.001 PHE A 351 TRP 0.007 0.001 TRP A 282 HIS 0.004 0.001 HIS A 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 ( 6485) covalent geometry : angle 0.55774 / 0.32 ( 8906) hydrogen bonds : bond 0.05210 / 3.33 ( 260) hydrogen bonds : angle 5.12092 / 3.63 ( 780) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8279 (OUTLIER) cc_final: 0.7225 (mt0) outliers start: 16 outliers final: 3 residues processed: 87 average time/residue: 0.5700 time to fit residues: 52.0152 Evaluate side-chains 81 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 77 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 128 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 52 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.170100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.134696 restraints weight = 6236.610| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.26 r_work: 0.3185 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 6485 Z= 0.215 Angle : 0.623 5.970 8906 Z= 0.350 Chirality : 0.047 0.257 994 Planarity : 0.004 0.036 1020 Dihedral : 16.452 162.604 1106 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 3.12 % Allowed : 12.15 % Favored : 84.73 % 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: -0.21 (0.32), residues: 686 helix: 0.70 (0.34), residues: 236 sheet: 1.06 (0.41), residues: 152 loop : -1.50 (0.35), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 11 TYR 0.020 0.002 TYR A 158 PHE 0.016 0.002 PHE A 351 TRP 0.009 0.001 TRP A 599 HIS 0.004 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.22 ( 6485) covalent geometry : angle 0.62294 / 0.35 ( 8906) hydrogen bonds : bond 0.05398 / 3.41 ( 260) hydrogen bonds : angle 4.85253 / 3.42 ( 780) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.248 Fit side-chains REVERT: A 41 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7261 (ttt-90) REVERT: A 55 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7162 (mt0) REVERT: A 80 ILE cc_start: 0.8073 (OUTLIER) cc_final: 0.7648 (tt) REVERT: A 653 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8212 (mt-10) outliers start: 19 outliers final: 5 residues processed: 87 average time/residue: 0.5646 time to fit residues: 51.6012 Evaluate side-chains 84 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 653 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 28 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.169988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.142297 restraints weight = 6262.770| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 1.87 r_work: 0.3186 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 6485 Z= 0.198 Angle : 0.610 6.121 8906 Z= 0.343 Chirality : 0.046 0.258 994 Planarity : 0.004 0.039 1020 Dihedral : 16.519 163.379 1106 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.78 % Allowed : 13.63 % Favored : 82.59 % 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: -0.12 (0.32), residues: 686 helix: 0.73 (0.34), residues: 239 sheet: 0.98 (0.41), residues: 153 loop : -1.34 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 11 TYR 0.017 0.001 TYR A 158 PHE 0.015 0.002 PHE A 351 TRP 0.009 0.001 TRP A 599 HIS 0.003 0.001 HIS A 696 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 ( 6485) covalent geometry : angle 0.61000 / 0.34 ( 8906) hydrogen bonds : bond 0.05049 / 3.17 ( 260) hydrogen bonds : angle 4.70211 / 3.30 ( 780) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.233 Fit side-chains REVERT: A 55 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7121 (mt0) REVERT: A 80 ILE cc_start: 0.8051 (OUTLIER) cc_final: 0.7572 (tt) REVERT: A 124 ILE cc_start: 0.8103 (mm) cc_final: 0.7881 (mp) REVERT: A 130 TYR cc_start: 0.7818 (m-80) cc_final: 0.6508 (m-80) REVERT: A 140 ILE cc_start: 0.8715 (OUTLIER) cc_final: 0.8151 (pt) REVERT: A 653 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8234 (mt-10) outliers start: 23 outliers final: 5 residues processed: 90 average time/residue: 0.5485 time to fit residues: 52.0681 Evaluate side-chains 83 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 653 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 18 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 19 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 67 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 467 HIS ** A 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.168607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.130285 restraints weight = 6297.460| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.42 r_work: 0.3191 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 6485 Z= 0.210 Angle : 0.623 6.358 8906 Z= 0.350 Chirality : 0.047 0.268 994 Planarity : 0.004 0.036 1020 Dihedral : 16.595 163.848 1106 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.12 % Allowed : 14.61 % Favored : 82.27 % 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: -0.15 (0.32), residues: 686 helix: 0.96 (0.35), residues: 232 sheet: 1.30 (0.43), residues: 132 loop : -1.57 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 105 TYR 0.012 0.002 TYR A 158 PHE 0.015 0.002 PHE A 351 TRP 0.009 0.001 TRP A 599 HIS 0.003 0.001 HIS A 710 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 ( 6485) covalent geometry : angle 0.62301 / 0.35 ( 8906) hydrogen bonds : bond 0.05185 / 3.25 ( 260) hydrogen bonds : angle 4.68317 / 3.29 ( 780) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.150 Fit side-chains revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7128 (mt0) REVERT: A 130 TYR cc_start: 0.7826 (m-80) cc_final: 0.6455 (m-80) REVERT: A 140 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8118 (pt) REVERT: A 148 PHE cc_start: 0.8295 (OUTLIER) cc_final: 0.8074 (p90) REVERT: A 653 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8233 (mt-10) REVERT: A 680 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8546 (mp) outliers start: 19 outliers final: 8 residues processed: 86 average time/residue: 0.5548 time to fit residues: 50.1641 Evaluate side-chains 87 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 148 PHE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 680 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 0.0870 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.171643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.133786 restraints weight = 6269.839| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.38 r_work: 0.3246 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6485 Z= 0.128 Angle : 0.550 7.507 8906 Z= 0.314 Chirality : 0.043 0.264 994 Planarity : 0.004 0.035 1020 Dihedral : 16.549 162.339 1106 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.28 % Allowed : 15.93 % Favored : 80.79 % 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: 0.08 (0.32), residues: 686 helix: 1.14 (0.35), residues: 237 sheet: 0.98 (0.40), residues: 153 loop : -1.39 (0.34), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 11 TYR 0.012 0.001 TYR A 158 PHE 0.016 0.001 PHE A 101 TRP 0.009 0.001 TRP A 282 HIS 0.002 0.000 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.13 ( 6485) covalent geometry : angle 0.54957 / 0.31 ( 8906) hydrogen bonds : bond 0.04080 / 2.57 ( 260) hydrogen bonds : angle 4.47030 / 3.13 ( 780) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.147 Fit side-chains revert: symmetry clash REVERT: A 130 TYR cc_start: 0.7737 (m-80) cc_final: 0.6471 (m-80) REVERT: A 140 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8097 (pt) REVERT: A 330 MET cc_start: 0.8555 (mmp) cc_final: 0.8211 (mmt) REVERT: A 653 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8100 (mt-10) outliers start: 20 outliers final: 7 residues processed: 85 average time/residue: 0.4839 time to fit residues: 43.3471 Evaluate side-chains 86 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 653 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 10 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 27 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 19 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.169269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.130663 restraints weight = 6246.724| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.42 r_work: 0.3205 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 6485 Z= 0.196 Angle : 0.609 7.084 8906 Z= 0.340 Chirality : 0.046 0.268 994 Planarity : 0.004 0.038 1020 Dihedral : 16.580 163.865 1106 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.63 % Allowed : 17.24 % Favored : 80.13 % 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: -0.04 (0.32), residues: 686 helix: 1.00 (0.35), residues: 238 sheet: 1.27 (0.42), residues: 132 loop : -1.47 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 11 TYR 0.014 0.001 TYR A 158 PHE 0.013 0.002 PHE A 101 TRP 0.009 0.001 TRP A 599 HIS 0.003 0.001 HIS A 696 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 ( 6485) covalent geometry : angle 0.60921 / 0.34 ( 8906) hydrogen bonds : bond 0.04862 / 3.05 ( 260) hydrogen bonds : angle 4.55415 / 3.20 ( 780) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7251 (mt0) REVERT: A 130 TYR cc_start: 0.7796 (m-80) cc_final: 0.6544 (m-80) REVERT: A 140 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8128 (pt) REVERT: A 653 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8158 (mt-10) REVERT: A 680 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8709 (mp) outliers start: 16 outliers final: 9 residues processed: 85 average time/residue: 0.4650 time to fit residues: 41.6550 Evaluate side-chains 89 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 680 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 10 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.170201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.131490 restraints weight = 6260.600| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.51 r_work: 0.3213 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6485 Z= 0.156 Angle : 0.589 9.021 8906 Z= 0.330 Chirality : 0.045 0.267 994 Planarity : 0.004 0.037 1020 Dihedral : 16.570 163.331 1106 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.28 % Allowed : 17.08 % Favored : 79.64 % 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: 0.02 (0.32), residues: 686 helix: 1.10 (0.35), residues: 237 sheet: 1.30 (0.42), residues: 132 loop : -1.46 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 11 TYR 0.012 0.001 TYR A 158 PHE 0.015 0.001 PHE A 101 TRP 0.009 0.001 TRP A 599 HIS 0.002 0.001 HIS A 696 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 ( 6485) covalent geometry : angle 0.58888 / 0.33 ( 8906) hydrogen bonds : bond 0.04433 / 2.79 ( 260) hydrogen bonds : angle 4.48288 / 3.14 ( 780) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7259 (mt0) REVERT: A 130 TYR cc_start: 0.7783 (m-80) cc_final: 0.6530 (m-80) REVERT: A 140 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8098 (pt) REVERT: A 653 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8137 (mt-10) REVERT: A 680 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8673 (mp) outliers start: 20 outliers final: 8 residues processed: 86 average time/residue: 0.4708 time to fit residues: 42.7132 Evaluate side-chains 87 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 680 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 43 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.168090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140889 restraints weight = 6310.772| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.66 r_work: 0.3185 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 6485 Z= 0.232 Angle : 0.666 9.705 8906 Z= 0.366 Chirality : 0.048 0.275 994 Planarity : 0.004 0.039 1020 Dihedral : 16.631 164.517 1106 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.10 % Favored : 94.75 % Rotamer: Outliers : 2.30 % Allowed : 18.72 % Favored : 78.98 % 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: -0.13 (0.32), residues: 686 helix: 0.91 (0.35), residues: 238 sheet: 1.19 (0.42), residues: 132 loop : -1.48 (0.33), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 11 TYR 0.012 0.002 TYR A 158 PHE 0.016 0.002 PHE A 736 TRP 0.009 0.001 TRP A 599 HIS 0.004 0.001 HIS A 696 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.23 ( 6485) covalent geometry : angle 0.66586 / 0.37 ( 8906) hydrogen bonds : bond 0.05327 / 3.33 ( 260) hydrogen bonds : angle 4.62803 / 3.25 ( 780) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.7243 (mt0) REVERT: A 130 TYR cc_start: 0.7834 (m-80) cc_final: 0.6579 (m-80) REVERT: A 140 ILE cc_start: 0.8716 (OUTLIER) cc_final: 0.8128 (pt) REVERT: A 653 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8265 (mt-10) REVERT: A 680 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8708 (mp) outliers start: 14 outliers final: 9 residues processed: 84 average time/residue: 0.4902 time to fit residues: 43.5090 Evaluate side-chains 88 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 680 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 50 optimal weight: 0.0770 chunk 61 optimal weight: 0.0070 chunk 68 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 41 optimal weight: 0.0970 chunk 6 optimal weight: 0.2980 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 541 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.173091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.136539 restraints weight = 6204.635| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.29 r_work: 0.3270 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 6485 Z= 0.119 Angle : 0.560 10.049 8906 Z= 0.317 Chirality : 0.043 0.268 994 Planarity : 0.004 0.037 1020 Dihedral : 16.571 162.222 1106 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.79 % Favored : 96.06 % Rotamer: Outliers : 1.97 % Allowed : 19.05 % Favored : 78.98 % 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: 0.13 (0.32), residues: 686 helix: 1.25 (0.35), residues: 237 sheet: 1.08 (0.40), residues: 146 loop : -1.42 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 11 TYR 0.013 0.001 TYR A 37 PHE 0.022 0.001 PHE A 101 TRP 0.011 0.001 TRP A 599 HIS 0.002 0.000 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.12 ( 6485) covalent geometry : angle 0.55958 / 0.32 ( 8906) hydrogen bonds : bond 0.03672 / 2.31 ( 260) hydrogen bonds : angle 4.37386 / 3.06 ( 780) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1372 Ramachandran restraints generated. 686 Oldfield, 0 Emsley, 686 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.227 Fit side-chains revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7225 (mt0) REVERT: A 130 TYR cc_start: 0.7712 (m-80) cc_final: 0.6518 (m-80) REVERT: A 140 ILE cc_start: 0.8622 (OUTLIER) cc_final: 0.8080 (pt) REVERT: A 653 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.8023 (mt-10) outliers start: 12 outliers final: 9 residues processed: 85 average time/residue: 0.5418 time to fit residues: 48.5849 Evaluate side-chains 87 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 75 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 53 TYR Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 80 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 653 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 142 ASN ** A 530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.172297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.133700 restraints weight = 6254.294| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.49 r_work: 0.3240 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6485 Z= 0.137 Angle : 0.579 9.949 8906 Z= 0.323 Chirality : 0.044 0.270 994 Planarity : 0.004 0.035 1020 Dihedral : 16.528 162.993 1106 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.81 % Allowed : 19.38 % Favored : 78.82 % 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: 0.18 (0.32), residues: 686 helix: 1.26 (0.35), residues: 237 sheet: 1.36 (0.42), residues: 132 loop : -1.37 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 11 TYR 0.010 0.001 TYR A 158 PHE 0.020 0.001 PHE A 101 TRP 0.009 0.001 TRP A 599 HIS 0.002 0.000 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 ( 6485) covalent geometry : angle 0.57925 / 0.32 ( 8906) hydrogen bonds : bond 0.03918 / 2.46 ( 260) hydrogen bonds : angle 4.34207 / 3.04 ( 780) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1995.65 seconds wall clock time: 34 minutes 41.95 seconds (2081.95 seconds total)