Starting phenix.real_space_refine on Thu Jul 2 23:33:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xk3_38414/07_2026/8xk3_38414.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xk3_38414/07_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_38414/07_2026/8xk3_38414.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xk3_38414/07_2026/8xk3_38414.map" model { file = "/net/cci-nas-00/data/ceres_data/8xk3_38414/07_2026/8xk3_38414.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xk3_38414/07_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-dev-6108/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, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 0 Ad-hoc single atom residues: {' MN': 1} Chain breaks: 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: 1.48, per 1000 atoms: 0.23 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 357.0 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: 0.48 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: 1.15 Time building geometry restraints manager: 0.66 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: 8725 1.89 - 3.78: 165 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 3.060 nonbonded pdb=" OP2 DT C 7 " pdb="MN MN A 802 " model vdw 2.085 3.060 nonbonded pdb=" OP1 DA B 3 " pdb="MN MN B 101 " model vdw 2.232 3.060 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: 1.090 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 6.980 Find NCS groups from input model: 0.030 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:7.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.970 ------------------------------------------------------------------------------- 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 : 0.606 9.442 8906 Z= 0.417 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 0.60558 / 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 : 0.162 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.5398 time to fit residues: 64.3065 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 : 0.153 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.174246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.136813 restraints weight = 6255.050| |-----------------------------------------------------------------------------| r_work (start): 0.3575 rms_B_bonded: 2.41 r_work: 0.3254 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6485 Z= 0.153 Angle : 0.564 5.683 8906 Z= 0.323 Chirality : 0.044 0.205 994 Planarity : 0.004 0.033 1020 Dihedral : 16.205 164.495 1106 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % 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: -0.02 (0.32), residues: 686 helix: 0.76 (0.35), residues: 240 sheet: 1.29 (0.40), residues: 156 loop : -1.45 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 11 TYR 0.015 0.001 TYR A 158 PHE 0.010 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 0.00315 / 0.15 ( 6485) covalent geometry : angle 0.56368 / 0.32 ( 8906) hydrogen bonds : bond 0.04935 / 3.18 ( 260) hydrogen bonds : angle 5.05263 / 3.58 ( 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 96 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7212 (mt0) REVERT: A 140 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8284 (mm) REVERT: A 638 ASN cc_start: 0.8503 (m-40) cc_final: 0.8285 (m-40) outliers start: 16 outliers final: 3 residues processed: 85 average time/residue: 0.4612 time to fit residues: 41.1277 Evaluate side-chains 81 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 140 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 52 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 23 optimal weight: 0.0970 chunk 15 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 61 optimal weight: 0.4980 chunk 33 optimal weight: 2.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.171679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.132959 restraints weight = 6218.262| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.38 r_work: 0.3232 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6485 Z= 0.166 Angle : 0.564 5.040 8906 Z= 0.322 Chirality : 0.045 0.235 994 Planarity : 0.004 0.034 1020 Dihedral : 16.428 162.000 1106 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.28 % Allowed : 11.17 % Favored : 85.55 % 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: -0.03 (0.32), residues: 686 helix: 0.79 (0.35), residues: 240 sheet: 1.11 (0.41), residues: 152 loop : -1.34 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 11 TYR 0.017 0.001 TYR A 158 PHE 0.013 0.002 PHE A 351 TRP 0.008 0.001 TRP A 599 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 ( 6485) covalent geometry : angle 0.56365 / 0.32 ( 8906) hydrogen bonds : bond 0.04804 / 3.04 ( 260) hydrogen bonds : angle 4.71562 / 3.32 ( 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 101 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.149 Fit side-chains REVERT: A 55 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7086 (mt0) REVERT: A 653 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8102 (mt-10) outliers start: 20 outliers final: 5 residues processed: 90 average time/residue: 0.4701 time to fit residues: 44.3102 Evaluate side-chains 82 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 GLU Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 80 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: 5.9990 chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 45 optimal weight: 0.6980 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 44 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.171269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.141871 restraints weight = 6246.343| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.05 r_work: 0.3205 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6485 Z= 0.170 Angle : 0.576 5.894 8906 Z= 0.326 Chirality : 0.045 0.230 994 Planarity : 0.004 0.035 1020 Dihedral : 16.461 164.166 1106 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.96 % Allowed : 13.46 % Favored : 83.58 % 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: 0.03 (0.32), residues: 686 helix: 0.92 (0.35), residues: 239 sheet: 1.05 (0.40), residues: 152 loop : -1.31 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 11 TYR 0.016 0.001 TYR A 158 PHE 0.014 0.002 PHE A 397 TRP 0.008 0.001 TRP A 599 HIS 0.003 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 ( 6485) covalent geometry : angle 0.57562 / 0.33 ( 8906) hydrogen bonds : bond 0.04597 / 2.89 ( 260) hydrogen bonds : angle 4.61496 / 3.25 ( 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 93 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.149 Fit side-chains revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8233 (OUTLIER) cc_final: 0.7115 (mt0) REVERT: A 140 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8113 (pt) REVERT: A 653 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.8165 (mt-10) outliers start: 18 outliers final: 6 residues processed: 85 average time/residue: 0.4803 time to fit residues: 42.8572 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 : 0.158 ------------------------------------------------------------------------------- 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: 10.0000 chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.3961 r_free = 0.3961 target = 0.171482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.141598 restraints weight = 6308.009| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.13 r_work: 0.3203 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6485 Z= 0.153 Angle : 0.556 6.411 8906 Z= 0.316 Chirality : 0.044 0.240 994 Planarity : 0.004 0.040 1020 Dihedral : 16.478 163.424 1106 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.63 % Allowed : 14.61 % Favored : 82.76 % 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: 1.04 (0.35), residues: 238 sheet: 1.12 (0.41), residues: 152 loop : -1.32 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 11 TYR 0.015 0.001 TYR A 158 PHE 0.011 0.002 PHE A 148 TRP 0.008 0.001 TRP A 599 HIS 0.002 0.001 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 ( 6485) covalent geometry : angle 0.55568 / 0.32 ( 8906) hydrogen bonds : bond 0.04334 / 2.72 ( 260) hydrogen bonds : angle 4.49992 / 3.16 ( 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 92 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.238 Fit side-chains REVERT: A 140 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8112 (pt) REVERT: A 259 GLN cc_start: 0.7294 (OUTLIER) cc_final: 0.7041 (pp30) REVERT: A 653 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8140 (mt-10) outliers start: 16 outliers final: 7 residues processed: 85 average time/residue: 0.4827 time to fit residues: 43.2128 Evaluate side-chains 83 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.141 ------------------------------------------------------------------------------- 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 80 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 259 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 19 optimal weight: 0.0170 chunk 59 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 54 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 13 optimal weight: 0.2980 chunk 33 optimal weight: 5.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- 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 = 0.3991 r_free = 0.3991 target = 0.174206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.137592 restraints weight = 6274.059| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.40 r_work: 0.3269 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 6485 Z= 0.114 Angle : 0.524 8.684 8906 Z= 0.299 Chirality : 0.042 0.239 994 Planarity : 0.004 0.039 1020 Dihedral : 16.420 162.918 1106 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.96 % Allowed : 14.78 % 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: 0.27 (0.32), residues: 686 helix: 1.20 (0.35), residues: 239 sheet: 1.26 (0.41), residues: 151 loop : -1.29 (0.35), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 11 TYR 0.017 0.001 TYR A 37 PHE 0.009 0.001 PHE A 397 TRP 0.008 0.001 TRP A 282 HIS 0.002 0.000 HIS A 465 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.11 ( 6485) covalent geometry : angle 0.52447 / 0.30 ( 8906) hydrogen bonds : bond 0.03553 / 2.25 ( 260) hydrogen bonds : angle 4.32409 / 3.03 ( 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 99 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.240 Fit side-chains REVERT: A 55 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7287 (mt0) REVERT: A 174 MET cc_start: 0.6990 (OUTLIER) cc_final: 0.6403 (ttm) REVERT: A 330 MET cc_start: 0.8580 (mmt) cc_final: 0.8226 (mmt) REVERT: A 653 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8020 (mt-10) REVERT: A 680 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8601 (mp) outliers start: 18 outliers final: 5 residues processed: 90 average time/residue: 0.4228 time to fit residues: 40.1199 Evaluate side-chains 88 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 174 MET 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 Chi-restraints excluded: chain A residue 680 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 10 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3951 r_free = 0.3951 target = 0.170315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.135400 restraints weight = 6250.778| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.22 r_work: 0.3207 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 6485 Z= 0.185 Angle : 0.593 8.702 8906 Z= 0.330 Chirality : 0.045 0.242 994 Planarity : 0.004 0.044 1020 Dihedral : 16.470 164.360 1106 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.96 % Allowed : 15.76 % Favored : 81.28 % 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: 0.16 (0.32), residues: 686 helix: 1.11 (0.35), residues: 239 sheet: 1.34 (0.42), residues: 137 loop : -1.32 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 11 TYR 0.009 0.001 TYR A 37 PHE 0.012 0.002 PHE A 736 TRP 0.007 0.001 TRP A 599 HIS 0.002 0.001 HIS A 696 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 ( 6485) covalent geometry : angle 0.59270 / 0.33 ( 8906) hydrogen bonds : bond 0.04540 / 2.85 ( 260) hydrogen bonds : angle 4.44377 / 3.12 ( 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 94 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.259 Fit side-chains REVERT: A 41 ARG cc_start: 0.7721 (mtt-85) cc_final: 0.7459 (mtt-85) REVERT: A 55 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7274 (mt0) REVERT: A 140 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8124 (pt) REVERT: A 174 MET cc_start: 0.7098 (OUTLIER) cc_final: 0.6525 (ttm) REVERT: A 653 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8129 (mt-10) REVERT: A 680 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8664 (mp) outliers start: 18 outliers final: 8 residues processed: 85 average time/residue: 0.4588 time to fit residues: 41.0270 Evaluate side-chains 90 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 174 MET 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: 0.8980 chunk 67 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 42 optimal weight: 9.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3966 r_free = 0.3966 target = 0.171799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.134351 restraints weight = 6246.436| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.37 r_work: 0.3259 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2171 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= 0.131 Angle : 0.560 9.364 8906 Z= 0.314 Chirality : 0.043 0.243 994 Planarity : 0.004 0.038 1020 Dihedral : 16.443 163.600 1106 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.30 % Allowed : 17.08 % Favored : 80.62 % 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: 0.26 (0.32), residues: 686 helix: 1.23 (0.35), residues: 239 sheet: 1.41 (0.42), residues: 136 loop : -1.30 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 11 TYR 0.012 0.001 TYR A 37 PHE 0.008 0.001 PHE A 86 TRP 0.008 0.001 TRP A 599 HIS 0.002 0.000 HIS A 696 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 ( 6485) covalent geometry : angle 0.56035 / 0.31 ( 8906) hydrogen bonds : bond 0.03871 / 2.44 ( 260) hydrogen bonds : angle 4.33563 / 3.04 ( 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 90 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.151 Fit side-chains REVERT: A 37 TYR cc_start: 0.7952 (t80) cc_final: 0.7662 (t80) REVERT: A 41 ARG cc_start: 0.7654 (mtt-85) cc_final: 0.7342 (mtt-85) REVERT: A 55 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7199 (mt0) REVERT: A 140 ILE cc_start: 0.8637 (OUTLIER) cc_final: 0.8084 (pt) REVERT: A 653 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8076 (mt-10) REVERT: A 680 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8582 (mp) REVERT: A 709 ILE cc_start: 0.8559 (OUTLIER) cc_final: 0.8284 (mp) outliers start: 14 outliers final: 6 residues processed: 81 average time/residue: 0.4564 time to fit residues: 38.8792 Evaluate side-chains 86 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 709 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 16 optimal weight: 0.1980 chunk 60 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3971 r_free = 0.3971 target = 0.172394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.143521 restraints weight = 6273.901| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.06 r_work: 0.3225 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6485 Z= 0.137 Angle : 0.563 9.629 8906 Z= 0.314 Chirality : 0.043 0.245 994 Planarity : 0.004 0.039 1020 Dihedral : 16.428 163.846 1106 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.13 % Allowed : 17.73 % 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: 0.28 (0.32), residues: 686 helix: 1.25 (0.35), residues: 239 sheet: 1.45 (0.42), residues: 136 loop : -1.30 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 11 TYR 0.011 0.001 TYR A 37 PHE 0.008 0.001 PHE A 365 TRP 0.007 0.001 TRP A 599 HIS 0.002 0.000 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 6485) covalent geometry : angle 0.56284 / 0.31 ( 8906) hydrogen bonds : bond 0.03902 / 2.45 ( 260) hydrogen bonds : angle 4.31213 / 3.03 ( 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: 13 poor density : 78 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7270 (mt0) REVERT: A 140 ILE cc_start: 0.8663 (OUTLIER) cc_final: 0.8094 (pt) REVERT: A 653 GLU cc_start: 0.8581 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: A 680 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8613 (mp) REVERT: A 709 ILE cc_start: 0.8709 (OUTLIER) cc_final: 0.8334 (mp) outliers start: 13 outliers final: 6 residues processed: 85 average time/residue: 0.4713 time to fit residues: 42.2624 Evaluate side-chains 86 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 653 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 709 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 50 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 68 optimal weight: 0.0470 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 43 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.173047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.135687 restraints weight = 6159.528| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.31 r_work: 0.3270 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6485 Z= 0.128 Angle : 0.569 9.966 8906 Z= 0.317 Chirality : 0.043 0.245 994 Planarity : 0.004 0.045 1020 Dihedral : 16.402 163.631 1106 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.97 % Allowed : 18.06 % Favored : 79.97 % 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: 0.31 (0.32), residues: 686 helix: 1.27 (0.35), residues: 240 sheet: 1.49 (0.42), residues: 136 loop : -1.30 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 11 TYR 0.015 0.001 TYR A 37 PHE 0.008 0.001 PHE A 86 TRP 0.008 0.001 TRP A 282 HIS 0.002 0.000 HIS A 355 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 ( 6485) covalent geometry : angle 0.56889 / 0.32 ( 8906) hydrogen bonds : bond 0.03645 / 2.30 ( 260) hydrogen bonds : angle 4.30119 / 3.03 ( 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 89 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.152 Fit side-chains revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.7181 (mt0) REVERT: A 140 ILE cc_start: 0.8645 (OUTLIER) cc_final: 0.8099 (pt) REVERT: A 653 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7998 (mt-10) REVERT: A 680 LEU cc_start: 0.8848 (OUTLIER) cc_final: 0.8569 (mp) REVERT: A 709 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8281 (mp) outliers start: 12 outliers final: 7 residues processed: 82 average time/residue: 0.4716 time to fit residues: 40.6687 Evaluate side-chains 89 residues out of total 617 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.151 ------------------------------------------------------------------------------- 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 384 THR Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 709 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 0.0770 chunk 29 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 51 optimal weight: 0.0670 chunk 22 optimal weight: 0.0050 chunk 37 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 overall best weight: 0.3690 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.175532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.137903 restraints weight = 6247.196| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 2.30 r_work: 0.3324 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 6485 Z= 0.115 Angle : 0.552 9.866 8906 Z= 0.307 Chirality : 0.043 0.245 994 Planarity : 0.004 0.044 1020 Dihedral : 16.354 163.256 1106 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.81 % Allowed : 18.72 % Favored : 79.47 % 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: 0.44 (0.33), residues: 686 helix: 1.38 (0.35), residues: 240 sheet: 1.62 (0.42), residues: 136 loop : -1.26 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 11 TYR 0.016 0.001 TYR A 37 PHE 0.008 0.001 PHE A 86 TRP 0.008 0.001 TRP A 282 HIS 0.002 0.000 HIS A 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 ( 6485) covalent geometry : angle 0.55189 / 0.31 ( 8906) hydrogen bonds : bond 0.03244 / 2.06 ( 260) hydrogen bonds : angle 4.23208 / 2.99 ( 780) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1786.43 seconds wall clock time: 31 minutes 2.27 seconds (1862.27 seconds total)